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2023

01. Hosokawa C, Yagi H, Segami S, Nagano AJ, Koumoto Y, Tamura K, Oka Y, Matsushita T, Shimada T. (2023) The Arabidopsis katamari2 Mutant Exhibits a Hypersensitive Seedling Arrest Response at the Phase Transition from Heterotrophic to Autotrophic Growth. Plant Cell Physiol. 7:pcad156. doi: 10.1093/pcp/pcad156.

02. Zeichner SS, Aponte JC, Bhattacharjee S, Dong G, Hofmann AE, Dworkin JP, Glavin DP, Elsila JE, Graham HV, Naraoka H, Takano Y, Tachibana S, Karp AT, Grice K, Holman AI, Freeman KH, Yurimoto H, Nakamura T, Noguchi T, Okazaki R, Yabuta H, Sakamoto K, Yada T, Nishimura M, Nakato A, Miyazaki A, Yogata K, Abe M, Okada T, Usui T, Yoshikawa M, Saiki T, Tanaka S, Terui F, Nakazawa S, Watanabe SI, Tsuda Y, Hamase K, Fukushima K, Aoki D, Hashiguchi M, Mita H, Chikaraishi Y, Ohkouchi N, Ogawa NO, Sakai S, Parker ET, McLain HL, Orthous-Daunay FR, Vuitton V, Wolters C, Schmitt-Kopplin P, Hertkorn N, Thissen R, Ruf A, Isa J, Oba Y, Koga T, Yoshimura T, Araoka D, Sugahara H, Furusho A, Furukawa Y, Aoki J, Kano K, Nomura SM, Sasaki K, Sato H, Yoshikawa T, Tanaka S, Morita M, Onose M, Kabashima F, Fujishima K, Yamazaki T, Kimura Y, Eiler JM. (2023) Polycyclic aromatic hydrocarbons in samples of Ryugu formed in the interstellar medium. Science. 382(6677):1411-1416. doi: 10.1126/science.adg6304.

03. Fujiwara K, Maekawa M, Iimori Y, Ogawa A, Urano T, Kono N, Takeda H, Higashiyama S, Arita M, Murai J. (2023) The crucial role of single-stranded DNA binding in enhancing sensitivity to DNA-damaging agents for Schlafen 11 and Schlafen 13. iScience. 26(12):108529. doi: 10.1016/j.isci.2023.108529.

04. Tanaka A, Sanada K, Miyaho K, Tachibana T, Kurokawa S, Ishii C, Noda Y, Nakajima S, Fukuda S, Mimura M, Kishimoto T, Iwanami A. (2023) The relationship between sleep, gut microbiota, and metabolome in patients with depression and anxiety: A secondary analysis of the observational study. PLoS One. 18(12):e0296047. doi: 10.1371/journal.pone.0296047.

05. Honda S, Imamura A, Seki Y, Chigira K, Iwasa M, Hayami K, Nomura T, Ohkubo S, Ookawa T, Nagano AJ, Matsuoka M, Tanaka Y, Adachi S. (2023) Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice. Photosynth Res. 19. doi: 10.1007/s11120-023-01065-3.

06. Kawamata T, Wakimoto A, Nishikawa T, Ikezawa M, Hamada M, Inoue Y, Kulathunga K, Salim FN, Kanai M, Nishino T, Gentleman K, Liu C, Mathis BJ, Obana N, Fukuda S, Takahashi S, Taya Y, Sakai S, Hiramatsu Y. (2023) Natto consumption suppresses atherosclerotic plaque progression in LDL receptor-deficient mice transplanted with iRFP-expressing hematopoietic cells. Sci Rep. 13(1):22469. doi: 10.1038/s41598-023-48562-y.

07. Nakayama T, Tanikawa M, Okushi Y, Itoh T, Shimmura T, Maruyama M, Yamaguchi T, Matsumiya A, Shinomiya A, Guh YJ, Chen J, Naruse K, Kudoh H, Kondo Y, Naoki H, Aoki K, Nagano AJ, Yoshimura T. (2023) A transcriptional program underlying the circannual rhythms of gonadal development in medaka. Proc Natl Acad Sci U S A. 120(52):e2313514120. doi: 10.1073/pnas.2313514120.

08. Suzuki Y, Fukazawa A, Sugawara K, Galipon J, Arakawa K. (2023) Complete genome sequence of PETase type IIa-harboring Marinobacter nanhaiticus D15-8W, isolated from a South China Sea sediment. Microbiol Resour Announc. 12(12):e0086823. doi: 10.1128/MRA.00868-23.

09. Nishimoto Y, Salim F, Yamauchi Y, Mori Y, Murakami S, Suzuki A, Fukuda S, Yamada T. (2023) Kale improves bowel movements in constipated women and affects some intestinal microbes and metabolites: a pilot study. Front Nutr. 10:1247683. doi: 10.3389/fnut.2023.1247683.

10. Nomura M, Ohuchi M, Sakamoto Y, Kudo K, Yaku K, Soga T, Sugiura Y, Morita M, Hayashi K, Miyahara S, Sato T, Yamashita Y, Ito S, Kikuchi N, Sato I, Saito R, Yaegashi N, Fukuhara T, Yamada H, Shima H, Nakayama KI, Hirao A, Kawasaki K, Arai Y, Akamatsu S, Tanuma SI, Sato T, Nakagawa T, Tanuma N. (2023) Niacin restriction with NAMPT-inhibition is synthetic lethal to neuroendocrine carcinoma. Nat Commun. 14(1):8095. doi: 10.1038/s41467-023-43630-3.

11. Naruki M, Watanabe A, Warashina T, Morita T, Arakawa K. (2024) Complete genome sequence of Limnobacter thiooxidans CS-K2T, isolated from freshwater lake sediments in Bavaria, Germany. Microbiol Resour Announc. 13(1):e0099223. doi: 10.1128/mra.00992-23.

12. Kato S, Arakaki S, Nagano AJ, Kikuchi K, Hirase S. (2023) Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes. Mol Ecol. 4. doi: 10.1111/mec.17216.

13. Haqani MI, Nakano M, Nagano AJ, Nakamura Y, Tsudzuki M. (2023) Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Sci Rep. 13(1):21307. doi: 10.1038/s41598-023-48293-0.

14. Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. (2023) Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics. Front Microbiol. 14:1261137. doi: 10.3389/fmicb.2023.1261137.

15. Oshibuchi K, Yang J, Obana N, Fukuda S, Arakawa K. (2024) Complete genome sequence of Solobacterium moorei JCM 10645T isolated from a human stool sample. Microbiol Resour Announc. 13(1):e0096523. doi: 10.1128/MRA.00965-23.

16. Tanaka S, Arakawa K. (2023) Reply to Tanaka and Kunieda: Control protein GFP also shows a mesh-like structure in desiccating tardigrade cells. Proc Natl Acad Sci U S A. 120(48):e2316451120. doi: 10.1073/pnas.2316451120.

17. Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. (2023) Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event. Mol Biol Evol.40(12):msad246. doi: 10.1093/molbev/msad246.

18. Kawashima T, Watanabe Y, Arakawa K. (2023) Complete genome sequence of Actinoplanes sichuanensis strain 03-723T. Microbiol Resour Announc. 12(12):e0066223. doi: 10.1128/MRA.00662-23.

19. Ito T, Kimura R, Wakamori H, Tanaka M, Tezuka A, Nagano AJ, Hamada Y, Kawamoto Y. (2023) Hybridization and its impact on the ontogenetic allometry of skulls in macaques. Evolution. 11:qpad206. doi: 10.1093/evolut/qpad206.

20. Nguyen LAC, Mori M, Yasuda Y, Galipon J. (2023) Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation. Mol Cell Biol. 43(11):611-628. doi: 10.1080/10985549.2023.2270406.

21. Harada S, Ohmomo H, Matsumoto M, Sata M, Iida M, Hirata A, Miyagawa N, Kuwabara K, Kato S, Toki R, Edagawa S, Sugiyama D, Sato A, Hirayama A, Sugimoto M, Soga T, Tomita M, Shimizu A, Okamura T, Takebayashi T. (2023) Metabolomics profiles alterations in cigarette smokers and heated tobacco product users. J Epidemiol. 4. doi: 10.2188/jea.JE20230170.

22. Shiraishi S, Sugimoto M, Tokuuye K. (2023) Salivary metabolites as novel independent predictors of radiation pneumonitis. J Cancer Res Clin Oncol. 149(19):17559-17566. doi: 10.1007/s00432-023-05479-3.

23. Nishimoto Y, Salim F, Yama K, Kumagai K, Jo R, Harada M, Maruyama Y, Aita Y, Fujii N, Inokuchi T, Kawamata R, Sako M, Ichiba Y, Tsutsumi K, Kimura M, Mori Y, Murakami S, Kakizawa Y, Kumagai T, Fukuda S. (2023) Integrated analysis of the oral and intestinal microbiome and metabolome of elderly people with more than 26 original teeth: a pilot study. Front Microbiol. 14:1233460. doi: 10.3389/fmicb.2023.1233460.

24. Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. (2023) Parallel nonfunctionalization of CK1 1δ/ε kinase ohnologs following a whole-genome duplication event. bioRxiv.2:2023.10.02.560513. doi: 10.1101/2023.10.02.560513.

25. Wang Y, Morishima T, Sezaki M, Sato R, Nakato G, Fukuda S, Kobiyama K, Ishii KJ, Li Y, Takizawa H. (2023) Akkermansia muciniphila induces slow extramedullary hematopoiesis via cooperative IL-1R/TLR signals. EMBO Rep. 24(12):e57485. doi: 10.15252/embr.202357485.

26. Kojima Y, Mishiro-Sato E, Fujishita T, Satoh K, Kajino-Sakamoto R, Oze I, Nozawa K, Narita Y, Ogata T, Matsuo K, Muro K, Taketo MM, Soga T, Aoki M. (2023) Decreased liver B vitamin-related enzymes as a metabolic hallmark of cancer cachexia. Nat Commun. 14(1):6246. doi: 10.1038/s41467-023-41952-w.

27. Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O. (2023) An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell. 186(22):4920-4935.e23. doi: 10.1016/j.cell.2023.08.031.

28. Probowati W, Koga S, Harada K, Nagano Y, Nagano AJ, Ishimaru K, Ohshima K, Fukuda S. (2023) RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized. Sci Rep. 13(1):16354. doi: 10.1038/s41598-023-43537-5.

29. Ichigaya N, Kawanishi N, Adachi T, Sugimoto M, Kimoto K, Hoshi N. (2023) Effects of Denture Treatment on Salivary Metabolites: A Pilot Study. Int J Mol Sci. 24(18):13959. doi: 10.3390/ijms241813959.

30. Jiang C, Saiki Y, Hirota S, Iwata K, Wang X, Ito Y, Murakami K, Imura T, Inoue J, Masamune A, Hirayama A, Goto M, Furukawa T. (2023) Ablation of Dual-Specificity Phosphatase 6 Protects against Nonalcoholic Fatty Liver Disease via Cytochrome P450 4A and Mitogen-Activated Protein Kinase. Am J Pathol. 193(12):1988-2000. doi: 10.1016/j.ajpath.2023.09.003.

31. Yamahira K, Kobayashi H, Kakioka R, Montenegro J, Masengi KWA, Okuda N, Nagano AJ, Tanaka R, Naruse K, Tatsumoto S, Go Y, Ansai S, Kusumi J. (2023) Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake. J Evol Biol. 36(10):1484-1493. doi: 10.1111/jeb.14223.

32. Hisatomi A, Kastawa NWEPG, Song I, Ohkuma M, Fukiya S, Sakamoto M. (2023) Claveliimonas bilis gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Sellimonas monacensis Zenner et al. 2021 as Claveliimonas monacensis comb. nov. Int J Syst Evol Microbiol. 73(9). doi: 10.1099/ijsem.0.006030.

33. Kopra K, Mahran R, Yli-Hollo T, Tabata S, Vuorinen E, Fujii Y, Vuorinen I, Ogawa-Iio A, Hirayama A, Soga T, Sasaki AT, Härmä H. (2023) Homogeneous luminescent quantitation of cellular guanosine and adenosine triphosphates (GTP and ATP) using QT-LucGTP&ATP assay. Anal Bioanal Chem. 415(27):6689-6700. doi: 10.1007/s00216-023-04944-9.

34. Yabushita T, Chinen T, Nishiyama A, Asada S, Shimura R, Isobe T, Yamamoto K, Sato N, Enomoto Y, Tanaka Y, Fukuyama T, Satoh H, Kato K, Saitoh K, Ishikawa T, Soga T, Nannya Y, Fukagawa T, Nakanishi M, Kitagawa D, Kitamura T, Goyama S. (2023) Mitotic perturbation is a key mechanism of action of decitabine in myeloid tumor treatment. Cell Rep. 42(9):113098. doi: 10.1016/j.celrep.2023.113098.

35. Ushio M, Saito H, Tojo M, Nagano AJ. (2023) An ecological network approach for detecting and validating influential organisms for rice growth. Elife. 12:RP87202. doi: 10.7554/eLife.87202.

36. Yama K, Nishimoto Y, Kumagai K, Jo R, Harada M, Maruyama Y, Aita Y, Fujii N, Inokuchi T, Kawamata R, Sako M, Ichiba Y, Tsutsumi K, Kimura M, Murakami S, Kakizawa Y, Kumagai T, Yamada T, Fukuda S. (2023) Dysbiosis of oral microbiome persists after dental treatment-induced remission of periodontal disease and dental caries. mSystems. 8(5):e0068323. doi: 10.1128/msystems.00683-23.

37. Ikeda Y, Davis MI, Sumita K, Zheng Y, Kofuji S, Sasaki M, Hirota Y, Pragani R, Shen M, Boxer MB, Takeuchi K, Senda T, Simeonov A, Sasaki AT. (2023) Multimodal action of KRP203 on phosphoinositide kinases in vitro and in cells. Biochem Biophys Res Commun. 679:116-121. doi: 10.1016/j.bbrc.2023.08.050.

38. Kitabatake K, Ishikawa S, Sugimoto M, Enomoto A, Kaneko M, Ota S, Edamatsu K, Yusa K, Hemmi T, Okuyama N, Iino M. (2023) Salivary metabolomics for oral leukoplakia with and without dysplasia. J Stomatol Oral Maxillofac Surg. 124(6S):101618. doi: 10.1016/j.jormas.2023.101618.

39. Shinzawa K, Matsumoto S, Sada R, Harada A, Saitoh K, Kato K, Ikeda S, Hirayama A, Yokoi K, Tanemura A, Nimura K, Ikawa M, Soga T, Kikuchi A. (2023) GREB1 isoform 4 is specifically transcribed by MITF and required for melanoma proliferation. Oncogene. 42(42):3142-3156. doi: 10.1038/s41388-023-02803-6.

40. Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H. (2023) Gut microbial carbohydrate metabolism contributes to insulin resistance. Nature. 621(7978):389-395. doi: 10.1038/s41586-023-06466-x.

41. Arakawa H, Kawanishi T, Shengyu D, Nishiuchi T, Meguro-Horike M, Horike SI, Sugimoto M, Kato Y. (2023) Renal Pharmacokinetic Adaptation to Cholestasis Causes Increased Nephrotoxic Drug Accumulation by Mrp6 Downregulation in Mice. J Pharm Sci. 112(12):3209-3215. doi: 10.1016/j.xphs.2023.08.008.

42. Saito M, Inose R, Sato A, Tomita M, Suzuki H, Kanai A. (2023) Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei. J Mol Evol. 91(5):669-686. doi: 10.1007/s00239-023-10128-x.

43. Englund E, Schmidt M, Nava AA, Klass S, Keiser L, Dan Q, Katz L, Yuzawa S, Keasling JD. (2023) Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries. Nat Commun. 14(1):4871. doi: 10.1038/s41467-023-40464-x.

44. Harigai W, Saito A, Zemmoto C, Karasawa S, Yokoi T, Nagano AJ, Suzuki H, Yamamoto M. (2023) History of the terrestrial isopod genus Ligidium in Japan based on phylogeographic analysis. BMC Ecol Evol. 23(1):38. doi: 10.1186/s12862-023-02144-8.

45. Perlee S, Kikuchi S, Nakadai T, Masuda T, Ohtsuki S, Matsumoto M, Rahmutulla B, Fukuyo M, Cifani P, Kentsis A, Roeder RG, Kaneda A, Hoshii T. (2023) SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3. EMBO Rep. 24(10):e57108. doi: 10.15252/embr.202357108.

46. Nose D, Matsui T, Otsuka T, Matsuda Y, Arimura T, Yasumoto K, Sugimoto M, Miura SI. (2023) Development of Machine Learning-Based Web System for Estimating Pleural Effusion Using Multi-Frequency Bioelectrical Impedance Analyses. J Cardiovasc Dev Dis. 10(7):291. doi: 10.3390/jcdd10070291.

47. Tanaka K, Tanigawa N, Song I, Komatsu T, Kuriki Y, Tanaka Y, Fukudo S, Urano Y, Fukuda S. (2023) A protease activity-based machine-learning approach as a complementary tool for conventional diagnosis of diarrhea-predominant irritable bowel syndrome. Front Microbiol. 14:1179534. doi: 10.3389/fmicb.2023.1179534.

48. Harada Y, Mizote Y, Suzuki T, Hirayama A, Ikeda S, Nishida M, Hiratsuka T, Ueda A, Imagawa Y, Maeda K, Ohkawa Y, Murai J, Freeze HH, Miyoshi E, Higashiyama S, Udono H, Dohmae N, Tahara H, Taniguchi N. (2023) Metabolic clogging of mannose triggers dNTP loss and genomic instability in human cancer cells. Elife. 12:e83870. doi: 10.7554/eLife.83870.

49. Yoichi W, Matsuzawa S, Tamaki I, Nagano AJ, Oh SH. (2023) Genetic differentiation and evolution of broad-leaved evergreen shrub and tree varieties of Daphniphyllum macropodum (Daphniphyllaceae). Heredity (Edinb). 131(3):211-220. doi: 10.1038/s41437-023-00637-2.

50. Iwai H, Kono N. (2023) Cuticular Hydrocarbon Profiling by Fractionation and GC-MS in Socially Parasitic Ants. Bio Protoc. 13(13):e4772. doi: 10.21769/BioProtoc.4772.

51. Watanabe Y, Arakawa K. (2023) Molecular mechanisms of the high performance of spider silks revealed through multi-omics analysis. Biophys Physicobiol. 20(1):e200014. doi: 10.2142/biophysico.bppb-v20.0014.

52. Sun J, Okada M, Tameshige T, Shimizu-Inatsugi R, Akiyama R, Nagano AJ, Sese J, Shimizu KK. (2023) A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat. NAR Genom Bioinform. 5(3):lqad067. doi: 10.1093/nargab/lqad067.

53. Matsumoto M, Ito H, Tateishi A, Kobayashi Y, Satoh K, Numata K, Miyakawa H. (2023) Effects of polycaprolactone degradation products on the water flea, Daphnia magna: Carbodiimide additives have acute and chronic toxicity. J Appl Toxicol. 43(12):1840-1848. doi: 10.1002/jat.4516.

54. Shiwa Y, Baba T, Sierra MA, Kim J, Mason CE, Suzuki H. (2023) Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces. BMC Res Notes. 16(1):142. doi: 10.1186/s13104-023-06417-9.

55. Nagai M, Moriyama M, Ishii C, Mori H, Watanabe H, Nakahara T, Yamada T, Ishikawa D, Ishikawa T, Hirayama A, Kimura I, Nagahara A, Naito T, Fukuda S, Ichinohe T. (2023) High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection. Nat Commun. 14(1):3863. doi: 10.1038/s41467-023-39569-0.

56. Aoki K, Nishito Y, Motoi N, Arai Y, Hiraoka N, Shibata T, Sonobe Y, Kayukawa Y, Hashimoto E, Takahashi M, Fujii E, Nishizawa T, Fukuda H, Ohashi K, Arai K, Mizoguchi Y, Yoshida Y, Watanabe SI, Yamashita M, Kitano S, Sakamoto H, Nagata Y, Mitsumori R, Ozaki K, Niida S, Kanai Y, Hirayama A, Soga T, Maruyama T, Tsukada K, Yabuki N, Shimada M, Kitazawa T, Natori O, Sawada N, Kato A, Yoshida T, Yasuda K, Mizuno H, Tsunoda H, Ochiai A. (2023) Tumor-infiltrating Leukocyte Profiling Defines Three Immune Subtypes of NSCLC with Distinct Signaling Pathways and Genetic Alterations. Cancer Res Commun. 3(6):1026-1040. doi: 10.1158/2767-9764.CRC-22-0415.

57. Takeuchi N, Hamada-Zhu S, Suzuki H. (2023) Prophages and plasmids can display opposite trends in the types of accessory genes they carry. Proc Biol Sci. 290(2001):20231088. doi: 10.1098/rspb.2023.1088.

58. Miyagi T, Ueda K, Sugimoto M, Yagi T, Ito D, Yamazaki R, Narumi S, Hayamizu Y, Uji-I H, Kuroda M, Kanekura K. (2023) Differential toxicity and localization of arginine-rich C9ORF72 dipeptide repeat proteins depend on de-clustering of positive charges. iScience. 26(6):106957. doi: 10.1016/j.isci.2023.106957.

59. Hibino S, Eto S, Hangai S, Endo K, Ashitani S, Sugaya M, Osawa T, Soga T, Taniguchi T, Yanai H. (2023) Tumor cell-derived spermidine is an oncometabolite that suppresses TCR clustering for intratumoral CD8+ T cell activation. Proc Natl Acad Sci U S A. 120(24):e2305245120. doi: 10.1073/pnas.2305245120.

60. Arakawa K, Hirose T, Inada T, Ito T, Kai T, Oyama M, Tomari Y, Yoda T, Nakagawa S. (2023) Nondomain biopolymers: Flexible molecular strategies to acquire biological functions. Genes Cells. 28(8):539-552. doi: 10.1111/gtc.13050.

61. Murai J, Ceribelli M, Fu H, Redon CE, Jo U, Murai Y, Aladjem MI, Thomas CJ, Pommier Y. (2023) Schlafen 11 (SLFN11) Kills Cancer Cells Undergoing Unscheduled Re-replication. Mol Cancer Ther. 22(8):985-995. doi: 10.1158/1535-7163.MCT-22-0552.

62. Kawamoto S, Uemura K, Hori N, Takayasu L, Konishi Y, Katoh K, Matsumoto T, Suzuki M, Sakai Y, Matsudaira T, Adachi T, Ohtani N, Standley DM, Suda W, Fukuda S, Hara E. (2023) Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota. Nat Cell Biol. 25(6):865-876. doi: 10.1038/s41556-023-01145-5.

63. Mandagi IF, K A Sumarto B, Nuryadi H, Mokodongan DF, Lawelle SA, Masengi KWA, Nagano AJ, Kakioka R, Kitano J, Ansai S, Kusumi J, Yamahira K. (2023) Multiple colonizations and hybridization of a freshwater fish group on a satellite island of Sulawesi. Mol Phylogenet Evol. 184:107804. doi: 10.1016/j.ympev.2023.107804.

64. Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. (2023) Facilitative interaction networks in experimental microbial community dynamics. Front Microbiol. 14:1153952. doi: 10.3389/fmicb.2023.1153952.

65. Hirayama A, Ishikawa T, Takahashi H, Yamanaka S, Ikeda S, Hirata A, Harada S, Sugimoto M, Soga T, Tomita M, Takebayashi T. (2023) Quality Control of Targeted Plasma Lipids in a Large-Scale Cohort Study Using Liquid Chromatography-Tandem Mass Spectrometry. Metabolites. 13(4):558. doi: 10.3390/metabo13040558.

66. Ajayi FF, Alnuaimi A, Hamdi M, Mostafa H, Wakayama M, Mudgil P, Maqsood S. (2023) Metabolomics approach for the identification of bioactive compounds released from young and mature soybean upon in vitro gastrointestinal digestion and their effect on health-related bioactive properties. Food Chem. 420:136050. doi: 10.1016/j.foodchem.2023.136050.

67. Yoshinaga N, Tateishi A, Kobayashi Y, Kubo T, Miyakawa H, Satoh K, Numata K. (2023) Effect of Oligomers Derived from Biodegradable Polyesters on Eco- and Neurotoxicity. Biomacromolecules. 24(6):2721-2729. doi: 10.1021/acs.biomac.3c00160.

68. Kitagawa A, Osawa T, Noda M, Kobayashi Y, Aki S, Nakano Y, Saito T, Shimizu D, Komatsu H, Sugaya M, Takahashi J, Kosai K, Takao S, Motomura Y, Sato K, Hu Q, Fujii A, Wakiyama H, Tobo T, Uchida H, Sugimachi K, Shibata K, Utsunomiya T, Kobayashi S, Ishii H, Hasegawa T, Masuda T, Matsui Y, Niida A, Soga T, Suzuki Y, Miyano S, Aburatani H, Doki Y, Eguchi H, Mori M, Nakayama KI, Shimamura T, Shibata T, Mimori K. (2023) Convergent genomic diversity and novel BCAA metabolism in intrahepatic cholangiocarcinoma. Br J Cancer. 128(12):2206-2217. doi: 10.1038/s41416-023-02256-4.

69. Yoichi W, Tamaki I, Oh SH, Nagano AJ, Uehara K, Tomaru N, Abe H. (2023) The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment. Am J Bot. 110(4):e16166. doi: 10.1002/ajb2.16166.

70. Nakamura H, Kono N, Mori M, Masunaga H, Numata K, Arakawa K. (2023) Composition of Minor Ampullate Silk Makes Its Properties Different from Those of Major Ampullate Silk. Biomacromolecules. 24(5):2042-2051. doi: 10.1021/acs.biomac.2c01474.

71. Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Iwayama K, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. (2023) Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics. Microbiome. 11(1):63. doi: 10.1186/s40168-023-01474-5.

72. Hayashi K, Kato N, Bashir K, Nomoto H, Nakayama M, Chini A, Takahashi S, Saito H, Watanabe R, Takaoka Y, Tanaka M, Nagano AJ, Seki M, Solano R, Ueda M. (2023) Subtype-selective agonists of plant hormone co-receptor COI1-JAZs identified from the stereoisomers of coronatine. Commun Biol. 6(1):320. doi: 10.1038/s42003-023-04709-1.

73. Ito Y, Uda S, Kokaji T, Hirayama A, Soga T, Suzuki Y, Kuroda S, Kubota H. (2023) Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures. Sci Rep. 13(1):4758. doi: 10.1038/s41598-023-31547-2.

74. Oba Y, Koga T, Takano Y, Ogawa NO, Ohkouchi N, Sasaki K, Sato H, Glavin DP, Dworkin JP, Naraoka H, Tachibana S, Yurimoto H, Nakamura T, Noguchi T, Okazaki R, Yabuta H, Sakamoto K, Yada T, Nishimura M, Nakato A, Miyazaki A, Yogata K, Abe M, Okada T, Usui T, Yoshikawa M, Saiki T, Tanaka S, Terui F, Nakazawa S, Watanabe SI, Tsuda Y; Hayabusa2-initial-analysis SOM team. (2023) Uracil in the carbonaceous asteroid (162173) Ryugu. Nat Commun. 14(1):1292. doi: 10.1038/s41467-023-36904-3.

75. Zhu X, Sakamoto S, Ishii C, Smith MD, Ito K, Obayashi M, Unger L, Hasegawa Y, Kurokawa S, Kishimoto T, Li H, Hatano S, Wang TH, Yoshikai Y, Kano SI, Fukuda S, Sanada K, Calabresi PA, Kamiya A. (2023) Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses. Nat Immunol.24(4):625-636. doi: 10.1038/s41590-023-01447-8.

76. Abhinand CS, Galipon J, Mori M, Ramesh P, Prasad TSK, Raju R, Sudhakaran PR, Tomita M. (2023) Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis. J Cell Commun Signal. 17(3):1067-1079. doi: 10.1007/s12079-023-00736-z.

77. Tabata S, Kojima Y, Sakamoto T, Igarashi K, Umetsu K, Ishikawa T, Hirayama A, Kajino-Sakamoto R, Sakamoto N, Yasumoto KI, Okano K, Suzuki Y, Yachida S, Aoki M, Soga T. (2023) L-2hydroxyglutaric acid rewires amino acid metabolism in colorectal cancer via the mTOR-ATF4 axis. Oncogene. 42(16):1294-1307. doi: 10.1038/s41388-023-02632-7.

78. Takeuchi K, Senda M, Ikeda Y, Okuwaki K, Fukuzawa K, Nakagawa S, Sasaki M, Sasaki AT, Senda T. (2023) Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ. FEBS J.290(18):4419-4428. doi: 10.1111/febs.16763.

79. Hirose S, Waku T, Tani M, Masuda H, Endo K, Ashitani S, Aketa I, Kitano H, Nakada S, Wada A, Hatanaka A, Osawa T, Soga T, Kobayashi A. (2023) NRF3 activates mTORC1 arginine-dependently for cancer cell viability. iScience. 26(2):106045. doi: 10.1016/j.isci.2023.106045.

80. Kawamura G, Kokaji T, Kawata K, Sekine Y, Suzuki Y, Soga T, Ueda Y, Endo M, Kuroda S, Ozawa T. (2023) Optogenetic decoding of Akt2-regulated metabolic signaling pathways in skeletal muscle cells using transomics analysis. Sci Signal. 16(773):eabn0782. doi: 10.1126/scisignal.abn0782.

81. Kono N. (2023) A Guide to Sequencing for Long Repetitive Regions. Methods Mol Biol. 2632:131-146. doi: 10.1007/978-1-0716-2996-3_10.

82. Arakawa K. (2023) A Nanopore Sequencing Course for Graduate School Curriculum. Methods Mol Biol. 2632:113-127. doi: 10.1007/978-1-0716-2996-3_9.

83. Takasuka K, Arakawa K. (2023) The Method of Eliminating the Wolbachia Endosymbiont Genomes from Insect Samples Prior to a Long-Read Sequencing. Methods Mol Biol. 2632:101-112. doi: 10.1007/978-1-0716-2996-3_8.

84. Arakawa K. (2023) Ultralow-Input Genome Library Preparation for Nanopore Sequencing with Droplet MDA. Methods Mol Biol. 2632:91-100. doi: 10.1007/978-1-0716-2996-3_7.

85. Nose D, Sugimoto M, Muta T, Miura SI. (2023) Salivary Polyamines Help Detect High-Risk Patients with Pancreatic Cancer: A Prospective Validation Study. Int J Mol Sci. 24(3):2998. doi: 10.3390/ijms24032998.

86. Shibuki T, Iida M, Harada S, Kato S, Kuwabara K, Hirata A, Sata M, Matsumoto M, Osawa Y, Okamura T, Sugiyama D, Takebayashi T. (2023) The association between sleep parameters and sarcopenia in Japanese community-dwelling older adults. Arch Gerontol Geriatr. 109:104948. doi: 10.1016/j.archger.2023.104948.

87. Muto N, Kawasaki T, Kakioka R, Nagano AJ, Shimizu Y, Inose S, Shimizu Y, Takahashi H. (2023) Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes). J Hered. 114(3):231-245. doi: 10.1093/jhered/esad007.

88. Tanaka Y, Yamashita R, Kawashima J, Mori H, Kurokawa K, Fukuda S, Gotoh Y, Nakamura K, Hayashi T, Kasahara Y, Sato Y, Fukudo S. (2023) Further notice of omics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation. J Gastroenterol. 58(4):427-428. doi: 10.1007/s00535-022-01951-y.

89. Hamada S, Kano S, Murai J, Suzuki T, Tsushima N, Mizumachi T, Suzuki M, Takashima T, Taniyama D, Sakamoto N, Fujioka Y, Ohba Y, Homma A. (2023) Schlafen family member 11 indicates favorable prognosis of patients with head and neck cancer following platinum-based chemoradiotherapy. Front Oncol. 12:978875. doi: 10.3389/fonc.2022.978875.

90. Hirabayashi T, Kawaguchi M, Harada S, Mouri M, Takamiya R, Miki Y, Sato H, Taketomi Y, Yokoyama K, Kobayashi T, Tokuoka SM, Kita Y, Yoda E, Hara S, Mikami K, Nishito Y, Kikuchi N, Nakata R, Kaneko M, Kiyonari H, Kasahara K, Aiba T, Ikeda K, Soga T, Kurano M, Yatomi Y, Murakami M. (2023) Hepatic phosphatidylcholine catabolism driven by PNPLA7 and PNPLA8 supplies endogenous choline to replenish the methionine cycle with methyl groups. Cell Rep. 42(2):111940. doi: 10.1016/j.celrep.2022.111940.

91. Matsuda H, Yamazaki Y, Moriyoshi E, Nakayasu M, Yamazaki S, Aoki Y, Takase H, Okazaki S, Nagano AJ, Kaga A, Yazaki K, Sugiyama A. (2023) Apoplast-Localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere. Plant Cell Physiol.64(5):486-500. doi: 10.1093/pcp/pcad012.

92. Hayasaka R, Tabata S, Hasebe M, Ikeda S, Hikita T, Oneyama C, Yoshitake J, Onoshima D, Takahashi K, Shibata T, Uchida K, Baba Y, Soga T, Tomita M, Hirayama A. (2023) Metabolomics of small extracellular vesicles derived from isocitrate dehydrogenase 1-mutant HCT116 cells collected by semi-automated size exclusion chromatography. Front Mol Biosci. 9:1049402. doi: 10.3389/fmolb.2022.1049402.

93. Chigira K, Yamasaki M, Adachi S, Nagano AJ, Ookawa T. (2023) Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi. Rice (N Y). 16(1):4. doi: 10.1186/s12284-023-00621-8.

94. Nishimoto Y, Kawai J, Mori K, Hartanto T, Komatsu K, Kudo T, Fukuda S. (2023) Dietary supplement of mushrooms promotes SCFA production and moderately associates with IgA production: A pilot clinical study. Front Nutr. 9:1078060. doi: 10.3389/fnut.2022.1078060.

95. Morita H, Kano C, Ishii C, Kagata N, Ishikawa T, Hirayama A, Uchiyama Y, Hara S, Nakamura T, Fukuda S. (2023) Bacteroides uniformisand its preferred substrate, α-cyclodextrin, enhance endurance exercise performance in mice and human males. Sci Adv.9(4):eadd2120. doi: 10.1126/sciadv.add2120.

96. Tanaka S, Aoki K, Arakawa K. (2023) In vivo expression vector derived from anhydrobiotic tardigrade genome enables live imaging in Eutardigrada. Proc Natl Acad Sci U S A. 120(5):e2216739120. doi: 10.1073/pnas.2216739120.

97. Nishimoto Y, Fujisawa K, Ukawa Y, Kudoh M, Funahashi K, Kishimoto Y, Fukuda S. (2023) Effect of urolithin A on the improvement of vascular endothelial function depends on the gut microbiota. Front Nutr. 9:1077534. doi: 10.3389/fnut.2022.1077534.

98. Kasuya K, Imura S, Ishikawa T, Sugimoto M, Inoue T. (2023) Relationship between Urinary Metabolomic Profiles and Depressive Episode in Antarctica. Int J Mol Sci. 24(2):943. doi: 10.3390/ijms24020943.

99. Noyes C, Kitajima S, Li F, Suita Y, Miriyala S, Isaac S, Ahsan N, Knelson E, Vajdi A, Tani T, Thai TC, Xu D, Murai J, Tapinos N, Takahashi C, Barbie DA, Yajima M. (2023) The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells. Commun Biol. 6(1):65. doi: 10.1038/s42003-023-04444-7.

100. Kijima Y, Evans-Yamamoto D, Toyoshima H, Yachie N. (2023) A universal sequencing read interpreter. Sci Adv. 9(1):eadd2793. doi: 10.1126/sciadv.add2793.

101. Ikizawa T, Ikeda K, Arita M, Kitajima S, Soga T, Ichijo H, Naguro I. (2023) Mitochondria directly sense osmotic stress to trigger rapid metabolic remodeling via regulation of pyruvate dehydrogenase phosphorylation. J Biol Chem. 299(2):102837. doi: 10.1016/j.jbc.2022.102837.

102. Rasmika Dewi DAP, Shiwa Y, Ryon K, Mason CE, Matsumoto T, Suzuki H. (2023) Urban Microbiomes in Narita, Chiba, Japan: Shotgun Metagenome Sequences of a Train Station. Microbiol Resour Announc. 12(1):e0109222. doi: 10.1128/mra.01092-22.

103. Maeda T, Sugano SS, Shirakawa M, Sagara M, Ito T, Kondo S, Nagano AJ. (2023) Single-Cell RNA Sequencing of Arabidopsis Leaf Tissues Identifies Multiple Specialized Cell Types: Idioblast Myrosin Cells and Potential Glucosinolate-Producing Cells. Plant Cell Physiol. 64(2):234-247. doi: 10.1093/pcp/pcac167.

104. Kondo F, Umeda K, Sudasinghe SP, Yamaguchi M, Aratani S, Kumanomido Y, Nemoto K, Nagano AJ, Matsushima K. (2023) Genetic analysis of pungency deficiency in Japanese chili pepper 'Shishito' (Capsicum annuum) revealed its unique heredity and brought the discovery of two genetic loci involved with the reduction of pungency. Mol Genet Genomics. 298(1):201-212. doi: 10.1007/s00438-022-01975-2.

105. Nakata S, Murai J, Okada M, Takahashi H, Findlay TH, Malebranche K, Parthasarathy A, Miyashita S, Gabdulkhaev R, Benkimoun I, Druillennec S, Chabi S, Hawkins E, Miyahara H, Tateishi K, Yamashita S, Yamada S, Saito T, On J, Watanabe J, Tsukamoto Y, Yoshimura J, Oishi M, Nakano T, Imamura M, Imai C, Yamamoto T, Takeshima H, Sasaki AT, Rodriguez FJ, Nobusawa S, Varlet P, Pouponnot C, Osuka S, Pommier Y, Kakita A, Fujii Y, Raabe EH, Eberhart CG, Natsumeda M. (2023)Epigenetic upregulation of Schlafen11 renders WNT- and SHH-activated medulloblastomas sensitive to cisplatin. Neuro Oncol.25(5):899-912. doi: 10.1093/neuonc/noac243.

106. Sugimoto M. (2023) Computational Simulation of Tumor-Induced Angiogenesis. Methods Mol Biol. 2553:275-283. doi: 10.1007/978-1-0716-2617-7_14.

107. Sugimoto M, Aizawa Y. (2023) Metabolomics Analysis of Blood, Urine, and Saliva Samples Based on Capillary Electrophoresis-Mass Spectrometry. Methods Mol Biol. 2571:83-94. doi: 10.1007/978-1-0716-2699-3_8.

108. Matsunami M, Murai-Hatano M, Kuwagata T, Matsushima U, Hashida Y, Tominaga Y, Masuya Y, Nagano AJ. (2023) Transcriptome dynamics of rice in natura: Response of above and below ground organs to microclimate. Plant Cell Environ. 46(4):1176-1194. doi: 10.1111/pce.14439.

109. Kikushige Y, Miyamoto T, Kochi Y, Semba Y, Ohishi M, Irifune H, Hatakeyama K, Kunisaki Y, Sugio T, Sakoda T, Miyawaki K, Kato K, Soga T, Akashi K. (2023) Human acute leukemia uses branched-chain amino acid catabolism to maintain stemness through regulating PRC2 function. Blood Adv. 7(14):3592-3603. doi: 10.1182/bloodadvances.2022008242.

110. Kure A, Tsukimi T, Ishii C, Aw W, Obana N, Nakato G, Hirayama A, Kawano H, China T, Shimizu F, Nagata M, Isotani S, Muto S, Horie S, Fukuda S. (2023) Gut environment changes due to androgen deprivation therapy in patients with prostate cancer. Prostate Cancer Prostatic Dis. 26(2):323-330. doi: 10.1038/s41391-022-00536-3.

2022

01. Yoshida Y, Shimizu I, Shimada A, Nakahara K, Yanagisawa S, Kubo M, Fukuda S, Ishii C, Yamamoto H, Ishikawa T, Kano K, Aoki J, Katsuumi G, Suda M, Ozaki K, Yoshida Y, Okuda S, Ohta S, Okamoto S, Minokoshi Y, Oda K, Sasaoka T, Abe M, Sakimura K, Kubota Y, Yoshimura N, Kajimura S, Zuriaga M, Walsh K, Soga T, Minamino T. (2022) Brown adipose tissue dysfunction promotes heart failure via a trimethylamine N-oxide-dependent mechanism. Sci Rep.12(1):14883.

02. Arakawa K, Kono N, Malay AD, Tateishi A, Ifuku N, Masunaga H, Sato R, Tsuchiya K, Ohtoshi R, Pedrazzoli D, Shinohara A, Ito Y, Nakamura H, Tanikawa A, Suzuki Y, Ichikawa T, Fujita S, Fujiwara M, Tomita M, Blamires SJ, Chuah JA, Craig H, Foong CP, Greco G, Guan J, Holland C, Kaplan DL, Sudesh K, Mandal BB, Norma-Rashid Y, Oktaviani NA, Preda RC, Pugno NM, Rajkhowa R, Wang X, Yazawa K, Zheng Z, Numata K. (2022) 1000 spider silkomes: Linking sequences to silk physical properties. Sci Adv.8(41):eabo6043.

03. Morita T, Majdalani N, Miura MC, Inose R, Oshima T, Tomita M, Kanai A, Gottesman S. (2022)Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli. mBio.13(6):e0237122.

04. Hoshii T, Perlee S, Kikuchi S, Rahmutulla B, Fukuyo M, Masuda T, Ohtsuki S, Soga T, Nabet B, Kaneda A. (2022)SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia.Cell Rep.41(9):111727.

05. Maeda T, Sugano SS, Shirakawa M, Sagara M, Ito T, Kondo S, Nagano AJ. (2022)Single-cell RNA Sequencing of Arabidopsis Leaf Tissues Identifies Multiple Specialized Cell Types: Idioblast Myrosin Cells and Potential Glucosinolate-producing Cells. Plant Cell Physiol.

06. Matsuta R, Yamamoto H, Tomita M, Saito R. (2022)iDMET: network-based approach for integrating differential analysis of cancer metabolomics. BMC Bioinformatics.23(1):508.

07. Miyakoshi M, Morita T, Kobayashi A, Berger A, Takahashi H, Gotoh Y, Hayashi T, Tanaka K. (2022)Glutamine synthetase mRNA releases sRNA from its 3'UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae. Elife.11.

08. Imajo M, Norikane T, Yamamoto Y, Maeda Y, Saitoh K, Kato K, Soga T, Okano K, Nishiyama Y. (2022)Relationship between [(18)F]FDG PET/CT and metabolomics in patients with colorectal cancer. Metabolomics.18(11):91.

09. Mori H, Yachie N. (2022)A framework to efficiently describe and share reproducible DNA materials and construction protocols. Nat Commun.13(1):2894.

10. Masuyama N, Konno N, Yachie N. (2022)Molecular recorders to track cellular events. Science.377(6605):469-70.

11. Tanaka S, Hashimoto K, Kobayashi Y, Yano K, Maeda T, Kameoka H, Ezawa T, Saito K, Akiyama K, Kawaguchi M. (2022)Asymbiotic mass production of the arbuscular mycorrhizal fungus Rhizophagus clarus. Commun Biol.5(1):43.

12. Tanaka H, Sun T, Kinashi H, Kamiya K, Yamaguchi M, Nobata H, Sakata F, Kim H, Mizuno M, Kunoki S, Sakai Y, Hirayama A, Soga T, Yoshikawa K, Ishimoto T, Ito Y. (2022) Interleukin-6 blockade reduces salt-induced cardiac inflammation and fibrosis in subtotal nephrectomized mice. Am J Physiol Renal Physiol.323(6):F654-F65.

13. Kokaji T, Eto M, Hatano A, Yugi K, Morita K, Ohno S, Fujii M, Hironaka KI, Ito Y, Egami R, Uematsu S, Terakawa A, Pan Y, Maehara H, Li D, Bai Y, Tsuchiya T, Ozaki H, Inoue H, Kubota H, Suzuki Y, Hirayama A, Soga T, Kuroda S. (2022)In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states. Sci Rep.12(1):13719.

14. Wada Y, Okano K, Sato K, Sugimoto M, Shimomura A, Nagao M, Matsukawa H, Ando Y, Suto H, Oshima M, Kondo A, Asano E, Kishino T, Kumamoto K, Kobara H, Kamada H, Masaki T, Soga T, Suzuki Y. (2022) Tumor metabolic alterations after neoadjuvant chemoradiotherapy predict postoperative recurrence in patients with pancreatic cancer. Jpn J Clin Oncol.52(8):887-95.

15. Ikeda Y, Hirayama A, Kofuji S, Hirota Y, Kamata R, Osaka N, Fujii Y, Sasaki M, Ikeda S, Smith EP, Bachoo R, Soga T, Sasaki AT. (2022) SI-MOIRAI: a new method to identify and quantify the metabolic fate of nucleotides. J Biochem. 170(6):699-711.

16. Miyazaki T, Chung S, Sakai H, Ohata H, Obata Y, Shiokawa D, Mizoguchi Y, Kubo T, Ichikawa H, Taniguchi H, Aoki K, Soga T, Nakagama H, Okamoto K. (2022) Stemness and immune evasion conferred by the TDO2-AHR pathway are associated with liver metastasis of colon cancer. Cancer Sci. 113(1):170-81.

17. Watanabe K, Iida M, Harada S, Kato S, Kuwabara K, Kurihara A, Takeuchi A, Sugiyama D, Okamura T, Suzuki A, Amano K, Hirayama A, Sugimoto M, Soga T, Tomita M, Kobayashi Y, Banno K, Aoki D, Takebayashi T. (2022) Metabolic profiling of charged metabolites in association with menopausal status in Japanese community-dwelling midlife women: Tsuruoka Metabolomic Cohort Study. Maturitas. 155:54-62.

18. Yoshida Y, Satoh T, Ota C, Tanaka S, Horikawa DD, Tomita M, Kato K, Arakawa K.(2022) Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades. BMC Genomics.23(1):405.

19. Evans-Yamamoto D, Rouleau FD, Nanda P, Makanae K, Liu Y, Despres PC, Matsuo H, Seki M, Dube AK, Ascencio D, Yachie N, Landry CR.(2022) Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery. Nucleic Acids Res.50(9):e54.

20. Yoshida Y, Shimizu I, Hsiao YT, Suda M, Katsuumi G, Seki M, Suzuki Y, Okuda S, Soga T, Minamino T.(2022) Differing impact of phosphoglycerate mutase 1-deficiency on brown and white adipose tissue. iScience.25(5):104268.

21. Saito Y, Matsuda S, Ohnishi N, Endo K, Ashitani S, Ohishi M, Ueno A, Tomita M, Ueda K, Soga T, Muthuswamy SK.(2022) Polarity protein SCRIB interacts with SLC3A2 to regulate proliferation and tamoxifen resistance in ER+ breast cancer. Commun Biol.5(1):403.

22. Ogawa T, Masumura K, Kohara Y, Kanai M, Soga T, Ohya Y, Blackwell TK, Mizunuma M.(2022) S-adenosyl-L-homocysteine extends lifespan through methionine restriction effects. Aging Cell.21(5):e13604.

23. Miyazawa K, Itoh SG, Yoshida Y, Arakawa K, Okumura H.(2022) Tardigrade Secretory-Abundant Heat-Soluble Protein Varies Entrance Propensity Depending on the Amino-Acid Sequence. J Phys Chem B.126(12):2361-8.

24. Kurihara Y, Iwai H, Kono N, Tomita M, Arakawa K.(2022) Initial parasitic behaviour of the temporary social parasitic ant Polyrhachis lamellidens can be induced by host-like cuticles in laboratory environment. Biol Open.11(3).

25. Ishihara S, Sato T, Fujikado N, Miyazaki H, Yoshimoto T, Yamamoto H, Fukuda S, Katagiri K.(2022) Rap1 prevents colitogenic Th17 cell expansion and facilitates Treg cell differentiation and distal TCR signaling. Commun Biol.5(1):206.

26. Akao Y, Kuranaga Y, Heishima K, Sugito N, Morikawa K, Ito Y, Soga T, Ito T.(2022) Plant hvu-MIR168-3p enhances expression of glucose transporter 1 (SLC2A1) in human cells by silencing genes related to mitochondrial electron transport chain complex I. J Nutr Biochem.101:108922.

27. Onji H, Murai J.(2022) Reconsidering the mechanisms of action of PARP inhibitors based on clinical outcomes. Cancer Sci.

28. Yamato M, Yamada H, Maeda T, Yamamoto K, Kusakabe R, Orihara T.(2022) Clonal spore populations in sporocarps of arbuscular mycorrhizal fungi. Mycorrhiza.

29. Pan M, Zorbas C, Sugaya M, Ishiguro K, Kato M, Nishida M, Zhang HF, Candeias MM, Okamoto A, Ishikawa T, Soga T, Aburatani H, Sakai J, Matsumura Y, Suzuki T, Proud CG, Lafontaine DLJ, Osawa T.(2022) Glutamine deficiency in solid tumor cells confers resistance to ribosomal RNA synthesis inhibitors. Nat Commun.13(1):3706.

30. Kuwabara H, Katsumata K, Iwabuchi A, Udo R, Tago T, Kasahara K, Mazaki J, Enomoto M, Ishizaki T, Soya R, Kaneko M, Ota S, Enomoto A, Soga T, Tomita M, Sunamura M, Tsuchida A, Sugimoto M, Nagakawa Y.(2022) Salivary metabolomics with machine learning for colorectal cancer detection. Cancer Sci.

31. Jangid A, Fukuda S, Seki M, Suzuki Y, Taylor TD, Ohno H, Prakash T.(2022) Gut microbiota alternation under the intestinal epithelium-specific knockout of mouse Piga gene. Sci Rep.12(1):10812.

32. Yamagishi R, Kamachi F, Nakamura M, Yamazaki S, Kamiya T, Takasugi M, Cheng Y, Nonaka Y, Yukawa-Muto Y, Thuy LTT, Harada Y, Arai T, Loo TM, Yoshimoto S, Ando T, Nakajima M, Taguchi H, Ishikawa T, Akiba H, Miyake S, Kubo M, Iwakura Y, Fukuda S, Chen WY, Kawada N, Rudensky A, Nakae S, Hara E, Ohtani N.(2022) Gasdermin D-mediated release of IL-33 from senescent hepatic stellate cells promotes obesity-associated hepatocellular carcinoma. Sci Immunol.7(72):eabl7209.

33. Suzuki Y, Hayasaka R, Hasebe M, Ikeda S, Soga T, Tomita M, Hirayama A, Kuroda H.(2022) Comparative Metabolomics of Small Molecules Specifically Expressed in the Dorsal or Ventral Marginal Zones in Vertebrate Gastrula. Metabolites.12(6).

34. Kadonosono T, Miyamoto K, Sakai S, Matsuo Y, Kitajima S, Wang Q, Endo M, Niibori M, Kuchimaru T, Soga T, Hirota K, Kizaka-Kondoh S.(2022) AGE/RAGE axis regulates reversible transition to quiescent states of ALK-rearranged NSCLC and pancreatic cancer cells in monolayer cultures. Sci Rep.12(1):9886.

35. Takeuchi K, Ikeda Y, Senda M, Harada A, Okuwaki K, Fukuzawa K, Nakagawa S, Yu HY, Nagase L, Imai M, Sasaki M, Lo YH, Ito D, Osaka N, Fujii Y, Sasaki AT, Senda T.(2022) The GTP responsiveness of PI5P4Kbeta evolved from a compromised trade-off between activity and specificity. Structure.30(6):886-99 e4.

36. Nakayama J, Konno Y, Maruyama A, Tomita M, Makinoshima H.(2022) Cinnamon bark extract suppresses metastatic dissemination of cancer cells through inhibition of glycolytic metabolism. J Nat Med.76(3):686-92.

37. Takeda T, Fukumitsu N, Yuzawa S, Arakawa K.(2022) Complete Genome Sequence of Streptomyces albus Strain G153. Microbiol Resour Announc.11(7):e0033222.

38. Ishikawa S, Huang M, Tomita A, Kurihara Y, Watanabe R, Iwai H, Arakawa K.(2022) Complete Genome Sequences of Four Bacteria Isolated from the Gut of a Spiny Ant (Polyrhachis lamellidens). Microbiol Resour Announc.11(7):e0033322.

39. Kudo R, Igarashi K, Soga T, Ishikawa T, Saito Y.(2022) Comprehensive metabolome analysis of intracellular metabolites in cultured cells. STAR Protoc.3(3):101531.

40. Imai T, Naruse M, Ochiai M, Matsumoto K, Ikeda S, Kani M, Kato Y, Hirayama A, Soga T, Hori Y, Yokoi A, Ochiai A.(2022) Different types of reactions to E7386 among colorectal cancer patient-derived organoids and corresponding CAFs. Oncol Lett.24(1):221.

41. Miki Y, Taketomi Y, Kidoguchi Y, Yamamoto K, Muramatsu K, Nishito Y, Park J, Hosomi K, Mizuguchi K, Kunisawa J, Soga T, Boilard E, SG BG, Ikeda K, Arita M, Murakami M.(2022) Group IIA secreted phospholipase A2 controls skin carcinogenesis and psoriasis by shaping the gut microbiota. JCI Insight.7(2).

42. Konishi A, Suzuki J, Kuwahara M, Matsumoto A, Nomura S, Soga T, Yorozuya T, Yamashita M.(2022) Glucocorticoid imprints a low glucose metabolism onto CD8 T cells and induces the persistent suppression of the immune response. Biochem Biophys Res Commun.588:34-40.

43. Kimura A, Hirayama A, Matsumoto T, Sato Y, Kobayashi T, Ikeda S, Maruyama M, Kaneko M, Shigeta M, Ito E, Soma T, Miyamoto K, Soga T, Tomita M, Oya A, Matsumoto M, Nakamura M, Kanaji A, Miyamoto T.(2022) Hao1 Is Not a Pathogenic Factor for Ectopic Ossifications but Functions to Regulate the TCA Cycle In Vivo. Metabolites.12(1).

44. Maruyama Y, Nishimoto Y, Umezawa K, Kawamata R, Ichiba Y, Tsutsumi K, Kimura M, Murakami S, Kakizawa Y, Kumagai T, Yamada T, Fukuda S.(2022) Comparison of oral metabolome profiles of stimulated saliva, unstimulated saliva, and mouth-rinsed water. Sci Rep.12(1):689.

45. Whitburn J, Rao SR, Morris EV, Tabata S, Hirayama A, Soga T, Edwards JR, Kaya Z, Palmer C, Hamdy FC, Edwards CM.(2022) Metabolic profiling of prostate cancer in skeletal microenvironments identifies G6PD as a key mediator of growth and survival. Sci Adv.8(8):eabf9096.

46. Uematsu S, Ohno S, Tanaka KY, Hatano A, Kokaji T, Ito Y, Kubota H, Hironaka KI, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S.(2022) Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. iScience.25(2):103787.

47. Arakawa K.(2022) Examples of Extreme Survival: Tardigrade Genomics and Molecular Anhydrobiology. Annu Rev Anim Biosci.10:17-37.

48. Richardson JJ, Liao W, Li J, Cheng B, Wang C, Maruyama T, Tardy BL, Guo J, Zhao L, Aw W, Ejima H.(2022) Rapid assembly of colorless antimicrobial and anti-odor coatings from polyphenols and silver. Sci Rep.12(1):2071.

49. Fujita S, Karasawa Y, Fujii M, Hironaka KI, Uda S, Kubota H, Inoue H, Sumitomo Y, Hirayama A, Soga T, Kuroda S.(2022) Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans. NPJ Syst Biol Appl.8(1):6.

50. Nishiumi S, Izumi Y, Hirayama A, Takahashi M, Nakao M, Hata K, Saigusa D, Hishinuma E, Matsukawa N, Tokuoka SM, Kita Y, Hamano F, Okahashi N, Ikeda K, Nakanishi H, Saito K, Hirai MY, Yoshida M, Oda Y, Matsuda F, Bamba T. (2022) Comparative Evaluation of Plasma Metabolomic Data from Multiple Laboratories. Metabolites.12(2).

51. Nishi M, Ogata T, Kobayakawa K, Kobayakawa R, Matsuo T, Cannistraci CV, Tomita S, Taminishi S, Suga T, Kitani T, Higuchi Y, Sakamoto A, Tsuji Y, Soga T, Matoba S.(2022) Energy-sparing by 2-methyl-2-thiazoline protects heart from ischaemia/reperfusion injury. ESC Heart Fail.9(1):428-41.

52. Okamoto L, Watanabe S, Deno S, Nie X, Maruyama J, Tomita M, Hatano A, Yugi K.(2022) Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach. Neurosci Res.175:82-97.

53. Jangid A, Fukuda S, Kato T, Seki M, Suzuki Y, Taylor TD, Ohno H, Prakash T.(2022) Impact of dietary fructooligosaccharides (FOS) on murine gut microbiota and intestinal IgA secretion. 3 Biotech.12(2):56.

54. Tsurumaki M, Saito M, Tomita M, Kanai A.(2022) Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis. RNA.28(8):1041-57.

55. Yukawa-Muto Y, Kamiya T, Fujii H, Mori H, Toyoda A, Sato I, Konishi Y, Hirayama A, Hara E, Fukuda S, Kawada N, Ohtani N.(2022) Distinct responsiveness to rifaximin in patients with hepatic encephalopathy depends on functional gut microbial species. Hepatol Commun.6(8):2090-104.

56. Shiroma H, Shiba S, Erawijantari PP, Takamaru H, Yamada M, Sakamoto T, Kanemitsu Y, Mizutani S, Soga T, Saito Y, Shibata T, Fukuda S, Yachida S, Yamada T.(2022) Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits. mSystems.7(2):e0001822.

57. Jangid A, Fukuda S, Suzuki Y, Taylor TD, Ohno H, Prakash T.(2022) Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice. Sci Rep.12(1):6748.

58. Kure A, Tsukimi T, Ishii C, Aw W, Obana N, Nakato G, Hirayama A, Kawano H, China T, Shimizu F, Nagata M, Isotani S, Muto S, Horie S, Fukuda S.(2022) Gut environment changes due to androgen deprivation therapy in patients with prostate cancer. Prostate Cancer Prostatic Dis.

59. Yoshida Y, Zheng T, Tanabe W, Tomoike F, Hashiya F, Suzuki T, Hirota S, Saiki Y, Horii A, Hirayama A, Soga T, Kimura Y, Abe H.(2022) Development of Fluorophosphoramidate as a Biocompatibly Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs. ChemMedChem:e202200188.

60. Nishimoto Y, Mizuguchi Y, Mori Y, Ito M, Miyazato S, Kishimoto Y, Yamada T, Fukuda S.(2022) Resistant Maltodextrin Intake Reduces Virulent Metabolites in the Gut Environment: A Randomized Control Study in a Japanese Cohort. Front Microbiol.13:644146.

61. Miura MC, Nagata S, Tamaki S, Tomita M, Kanai A.(2022) Distinct Expansion of Group II Introns During Evolution of Prokaryotes and Possible Factors Involved in Its Regulation. Front Microbiol.13:849080.

2021

01. Ishii N., Tajika Y., Murakami T., Galipon J., Shirahata H., Mukai R., Uehara D., Kaneko R., Yamazaki Y., Yoshimoto Y., Iwasaki H. (2021) Correlative microscopy and block-face imaging (CoMBI) method for both paraffin-embedded and frozen specimens. Scientific Reports, 11(1):13108. doi: 10.1038/s41598-021-92485-5.

02. Guo P., Zhang K., Yasuda Y., Yang W., Galipon J., Rival D.E. (2021) On the influence of biomimetic shark skin in dynamic flow separation. Bioinspiration & Biomimetics, 16(3). doi: 10.1088/1748-3190/abdf31.

03. Saito Y., Soga T. (2021) Amino acid transporters as emerging therapeutic targets in cancer. Cancer Science, doi: 10.1111/cas.15006.

04. Fujiwara, M., Kono, N., Hirayama, A., Malay, A.D., Nakamura, H., Ohtoshi, R., Numata, K., Tomita, M., Arakawa, K. (2021) Xanthurenic Acid Is the Main Pigment of Trichonephila clavata Gold Dragline Silk. Biomolecules. 11(4):563. doi: 10.3390/biom11040563.

05. Berger, C.A, Brewer, M.S., Kono, N., Nakamura, H., Arakawa, K., Kennedy, S.R., Wood, H.M., Adams, S.A., Gillespie, R.G. (2021) Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders. BMC Ecol Evol. 21(1):48. doi: 10.1186/s12862-021-01779-9.

06. Arakawa, K., Mori, M., Kono, N., Suzuki, T., Gotoh, T., Shimano, S. (2021) Proteomic evidence for the silk fibroin genes of spider mites (Order Trombidiformes: Family Tetranychidae). J Proteomics. 239:104195. doi: 10.1016/j.jprot.2021.104195.

07. Murai Y., Jo U., Murai J., Jenkins L.M., Huang S.N., Chakka S., Chen L., Cheng K., Fukuda S., Takebe N., Pommier Y. (2021) SLFN11 inactivation induces proteotoxic stress and sensitizes cancer cells to ubiquitin activating enzyme inhibitor TAK-243. Cancer Research. 81(11):3067-3078. doi: 10.1158/0008-5472.CAN-20-2694.

08. Takashima T., Taniyama D., Sakamoto N., Yasumoto M., Asai R., Hattori T., Honma R., Thang P.Q., Ukai S., Maruyama R., Harada K., Kuraoka K., Tanabe K, Sasaki A.T., Ohdan H., Morii E., Murai J., Yasui W. (2021) Schlafen 11 predicts response to platinum-based chemotherapy in gastric cancers. British journal of Cancer. 125(1):65-77. doi: 10.1038/s41416-021-01364-3.

09. Takashima T., Sakamoto N., Murai J., Taniyama D., Honma R., Ukai S., Maruyama R., Kuraoka K., Rajapakse V.N., Pommier Y., Yasui W. (2021) Immunohistochemical analysis of SLFN11 expression uncovers potential non-responders to DNA-damaging agents overlooked by tissue RNA-seq. Virchows Archiv. 478(3):569-579. doi: 10.1007/s00428-020-02840-6

10. Jo U., Murai Y., Chakka S., Chen L., Cheng K., Murai J., Saha L.K., Miller Jenkins L.M., Pommier Y. (2021) SLFN11 promotes CDT1 degradation by CUL4 in response to replicative DNA damage, while its absence leads to synthetic lethality with ATR/CHK1 inhibitors. Proceedings of the National Academy of Sciences. 118(6):e2015654118. doi: 10.1073/pnas.2015654118.

11. Moribe F., Nishikori M., Takashima T., Taniyama D, Onishi N, Arima H, Sasanuma H, Akagawa R, Elloumi F., Takeda S., Pommier Y., Morii E., Takaori-Kondo A., Murai J. (2021) Epigenetic suppression of SLFN11 in germinal center B-cells during B-cell development. PLoS One. 16(1):e0237554. doi: 10.1371/journal.pone.0237554

12. Takahashi H., Yang J., Yamamoto H., Fukuda S., Arakawa K. (2021) Complete Genome Sequence of Adlercreutzia equolifaciens subsp. celatus DSM 18785. Microbiology Resource Announcements. 10(19): e00354-21. doi: 10.1128/MRA.00354-21.

13. Yoshida Y., Horikawa DD., Sakashita T., Yokota Y., Kobayashi Y., Tomita M., Arakawa K. (2021) RNA sequencing data for gamma radiation response in the extremotolerant tardigrade Ramazzottius varieornatus. Data in Brief. 36:107111. doi: 10.1016/j.dib.2021.107111.

14. Warashina T., Yamamura S., Suzuki H., Amachi S., Arakawa K. (2021) Complete Genome Sequence of Geobacter sp. Strain SVR, an Antimonate-Reducing Bacterium Isolated from Antimony-Rich Mine Soil. Microbiology Resource Announcements. 10(14):e00142-21. doi: 10.1128/MRA.00142-21.

15. Nishimura K., Ikarashi M., Yasuda Y., Sato M., Cano Guerrero M., Galipon J., Arakawa K. (2021) Complete Genome Sequence of Sphingomonas paucimobilis Strain Kira, Isolated from Human Neuroblastoma SH-SY5Y Cell Cultures Supplemented with Retinoic Acid. Microbiology Resource Announcements. 10(6):e01156-20. doi: 10.1128/MRA.01156-20.

16. Arakawa K., Numata K. (2021) Reconsidering the "glass transition" hypothesis of intrinsically unstructured CAHS proteins in desiccation tolerance of tardigrades. Molecular Cell. 81(3):409-410. doi: 10.1016/j.molcel.2020.12.007

17. Fleming J.F., Arakawa K. (2021) Systematics of tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al. (2019). Zoologica Scripta. 50(3): 376-382. doi: 10.1111/zsc.12476

18. Igarashi K., Ota S., Kaneko M., Hirayama A., Enomoto M., Katumata K., Sugimoto M., Soga T. (2021) High-throughput Screening of Salivary Polyamine Markers for Discrimination of Colorectal Cancer by Multisegment Injection Capillary Electrophoresis Tandem Mass Spectrometry. J. Chromatogr. A. 1652, 462355, doi:10.1016/j.chroma.2021.462355. doi: 10.1016/j.chroma.2021.462355

19. Kozawa K., Sekai M., Ohba K., Ito S., Sako H., Maruyama T., Kakeno M., Shirai T., Kuromiya K., Kamasaki T., Kohashi K., Tanaka S., Ishikawa S., Sato N., Asano S., Suzuki H., Tanimura N., Mukai Y., Gotoh N., Tanino M., Tanaka S., Natsuga K., Soga T., Nakamura T., Yabuta Y., Saitou M., Ito T., Matsuura K., Tsunoda M., Kikumori T., Iida T., Mizutani Y., Miyai Y., Kaibuchi K., Enomoto A., Fujita Y. (2021) The CD44/COL17A1 pathway promotes the formation of multilayered, transformed epithelia. Curr Biol. 31(14):3086-3097.e7. doi: 10.1016/j.cub.2021.04.078.

20. Akiyama Y., Kikuchi K., Toyohara T., Mishima E., Suzuki C., Suzuki T., Nakayama M., Tomioka Y., Soga T., Abe T. (2021) CE-MS-based Identification of Uremic Solutes Specific to Hemodialysis Patients. Toxins.13(5):324. doi: 10.3390/toxins13050324.

21. Miyamoto K., Hirayama A., Sato Y., Ikeda S., Maruyama M., Soga T., Tomita M., Nakamura M., Matsumoto M., Yoshimura N., Miyamoto T. (2021) A Metabolomic Profile Predictive of New Osteoporosis or Sarcopenia Development. Metabolites. 11(5): 278. doi: 10.3390/metabo11050278.

22. Shimizu T., Kimura K., Sugihara E., Yamaguchi-Iwai S., Nobuse H., Sampetrean O., Otsuki Y., Fukuchi Y., Saitoh K., Kato K., Soga T., Muto A., Saya H. (2021) MEK inhibition preferentially suppresses anchorage-independent growth in osteosarcoma cells and decreases tumors in vivo. J. Orthop. Res. doi: 10.1002/jor.25023.

23. Nishida H., Okada M., Yang L., Takano T., Tabata S., Soga T., Ho D.M., Chung J., Minami Y., Yoo S.K., (2021)Methionine restriction breaks obligatory coupling of cell proliferation and death by an oncogene Src in Drosophila. ELife. 10: e59809. doi: 10.7554/eLife.59809.

24. Ishibashi Y., Harada S., Takeuchi A., Iida M., Kurihara A., Kato S., Kuwabara K., Hirata A., Shibuki T., Okamura T., Sugiyama D., Sato A, Amano K., Hirayama A., Sugimoto M., Soga T., Tomita M., Takebayashi, T. (2021) Reliability of urinary charged metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry. Sci. Rep. 11(1): 7407. doi: 10.1038/s41598-021-86600-9.

25. Hayasaka R., Tabata S., Hasebe M., Ikeda S., Ohnuma S., Mori M., Soga T., Tomita M., Hirayama A. (2021) Metabolomic Analysis of Small Extracellular Vesicles Derived from Pancreatic Cancer Cells Cultured under Normoxia and Hypoxia. Metabolites. 11(4): 215. doi: 10.3390/metabo11040215.

26. Hsiao Y.T., Shimizu I., Wakasugi T., Yoshida Y., Ikegami R., Hayashi Y., Suda M., Katsuumi G., Nakao M., Ozawa T., Izumi D., Kashimura T., Ozaki K., Soga T., Minamino T. (2021) Cardiac Mitofusin-1 is Reduced in Non-responding Patients with Idiopathic Dilated Cardiomyopathy. Sci. Rep. 11(1): 6722. doi: 10.1038/s41598-021-86209-y.

27. Egami R., Kokaji T., Hatano A., Yugi K., Eto M., Morita K., Ohno S., Fujii M., Hironaka K., Uematsu S., Terakawa A., Bai Y., Pan Y., Tsuchiya T., Ozaki H., Inoue H., Uda S., Kubota H., Suzuki Y., Matsumoto M., Nakayama K., Hirayama A., Soga T., Kuroda S., (2021) Trans-Omic Analysis Reveals Obesity-Associated Dysregulation of Inter-Organ Metabolomic Cycles between the Liver and Skeletal Muscle. iScience. 24(3): 102217. doi: 10.1016/j.isci.2021.102217.

28. Guo J., Wang J., Iino K., Tomita M., Soga T. (2021) Quantitative and Molecular Similarity Analyses of the Metabolites of Cold- and Hot-Natured Chinese Herbs. Evid. Based. Complement. Alternat. Med. 2021:6646507. doi: 10.1155/2021/6646507.

29. Guo J., Satoh K., Tabata S., Mori M., Tomita M., Soga T. (2021) Reprogramming of glutamine metabolism via glutamine synthetase silencing induces cisplatin resistance in A2780 ovarian cancer cells. BMC Cancer. 21(1): 174. doi: 10.1186/s12885-021-07879-5.

30. Shibutami E., Ishii R., Harada S., Kurihara A., Kuwabara K., Kato S., Iida M., Akiyama M., Sugiyama D., Hirayama A., Sato A., Amano K., Sugimoto M., Soga T., Tomita M., Takebayashi T. (2021) Charged metabolite biomarkers of food intake assessed via plasma metabolomics in a population-based observational study in Japan. PLoS One. 16(2): e0246456. doi: 10.1371/journal.pone.0246456.

31. Matsuo T., Isosaka T., Tang L., Soga T., Kobayakawa R., Kobayakawa K. (2021) Artificial hibernation/life-protective state induced by thiazoline-related innate fear odors. Commun Biol. 4(1): 101. doi: 10.1038/s42003-020-01629-2.

32. Sato M., Harada-Shoji N., Toyohara T., Soga T., Itoh M., Miyashita M., Tada H., Amari M., Anzai N., Furumoto S., Abe T., Suzuki T., Ishida T., Sasano H. (2021) L-type amino acid transporter 1 is associated with chemoresistance in breast cancer via the promotion of amino acid metabolism. Sci. Rep. 11(1): 589. doi: 10.1038/s41598-020-80668-5.

33. Saito R., Sugimoto M., Hirayama A., Soga T., Tomita M., Takebayashi T. (2021) Quality Assessment of Untargeted Analytical Data in a Large-Scale Metabolomic Study. J Clin Med 10(9): :1826. doi: 10.3390/jcm10091826.

34. Nakasuka F., Tabata S., Sakamoto T., Hirayama A., Ebi H., Yamada T., Umetsu K., Ohishi M., Ueno A., Goto H., Sugimoto M., Nishioka Y., Yamada Y., Tomita M., Sasaki A., Yano S., Soga T. (2021) TGF-β-dependent reprogramming of amino acid metabolism induces epitherial-mesenchymal transition in non-small cell lung cancers. Communications Biology. 4(1):782. doi: 10.1038/s42003-021-02323-7.

35. Takasuka K. (2021) The northernmost record of Eriostethus rufus (Uchida, 1932) (Hymenoptera, Ichneumonidae) with an indication of new host, Trichonephila clavata (Koch, 1878) (Araneae, Araneidae) and its web manipulation. Entomological Communications (2021) 3 ec03015. doi: 10.37486/2675-1305.ec03015.

36. Kitajima S., Sun W., Lee K.L., Ho J.C., Oyadomari S., Okamoto T., Masai H., Poellinger L., Kato H. A KDM6 inhibitor potently induces ATF4 and its target gene expression through HRI activation and by UTX inhibition Scientific Reports. 11(1):4538. doi: 10.1038/s41598-021-83857-y

37. International MetaSUB Consortium (2021) A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. 184(13):3376-3393.e17. doi: 10.1016/j.cell.2021.05.002.

38. MetaSUB Consortium (2021) COVID-19 drug practices risk antimicrobial resistance evolution. Lancet Microbe. 2(4):e135-e136. doi: 10.1016/S2666-5247(21)00039-2.

39. Yatsuoka W., Ueno T., Miyano K., Enomoto A., Ota S., Sugimoto M., Uezono Y. (2021) Time-Course of Salivary Metabolomic Profiles during Radiation Therapy for Head and Neck Cancer. J Clin Med. 10(12):2631. doi: 10.3390/jcm10122631.

40. Kato H., Sugimoto M., Enomoto A., Kaneko M., Hara Y., Saito N., Shiomi A., Ohnuki H., Izumi K. Metabolomic Alteration of Oral Keratinocytes and Fibroblasts in Hypoxia. J Clin Med. 10(6):1156. doi: 10.3390/jcm10061156.

41. Kumar N., Hoque M.A., Sugimoto M. (2021) Kernel weighted least square approach for imputing missing values of metabolomics data. Sci Rep. 11(1):11108. doi: 10.1038/s41598-021-90654-0.

42. Saito R, Hirayama A, Akiba A, Kamei Y, Kato Y, Ikeda S, Kwan B, Pu M, Natarajan L, Shinjo H, Akiyama S, Tomita M, Soga T, Maruyama S. (2021) Urinary Metabolome Analyses of Patients with Acute Kidney Injury Using Capillary Electrophoresis-Mass Spectrometry. Maturitas. 11(10).

43. Nakao M, Shimizu I, Katsuumi G, Yoshida Y, Suda M, Hayashi Y, Ikegami R, Hsiao YT, Okuda S, Soga T, Minamino T. (2021) Empagliflozin maintains capillarization and improves cardiac function in a murine model of left ventricular pressure overload. Sci Rep. 11(1):18384.

44. Heishima K, Sugito N, Soga T, Nishikawa M, Ito Y, Honda R, Kuranaga Y, Sakai H, Ito R, Nakagawa T, Ueda H, Akao Y. (2021) Petasin potently inhibits mitochondrial complex I-based metabolism that supports tumor growth and metastasis. J Clin Invest. 131(17).

45. Ryuge A, Kosugi T, Maeda K, Banno R, Gou Y, Zaitsu K, Ito T, Sato Y, Hirayama A, Tsubota S, Honda T, Nakajima K, Ozaki T, Kondoh K, Takahashi K, Kato N, Ishimoto T, Soga T, Nakagawa T, Koike T, Arima H, Yuzawa Y, Minokoshi Y, Maruyama S, Kadomatsu K. (2021) Basigin deficiency prevents anaplerosis and ameliorates insulin resistance and hepatosteatosis. JCI Insight. 6(20).

46. Murai Y, Jo U, Murai J, Fukuda S, Takebe N, Pommier Y. (2021) Schlafen 11 expression in human acute leukemia cells with gain-of-function mutations in the interferon-JAK signaling pathway. iScience. 24(10):103173.

47. Kono N, Nakamura H, Ohtoshi R, Arakawa K. (2021) Transcriptomic data during development of a two-spotted cricket Gryllus bimaculatus. Data Brief. 38:107388.

48. Taniyama D, Sakamoto N, Takashima T, Takeda M, Pham QT, Ukai S, Maruyama R, Harada K, Babasaki T, Sekino Y, Hayashi T, Sentani K, Pommier Y, Murai J, Yasui W. (2021) Prognostic impact of Schlafen 11 in bladder cancer patients treated with platinum-based chemotherapy. Cancer Sci.

49. Connell S, Kawashima M, Nakamura S, Imada T, Yamamoto H, Tsubota K, Fukuda S. (2021) Lactoferrin Ameliorates Dry Eye Disease Potentially through Enhancement of Short-Chain Fatty Acid Production by Gut Microbiota in Mice. Int J Mol Sci. 22(22).

50. Murai Y, Yagi-Utsumi M, Fujiwara M, Tanaka S, Tomita M, Kato K, Arakawa K. (2021) Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada. BMC Genomics. 22(1):813.

51. Yagi-Utsumi M, Aoki K, Watanabe H, Song C, Nishimura S, Satoh T, Yanaka S, Ganser C, Tanaka S, Schnapka V, Goh EW, Furutani Y, Murata K, Uchihashi T, Arakawa K, Kato K. (2021) Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade. Sci Rep. 11(1):21328.

52. Shibata S, Sogabe S, Miwa M, Fujimoto T, Takakura N, Naotsuka A, Kitamura S, Kawamoto T, Soga T. (2021) Identification of the first highly selective inhibitor of human lactate dehydrogenase B. Sci Rep. 11(1):21353.

53. Yokoyama Y, Shinohara K, Kitamura N, Nakamura A, Onoue A, Tanaka K, Hirayama A, Aw W, Nakamura S, Ogawa Y, Fukuda S, Tsubota K, Watanabe M. (2021) Metabolic Effects of Bee Larva-Derived Protein in Mice: Assessment of an Alternative Protein Source. Foods. 11(1):21353.

54. Maruyama A, Sato Y, Nakayama J, Murai J, Ishikawa T, Soga T, Makinoshima H. (2021) De novo deoxyribonucleotide biosynthesis regulates cell growth and tumor progression in small-cell lung carcinoma. Sci Rep. 11(1):13474.

55. Miyauchi K, Adachi Y, Tonouchi K, Yajima T, Harada Y, Fukuyama H, Deno S, Iwakura Y, Yoshimura A, Hasegawa H, Yugi K, Fujii SI, Ohara O, Takahashi Y, Kubo M. (2021) Influenza virus infection expands the breadth of antibody responses through IL-4 signalling in B cells. Nat Commun. 12(1):3789.

56. Kono N, Nakamura H, Tateishi A, Numata K, Arakawa K. (2021) The balance of crystalline and amorphous regions in the fibroin structure underpins the tensile strength of bagworm silk. Zoological Lett. 7(1):11.

57. Suzuki G, Saito Y, Seki M, Evans-Yamamoto D, Negishi M, Kakoi K, Kawai H, Landry CR, Yachie N, Mitsuyama T. (2021) Machine learning approach for discrimination of genotypes based on bright-field cellular images. NPJ Syst Biol Appl. 7(1):31.

58. Watanabe Y, Arakawa K. (2021) Complete Genome Sequences of Two Lysobacter Strains, Isolated from Seawater (Lysobacter caseinilyticus) and Soil (Lysobacter helvus) in South Korea. Microbiol Resour Announc. 10(28):e0033721.

59. Watanabe Y, Takeuchi N, Yang J, Obana N, Morinaga K, Kusada H, Tamaki H, Fukuda S, Arakawa K. (2021) Complete Genome Sequence of Atopobiaceae Bacterium Strain P1, Isolated from Mouse Feces. Microbiol Resour Announc. 10(28):e0062721.

60. Tomizawa Y, Kurokawa S, Ishii D, Miyaho K, Ishii C, Sanada K, Fukuda S, Mimura M, Kishimoto T. (2021) Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting. Int J Neuropsychopharmacol. 24(2):97-107.

61. Furusawa C, Tanabe K, Ishii C, Kagata N, Tomita M, Fukuda S. (2021) Decoding gut microbiota by imaging analysis of fecal samples. iScience. 24(12):103481.

62. Shindo H, Harada-Shoji N, Ebata A, Sato M, Soga T, Miyashita M, Tada H, Kawai M, Kosaka S, Onuki K, Usami S, Furumoto S, Hayashi S, Abe T, Suzuki T, Ishida T, Sasano H. (2021) Targeting Amino Acid Metabolic Reprogramming via L-Type Amino Acid Transporter 1 (LAT1) for Endocrine-Resistant Breast Cancer. Cancers (Basel). 13(17).

63. Matsuzaki F, Uda S, Yamauchi Y, Matsumoto M, Soga T, Maehara K, Ohkawa Y, Nakayama KI, Kuroda S, Kubota H. (2021) An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver. Cell Rep. 36(8):109569.

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2020

01. Toju, H., Abe S, M., Ishii, C., Hori, Y., Fujita H., and Fukuda, S. (2020) Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes. Frontiers in Microbiology, 11, 1361. doi: 10.3389/fmicb.2020.01361.

02. Zhang C, Amanda S, Wang C, Tan TK, Ali MZ, Leong WZ, Ng LM, Kitajima S, Li Z, Yeoh AEJ, Tan SH, Sanda T. (2020) Oncorequisite role of an aldehyde dehydrogenase in the pathogenesis of T-cell acute lymphoblastic leukemia. Haematologica May 2020 : haematol.2019.245639; doi: 10.3324/haematol.2019.245639

03. Kato H., Asamitsu K., Sun W., Kitajima S., Yoshizawa-Sugata N., Okamoto T., Masai H., Poellinger L. (2020) Cancer-derived UTX TPR Mutations G137V and D336G Impair Interaction with MLL3/4 complexes and Affect UTX Subcellular Localization. Oncogene, 39, 3322-3335.PMID: 32071397DOI: 10.1038/s41388-020-1218-3

04. Hikichi,S., Sugimoto,M., Tomita,M.(2020) Correlation-centred variable selection of a gene expression signature to predict breast cancer metastasis. Sci Rep. 2020;10(1):7923. doi:10.1038/s41598-020-64870-z

05. Tokuda M, Suzuki H, Yanagiya K, Yuki M, Inoue K, Ohkuma M, Kimbara K and Shintani M (2020) Determination of Plasmid pSN1216-29 Host Range and the Similarity in Oligonucleotide Composition Between Plasmid and Host Chromosomes. Front. Microbiol. 11:1187. doi: 10.3389/fmicb.2020.01187

06. Takashima, T., Sakamoto, N., Murai, J., Taniyama, D., Honma, R., Ukai, S., Yasui, W.v. Immunohistochemical analysis of SLFN11 expression uncovers potential non-responders to DNA-damaging agents overlooked by tissue RNA-seq. Virchows Archiv: an International Journal of Pathology.doi:10.1007/s00428-020-02840-6,

08. Rathkey, D., Khanal, M., Murai, J., Zhang, J., Sengupta, M., Jiang, Q., Chung, H. J. (2020) Sensitivity of mesothelioma cells to PARP inhibitors is not dependent on BAP1 but is enhanced by temozolomide in cells with high-schlafen 11 and low-O6-methylguanine-DNA methyltransferase expression. Journal of Thoracic Oncology. doi:10.1016/j.jtho.2020.01.012,

09. Erawijantari PP, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Saito Y, Fukuda S, Yachida S, Yamada T. (2020) Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles. Gut. 2020 Aug;69(8):1404-1415. doi: 10.1136/gutjnl-2019-319188. Epub 2020 Jan 16.

10. Imamoto A, Ki S, Li L, Iwamoto K, Maruthamuthu V, Devany J, Lu O, Kanazawa T, Zhang S, Yamada T, Hirayama A, Fukuda S, Suzuki Y, Okada M. (2020) Essential role of the Crk family-dosage in DiGeorge-like anomaly and metabolic homeostasis. Life Sci Alliance. 2020 Feb 10;3(2):e201900635. doi: 10.26508/lsa.201900635. Print 2020 Feb.

11. Nagao-Kitamoto H, Leslie JL, Kitamoto S, Jin C, Thomsson KA, Gillilland MG 3rd, Kuffa P, Goto Y, Jenq RR, Ishii C, Hirayama A, Seekatz AM, Martens EC, Eaton KA, Kao JY, Fukuda S, Higgins PDR, Karlsson NG, Young VB, Kamada N. (2020) Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nat Med. 2020 Apr;26(4):608-617. doi: 10.1038/s41591-020-0764-0. Epub 2020 Feb 17.

12. Jangid A, Fukuda S, Seki M, Horiuchi T, Suzuki Y, Taylor TD, Ohno H, Prakash T. (2020) Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice. PLoS One. 2020 Mar 24;15(3):e0228358. doi:10.1371/journal.pone.0228358.eCollection2020.

13. Aw W, Jia H, Lyu W, Fukuda S, Tomita M, Otani L, Kato H. (2020) Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum). NPJ Sci Food. 2020 Mar 31;4:5. doi: 10.1038/s41538-020-0065-5. eCollection 2020.

14. Tsukimi T, Watabe T, Tanaka K, Sato MP, Suzuki H, Tomita M, Fukuda S. (2020) Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals. J Genomics. 2020 Apr 6;8:37-42. doi: 10.7150/jgen.38516. eCollection 2020.

15. Seong KH, Ly NH, Katou Y, Yokota N, Nakato R, Murakami S, Hirayama A, Fukuda S, Kang S, Soga T, Shirahige K, Ishii S. (2020) Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells. Commun Biol. 2020 May 4;3(1):208. doi: 10.1038/s42003-020-0935-z.

16. Yang J, Yang Y, Ishii M, Nagata M, Aw W, Obana N, Tomita M, Nomura N, Fukuda S. (2020) Does the Gut Microbiota Modulate Host Physiology through Polymicrobial Biofilms? Microbes Environ. 2020;35(3). doi: 10.1264/jsme2.ME20037.

17. Vu, T.-D., Iwasaki, Y., Shigenobu, S., Maruko, A., Oshima, K., Iioka E., Huang, C.-L., Abe, T., Tamaki, S., Lin, Y.-W., Chen, C.-K., Lu, M.-Y., Hojo, M., Wang, H.-V., Tzeng, S.-F., Huang, H.-J., Kanai, A., Gojobori, T., Chiang, T.-Y., Sun, H. S., Li, W.-H., and Okada, N. (2020) Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens. PLOS Genetics.doi:10.1371/journal.pgen.1008831

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20. Kurihara Y, Kawai S, Ayano Sakai, Galipon J, Arakawa K. (2020) Complete Genome Sequence of Halomonas meridiana Strain Eplume2, Isolated from a Hydrothermal Plume in the Northeast Pacific Ocean. Microbiology Resource Announcements, 2020,May 14; 9(20): e00330-20. doi:10.1128/MRA.00330-20

21. Seo K, Tanaka K, Fukuda S, Arakawa K. (2020)Complete Genome Sequences of Two Cutibacterium acnes Strains Isolated from an Orthopedic Surgical Site. Microbiology Resource Announcements, 2020, Apr 23;9(17):e00290-20. doi:10.1128/MRA.00290-20

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23. Takahashi Y, Takahashi H, Galipon J, Arakawa K, (2020) Complete Genome Sequence of Halomonas meridiana Strain Slthf1, Isolated from a Deep-Sea Thermal Vent, Microbiology Resource Announcements, 2020, Apr 16;9(16):e00292-20. doi:10.1128/MRA.00292-20

24. Murai Y, Masuda T,Onuma Y,Yamamoto D.E,Takeuchi N,Mori H,Masuyama N,Ishiguro S, Yachie N, Arakawa K, (2020) Complete Genome Sequence of Bacillus sp. Strain KH172YL63, Isolated from Deep-Sea Sediment, Microbiology Resource Announcements, 2020, Apr 16; 9(16):e00291-20. doi:10.1128/MRA.00291-20

25. Takeyama N,Huang M,Sato K, Galipon J, Arakawa K, (2020) Complete Genome Sequence of Halomonas hydrothermalis Strain Slthf2, a Halophilic Bacterium Isolated from a Deep-Sea Hydrothermal-Vent Environment, Microbiology Resource Announcements, 2020, Apr 9;9 (15): e00294-20. doi:10.1128/MRA.00294-20

26. Arakawa K, (2020) Simultaneous Metabarcoding of Eukaryotes and Prokaryotes to Elucidate the Community Structures within Tardigrade Microhabitats, Diversity, 2020, 12(3):110. doi:10.3390/d12030110

27. Mapalo MA, Arakawa K, Baker CM, Persson DK, Mirano-Bascos D, Giribet G, (2020) The Unique Antimicrobial Recognition and Signaling Pathways in Tardigrades with a Comparison Across Ecdysozoa, G3(Bethesda), 2020 Jan 22, 10(3):1137-1148. doi:10.1534/g3.119.400734

28. Tadokoro H, Hirayama A, Kudo R, Hasebe M, Yoshioka Y, Matsuzaki J, Yamamoto Y, Sugimoto M, Soga T, Ochiya T. (2020)Adenosine leakage from perforin-burst extracellular vesicles inhibits perforin secretion by cytotoxic T-lymphocytes. PLoS One. 2020 Apr 10;15(4):e0231430. doi: 10.1371/journal.pone.0231430.

29. Endoh M, Baba M, Endoh T, Hirayama A, Nakamura-Ishizu A, Umemoto T, Hashimoto M, Nagashima K, Soga T, Lang M, Schmidt LS, Linehan WM, Suda T. (2020) A FLCN-TFE3 Feedback Loop Prevents Excessive Glycogenesis and Phagocyte Activation by Regulating Lysosome Activity. Cell Rep. 2020 Feb 11;30(6):1823-1834.e5. doi: 10.1016/j.celrep.2020.01.042.

30. Quek LE, Krycer JR, Ohno S, Yugi K, Fazakerley DJ, Scalzo R, Elkington SD, Dai Z, Hirayama A, Ikeda S, Shoji F, Suzuki K, Locasale JW, Soga T, James DE, Kuroda S. (2020) Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin. iScience. 2020 Feb 21;23(2):100855. doi: 10.1016/j.isci.2020.100855.

31. Hirayama A, Tabata S, Kudo R, Hasebe M, Suzuki K, Tomita M, Soga T. (2020) The use of a double coaxial electrospray ionization sprayer improves the peak resolutions of anionic metabolites in capillary ion chromatography-mass spectrometry. J Chromatogr A. 2020 May 24;1619:460914. doi: 10.1016/j.chroma.2020.460914.

32. Ogura, T., Wakayama, M., Ashino, Y., Kadowaki, R., Sato, M., Soga, T., Tomita, M. (2020) Effects of feed crops and boiling on chicken egg yolk and white determined by a metabolome analysis Food Chem. 327, 127077, doi:10.1016/j.foodchem.2020.127077, 2020.

33. Hamid, S.S., Wakayama, M., Ashino, Y., Kadowaki, R., Soga, T., Tomita, M. (2020) Effect of blanching on the concentration of metabolites in two parts of Undaria pinnatifida, Wakame (leaf) and Mekabu (sporophyll) Algal Res. 47, 101829, doi:10.1016/j.algal.2020.101829, 2020.

34. Sugimoto, M., Sugawara, T., Obiya, S., Enomoto, A., Kaneko, M., Ota, S., Soga, T., Tomita, M. (2020) Sensory properties and metabolomic profiles of dry-cured ham during the ripening process Food Res Int. 129, 108850, doi:10.1016/j.foodres.2019.108850, 2020.

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48. Malay AD, Suzuki T, Katashima T, Kono N, Arakawa K, Numata K. (2020) Spider silk self-assembly via modular liquid-liquid phase separation and nanofibrillation. Science Advance.2020 Nov 4;6(45):eabb6030. doi: 10.1126/sciadv.abb6030.

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50. Kondo K, Mori M, Tomita M, Arakawa K, (2020) Pre‐treatment with D942, a furancarboxylic acid derivative, increases desiccation tolerance in an anhydrobiotic tardigrade Hypsibius exemplaris. FEBS Open Bio 2020 Sep 10(9):1774-1781. doi: 10.1002/2211-5463.12926.

51. Ishikawa S, Hiraka T, Kirii K, Sugimoto M, Shimamoto H, Sugano A, Kitabatake K, Toyoguchi Y, Kanoto M, Nemoto K, Soga T, Tomita M, Iino M. (2020) Relationship between Standard Uptake Values of Positron Emission Tomography/Computed Tomography and Salivary Metabolites in Oral Cancer: A Pilot Study. J Clin Med. 2020 Dec 7; 9(12):E3958. doi: 10.3390/jcm9123958.

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65. Sugimoto M., Ota S., Kaneko M., Enomoto A., Soga T. (2020) Quantification of Salivary Charged Metabolites using Capillary Electrophoresis Time-of-flight-mass Spectrometry. Bio Protoc. 20;10(20):e3797. doi: 10.21769/BioProtoc.3797.

66. Hayashi Y., Mori M., Igarashi K., Tanaka K., Takehara A., Ito-Matsuoka Y., Kanai A., Yaegashi N., Soga T., Matsui Y. (2020) Proteomic and metabolomic analyses uncover sex-specific regulatory pathways in mouse fetal germline differentiation. Biol. Reprod. 103(4): 717-735. doi: 10.1093/biolre/ioaa115.

67. Kohno S., Linn P., Nagatani N., Watanabe Y., Kumar S., Soga T., Takahashi C. (2020) Pharmacologically targetable vulnerability in prostate cancer carrying RB1-SUCLA2 deletion. Oncogene.39(34): 5690-5707. doi: 10.1038/s41388-020-1381-6. 

68. Ohno S., Quek L.E., Krycer J.R., Yugi K., Hirayama A., Ikeda S., Shoji F., Suzuki K., Soga T., James D.E., Kuroda S., (2020) Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes. iScience. 23(9): 101479. doi: 10.1016/j.isci.2020.101479. 

69. Murai J., Zhang H., Pongor L., Tang S.W., Jo U., Moribe F., Ma Y., Tomita M., Pommier Y. (2020) Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress Cell Rep. 30(12):4137-4151.e6. doi: 10.1016/j.celrep.2020.02.117.

70. Ozawa H., Hirayama A., Ishikawa T., Kudo R., Maruyama M., Shoji F., Doke T., Ishimoto T., Maruyama S., Soga T., Tomita M. (2020) Comprehensive Dipeptide Profiling and Quantitation by Capillary Electrophoresis and Liquid Chromatography Coupled with Tandem Mass Spectrometry Anal Chem. 92(14):9799-9806. doi: 10.1021/acs.analchem.0c01258.

71. Stec D., Krzywański Ł., Arakawa K., Michalczyk Ł. (2020) A new redescription of Richtersius coronifer, supported by transcriptome, provides resources for describing concealed species diversity within the monotypic genus Richtersius (Eutardigrada). Zoological Lett. 6:2. doi: 10.1186/s40851-020-0154-y.

72. Malay A.D., Suzuki T., Katashima T., Kono N., Arakawa K., Numata K. (2020) Spider silk self-assembly via modular liquid-liquid phase separation and nanofibrillation. Science Advances. 6(45):eabb6030. doi: 10.1126/sciadv.abb6030.

2019

01. Deveaux,W., Hayashi,K., Selvarajoo,K.(2019) Defining rules for cancer cell proliferation in TRAIL stimulation. NPJ Syst Biol Appl. 2019 Feb 15;5:5. doi: 10.1038/s41540-019-0084-5. eCollection 2019.

02. Yasuda Y, Zhang K, Sasaki O, Tomita M, Rival D, Galipon J. (2019) Manufacturing of biomimetic silicone rubber films for experimental fluid mechanics: 3D printed shark skin molds. Journal of The Electrochemical Society 2019 volume 166, issue 9, B3302-B3308 doi: 10.1149/2.0461909jes

03. Yang J, Tsukimi T, Yoshikawa M, Suzuki K, Takeda T, Tomita M, Fukuda S. (2019) Cutibacterium acnes (Propionibacterium acnes) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification. mSystems. 2019 Nov 26;4(6). pii: e00594-19. doi: 10.1128/mSystems.00594-19.

04. Kitamoto S, Alteri CJ, Rodrigues M, Nagao-Kitamoto H, Sugihara K, Himpsl SD, Bazzi M, Miyoshi M, Nishioka T, Hayashi A, Morhardt TL, Kuffa P, Grasberger H, El-Zaatari M, Bishu S, Ishii C, Hirayama A, Eaton KA, Dogan B, Simpson KW, Inohara N, Mobley HLT, Kao JY, Fukuda S, Barnich N, Kamada N. (2019) Dietary L-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut. Nat Microbiol. 2019 Nov 4. doi: 10.1038/s41564-019-0591-6.

05. Jo R, Nishimoto Y, Umezawa K, Yama K, Aita Y, Ichiba Y, Murakami S, Kakizawa Y, Kumagai T, Yamada T, Fukuda S. (2019) Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water. Sci Rep. 2019 Nov 6;9(1):16124. doi: 10.1038/s41598-019-52445-6.

06. Aw W and Fukuda S. (2019) Protective effects of bifidobacteria against enteropathogens. Microb Biotechnol. 2019 Nov;12(6):1097-1100. doi: 10.1111/1751-7915.13460.

07. Orimo T, Sasaki I, Hemmi H, Ozasa T, Fukuda-Ohta Y, Ohta T, Morinaka M, Kitauchi M, Yamaguchi T, Sato Y, Tanaka T, Hoshino K, Katayama KI, Fukuda S, Miyake K, Yamamoto M, Satoh T, Furukawa K, Kuroda E, Ishii KJ, Takeda K, Kaisho T. (2019) Cholera toxin B induces interleukin-1β production from resident peritoneal macrophages through the pyrin inflammasome as well as the NLRP3 inflammasome. Int Immunol. 2019 Sep 18;31(10):657-668. doi: 10.1093/intimm/dxz004.

08. Kikuchi K, Saigusa D, Kanemitsu Y, Matsumoto Y, Thanai P, Suzuki N, Mise K, Yamaguchi H, Nakamura T, Asaji K, Mukawa C, Tsukamoto H, Sato T, Oikawa Y, Iwasaki T, Oe Y, Tsukimi T, Fukuda NN, Ho HJ, Nanto-Hara F, Ogura J, Saito R, Nagao S, Ohsaki Y, Shimada S, Suzuki T, Toyohara T, Mishima E, Shima H, Akiyama Y, Akiyama Y, Ichijo M, Matsuhashi T, Matsuo A, Ogata Y, Yang CC, Suzuki C, Breeggemann MC, Heymann J, Shimizu M, Ogawa S, Takahashi N, Suzuki T, Owada Y, Kure S, Mano N, Soga T, Wada T, Kopp JB, Fukuda S, Hozawa A, Yamamoto M, Ito S, Wada J, Tomioka Y, Abe T. (2019) Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease. Nat Commun. 2019 Apr 23;10(1):1835. doi: 10.1038/s41467-019-09735-4.

09. Nagata N, Tohya M, Fukuda S, Suda W, Nishijima S, Takeuchi F, Ohsugi M, Tsujimoto T, Nakamura T, Shimomura A, Yanagisawa N, Hisada Y, Watanabe K, Imbe K, Akiyama J, Mizokami M, Miyoshi-Akiyama T, Uemura N, Hattori M. (2019) Effects of bowel preparation on the human gut microbiome and metabolome. Sci Rep. 2019 Mar 11;9(1):4042. doi: 10.1038/s41598-019-40182-9.

10. Kushida M, Sugawara S, Asano M, Yamamoto K, Fukuda S, Tsuduki T. (2019) Effects of the 1975 Japanese diet on the gut microbiota in younger adults. J Nutr Biochem. 2019 Feb;64:121-127. doi: 10.1016/j.jnutbio.2018.10.011.

11. Murai J and Pommier Y (2019) Phosphatase 1 Nuclear Targeting Subunit, a Novel DNA Repair Partner of PARP1. Cancer Res. 2019 May 15;79(10):2460-2461. doi: 10.1158/0008-5472.CAN-19-0798.

12. Murai J and Pommier Y (2019) PARP trapping beyond homologous recombination and platinum sensitivity in cancers. Annual Review of Cancer Biology. Vol. 3:131-150 (Volume publication date March 2019) First published as a Review in Advance on November 7, 2018

13. Saito, M., Sato, A., Nagata, S., Tamaki, S., Tomita, M., Suzuki, H., and Kanai, A. (2019) Large-scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life. Genome Biol Evol. 2019 Oct 1;11(10):2713-2726. doi: 10.1093/gbe/evz195.

14. Kanai, A. and Yoshihisa, T. (2019) Editorial: Current Advances in the Research of RNA Regulatory Enzymes. Front Genet. 2019 Oct 9;10:973. doi: 10.3389/fgene.2019.00973. eCollection 2019.

15. Harada-Shoji, N., Soga, T., Tada, H., Miyashita, M., Harada, M., Watanabe, G., Hamanaka, Y., Sato, A., Suzuki, T., Suzuki, A., Ishida, T. (2019) A metabolic profile of routine needle biopsies identified tumor type specific metabolic signatures for breast cancer stratification: a pilot study. Metabolomics. 2019 Nov 4;15(11):147. doi: 10.1007/s11306-019-1610-6.

16. Louphrasitthiphol P., Ledaki I., Chauhan J., Falletta P., Siddaway R., Buffa FM., Mole DR., Soga T., *Goding CR., (2019) MITF controls the TCA cycle to modulate the melanoma hypoxia response. Pigment Cell Melanoma Res. 2019 Nov;32(6):792-808. doi: 10.1111/pcmr.12802.

17. Hashimoto, N., Nakamichi, N., Nanmo, H., Kimura, K., Masuo, Y., Sakai, Y., Schinkel, A.H., Sato, S., Soga, T., Kato, Y., (2019) Metabolome Analysis Reveals Dermal Histamine Accumulation in Murine Dermatitis Provoked by Genetic Deletion of P-Glycoprotein and Breast Cancer Resistance Protein. Pharm. Res. 2019 Sep 11;36(11):158. doi: 10.1007/s11095-019-2695-3.

18. Fukushima, K., Harada, S., Takeuchi, A., Kurihara, A., Iida, M., Fukai, K., Kuwabara, K., Kato, S., Matsumoto, M., Hirata, A., Akiyama, M., Tomita, M., Hirayama, A., Sato, A., Suzuki, C., Sugimoto, M., Soga, T., Sugiyama, D.,Okamura, T., Takebayashi, T., (2019) Association between dyslipidemia and plasma levels of branched-chain amino acids in the Japanese population without diabetes mellitus. J. Clini. Lipidol 13(6), 932-939, doi:10.1016/j.jacl.2019.09.002, 2019.

19. Hayasaki, T., Ishimoto, T., Doke, T., Hirayama, A., Soga, T., Furuhashi, K., Kato, N., Kosugi, T., Tsuboi, N., Lanaspa, MA., Johnson, RJ., Maruyama, S., Kadomatsu, K., (2019) Fructose Increases the Activity of Sodium Hydrogen Exchanger in Renal Proximal Tubules that is Dependent on Ketohexokinase. J. Nutr. Biochem. 2019 Sep;71:54-62. doi: 10.1016/j.jnutbio.2019.05.017.

20. Yoneshiro T., Wang, Q., Tajima K., Matsushita M., Maki H., Igarashi K., Dai Z., White PJ., McGarrah RW., Ilkayeva OR., Deleye Y., Oguri Y., Kuroda M., Ikeda K., Li H., Ueno A., Ohishi M., Ishikawa T., Kim K., Chen Y., Sponton CH., Pradhan RN., Majd H., Greiner VJ., Yoneshiro M., Brown Z., Chondronikola M., Takahashi H., Goto T., Kawada T., Sidossis L., Szoka FC., McManus MT., Saito M., Soga T., Kajimura S., (2019) BCAA catabolism in brown fat controls energy homeostasis through SLC25A44. Nature. 2019 Aug;572(7771):614-619. doi: 10.1038/s41586-019-1503-x.

21. Yatsuoka, W., Ueno, T., Miyano, K., Uezono, Y., Enomoto, A., Kaneko, M., Ota, S., Soga, T., Sugimoto, M., Ushijima, T., (2019) Metabolomic profiling reveals salivary hypotaurine as a potential early detection marker for medication-related osteonecrosis of the jaw. PLoS One. 2019 Aug 12;14(8):e0220712. doi: 10.1371/journal.pone.0220712. eCollection 2019.

22. Kofuji, S., Hirayama, A., Eberhardt, A.O., Kawaguchi R., Sugiura, Y., Sampetrean, O., Ikeda, Y., Warren, M., Sakamoto, N., Kitahara, S., Yohino, H., Yamashita, D., Sumita, K., Wofe, K., Lange, L., Ikeda, S., Shimada, H., Minami, N., Malhotra, A., Morioka, S., Ban, Y., Asano, M., Flanary, V.L., Ramkissoon, A., Chow, L.M.L., Kiyokawa, J., Mahimo, T., Lucey, G., Mareninov, S., Ozawa, T., Onishi, N., Okumura, K., Terakawa, J., Daikoku, T., Wise-Draper, T., Majd, N., Kofuji, K., Sasaki, M., Mori, M., Kanemura, Y., Smith, E.P., Anastasiou, D., Wakimoto, H., Holland, E.C., Yong, W.H., Horbinski, C., Nakano, I., Deberardinis, R.J., Bachoo, R., Mischel, P.S., Yasui, W., Suematsu, M., Saya, H., Soga, T., Grummt, I., Bierhoff, H., Sasaki, AT., (2019) IMP dehydrogenase-2 drives aberrant nucleolar activity and promotes tumorigenesis in glioblastoma. Nat. Cell Biol. 2019 Aug;21(8):1003-1014. doi: 10.1038/s41556-019-0363-9.

23. Valli, A., Morotti, M., Zois, CE., Albers, PK., Soga, T., Feldinger, K., Fischer, R., Frejno, M., McIntyre, A., Bridges, E., Haider, S., Buffa, FM., Baban, D., Rodriguezm, M., Yanes, O., Whittington, HJ., Lake, HA., Zervou, S., Lygate, CA., Kessler, BM., Harris, AL., (2019) Adaptation to HIF1α deletion in hypoxic cancer cells by upregulation of GLUT14 and creatine metabolism. Mol. Cancer Res. 2019 Jul;17(7):1531-1544. doi: 10.1158/1541-7786.MCR-18-0315.

24. *Osada-Oka, M., Goda, N., Saiga, H., Yamamoto, M., Takeda, K., Ozeki, Y., Yamagchi, T., Soga, T., Tateishi, Y., Miura, K., Okuzaki, D., Kobayashi, K., *Matsumoto, S., (2019) Metabolic adaptation to glycolysis is a basic defense mechanism of macrophages for Mycobacterium tuberculosis infection. Int. Immunol. 2019 Nov 8;31(12):781-793. doi: 10.1093/intimm/dxz048.

25. Yachida, S., Mizutani, S., Shiroma, H., Shiba, S., Nakajima, T., Sakamoto, T., Watanabe, H., Masuda, K., Nishimoto, Y., Kubo, M., Hosoda, F., Rokutan, H., Matsumoto, M., Takamaru, H., Yamada, M., Matsuda, T., Iwasaki, M., Yamaji, T., Yachida, T., Soga, T., Kurokawa, K., Toyoda, A., Ogura, Y., Hayashi, T., Hatakeyama, M., Nakagama, H., Saito, Y., Fukuda, S., Shibata, T., Yamada, T., (2019) Metagenomic and metabolimic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nat. Med. 2019 Jun;25(6):968-976. doi: 10.1038/s41591-019-0458-7.

26. Takai, T., Tsujino, T., Yoshikawa, Y., Inamoto, T., Sugito, N., Kuranaga, Y., Heishima, K., Soga, T., Hayashi, K., Miyata, K., Kataoka, K., Azuma, H., Akao, Y., (2019) Synthetic miR-143 Exhibited an Anti-Cancer Effect via the Downregulation of K-RAS Networks of Renal Cell Cancer Cells In Vitro and In Vivo. Mol. Ther. 2019 May 8;27(5):1017-1027. doi: 10.1016/j.ymthe.2019.03.004.

27. Furukawa, T., Yamasaki, Y., Hara, Y., Otsuki, C., Maki, H., Soga, T., Moriyama, Y., Kuroda, H., (2019) Axis elongation during Xenopus tail-bud stage is regulated by GABA expressed in the anterior-to-mid neural tube. Int. J. Dev. Biol. 2019;63(1-2):37-43. doi: 10.1387/ijdb.180384hk.

28. Saito, T., Kuma, A., Sugiura, Y., Ichimura, Y., Obata, M., Kitamura, H., Okuda, S., Lee, HC., Ikeda, K., Kanegae, Y., Saito, I., Auwerx, J., Motohashi, H., Suematsu, M., Soga, T., Yokomizo, T., Waguri, S., Mizushima, N., Komatsu M., (2019) Autophagy regulates lipid metabolism through selective turnover of NCoR1. Nat. Commun 2019 Apr 5;10(1):1567. doi: 10.1038/s41467-019-08829-3.

29. Wakasugi, T., Shimizu, I., Yoshida, Y., Hayashi, Y., Ikegami, R., Suda, M., Katsuumi, G., Nakao, M., Hoyano, M., Kashimura, T., Nakamura, K., Ito, H., Nojiri, T., Soga, T., Minamino, T., (2019) Role of smooth muscle cell p53 in pulmonary arterial hypertension. PLoS One 2019 Feb 26;14(2):e0212889. doi: 10.1371/journal.pone.0212889. eCollection 2019.

30. Saito, Y., Li L., Coyaud E., Luna A., Sander C., Raught B., Asara J.M., Brown M., Muthuswamy S.K. LLGL2 rescues nutrient stress by promoting Leu uptake in ER+ breast cancer. Nature 2019 May;569(7755):275-279. doi: 10.1038/s41586-019-1126-2.

31. Ii KM, Kono N, Paulino-Lima IG, Tomita M, Rothschild LJ, Arakawa K(2019) Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert. J Genomics 2019 Feb 18;7:18-25. doi: 10.7150/jgen.32194. eCollection 2019.

32. Ohshima Y., Kono N., Yokota Y., Watanabe S., Sasaki I., Ishioka NS., Sakashita T., Arakawa K. (2019) Anti-tumor effects and potential therapeutic response biomarkers in α-emitting meta-211At-astato-benzylguanidine therapy for malignant pheochromocytoma explored by RNA-sequencing. Theranostics 2019 Feb 27;9(6):1538-1549. doi: 10.7150/thno.30353. eCollection 2019.

33. Sugiura K., Minato H., Suzuki AC., Arakawa K., Kunieda T., Matsumoto M. (2019) Comparison of Sexual Reproductive Behaviors in Two Species of Macrobiotidae (Tardigrada: Eutardigrada). Zoological Science 2019 Apr 1;36(2):120-127. doi: 10.2108/zs180103.

34. Evans-Yamamoto D., Takeuchi N., Masuda T., Murai Y., Onuma Y., Mori H., Masuyama N., Ishiguro S., Yachie N., Arakawa K., (2019) Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan. Microbiol Resour Announc. 2019 Apr 18;8(16). pii: e00326-19. doi: 10.1128/MRA.00326-19.

35. Kono N., Nakamura H., Ohtoshi R., Tomita M., Numata K., Arakawa K.(2019) The bagworm genome reveals a unique fibroin gene that provides high tensile strength. Communications Biology Apr 29;2:148. doi: 10.1038/s42003-019-0412-8. eCollection 2019.

36. Kono N., Arakawa K., (2019) Nanopore sequencing: Review of potential applications in functional genomics. Develop Growth Differ. 2019 Jun;61(5):316-326. doi: 10.1111/dgd.12608.

37. Saito M., Nishigata A., Galipon J., Arakawa K. (2019) Complete Genome Sequence of Halomonas sulfidaeris Strain Esulfide1 Isolated from a Metal Sulfide Rock at a Depth of 2,200 Meters, Obtained Using Nanopore Sequencing. Microbiol Resour Announc. 2019 Jun 6;8(23). pii: e00327-19. doi: 10.1128/MRA.00327-19.

38. Nagata S., Ii KM., Tsukimi T., Miura MC., Galipon J., Arakawa K.(2019) Complete Genome Sequence of Halomonas olivaria, a Moderately Halophilic Bacterium Isolated from Olive Processing Effluents, Obtained by Nanopore Sequencing. Microbiol Resour Announc. 2019 May 2;8(18). pii: e00144-19. doi: 10.1128/MRA.00144-19.

39. Kono N., Nakamura H., Ohtoshi R., Pedrazzoli Moran DA., Shinohara A., Yoshida Y., Fujiwara M., Mori M., Tomita M., Arakawa K. (2019) Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue. Scientific Reports 2019 Jun. 10;9(1):8380. doi: 10.1038/s41598-019-44775-2.

40. Masuda T., Kono N., Tomita M., Arakawa K.(2019) Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coligenomes. Bio-protocol 2019 Aug. 9(15): e3329. DOI: 10.21769/BioProtoc.3329.

41. Yoshida Y., Novel RW., Arakawa K., Baxter M. (2019) Horizontal Gene Transfer in Metazoa: Examples and Methods. Horizontal Gene Transfer 2019 Aug. 203-226. doi: https://doi.org/10.1007/978-3-030-21862-1_7

42. Craig RJ., Böndel KB., Arakawa K., Nakada T., Ito T., Bell G., Colegrave N., Keightley PD., Ness RB. (2019) Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii. Molecular Ecology 2019 Sep;28(17):3977-3993. doi: 10.1111/mec.15193.

43. Kondo K., Mori M., Tomita M., Arakawa K. (2019) AMPK activity is required for the induction of anhydrobiosis in a tardigrade Hypsibius exemplaris, and its potential up-regulator is PP2A. Genes to Cells 2019Oct 14. doi: 10.1111/gtc.12726.

44. Izumi Y, Matsuda F, Hirayama A, Ikeda K, Kita Y, Horie K, Saigusa D, Saito K, Sawada Y, Nakanishi H, Okahashi N, Takahashi M, Nakao M, Hata K, Hoshi Y, Morihara M, Tanabe K, Bamba T, Oda Y. Inter-Laboratory Comparison of Metabolite Measurements for Metabolomics Data Integration. Metabolites. 2019 Oct 31;9(11).pii: E257. doi: 10.3390/metabo9110257.

45. Masuda, T., Sugiyama, N., Tomita, M., Ohtsuki, S. and *Ishihama, Y. Mass Spectrometry-compatible Subcellular Fractionation for Proteomics. J Proteome Res. (2019 Oct 17)doi: 10.1021/acs.jproteome.9b00347.

46. Tanaka, K., Watabe, T., Kato, K., Tsukimi, T., Sato, MP., Odamaki, T., Tomita, M. and Fukuda, S. Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals. Microbiol Resour Announc. (2019 Oct 3)8(40). pii: e00832-19.doi: 10.1128/MRA.00832-19.

47. Murata, T., Yanagisawa, T., Kurihara, T., Kaneko, M., Ota, S., Enomoto, A., Tomita, M., Sugimoto, M., Sunamura, M., Hayashida, T., Kitagawa, Y. and Jinno, H. Salivary metabolomics with alternative decision tree-based machine learning methods for breast cancer discrimination. Breast Cancer Res Treat. 2019 Oct;177(3):591-601. doi: 10.1007/s10549-019-05330-9.

48. Takasuka, K., Matsumoto, R. & Maeto, K. (2019) Oviposition behaviour by a spider-ectoparasitoid, Zatypota maculata, exploits the specialised prey capture technique of its spider host. Journal of Zoology 2019 Jul. 308, 221-230. doi: 10.1111/jzo.12668

49. Koshidaka, N. & Takasuka, K. (2019) Discovery of a bagworm devouring an orb-web. Arachnology 2019 Aug. 18, 147-149. doi: 10.13156/arac.2018.18.2.147

50. Takasuka K. (2019) Evaluation of manipulative effects by an ichneumonid spider-ectoparasitoid larva upon an orb-weaving spider host (Araneidae, Cyclosa argenteoalba) by means of surgical removal and transplantation. Journal of Arachnology 2019 Sep. 47, 181-189. doi: 10.1636/JoA-S-18-082

51. Takasuka K. (2019) The second record of Allagelena opulenta (Araneae, Agelenidae) parasitized by the spider-ectoparasitoid, Brachyzapus nikkoensis (Hymenoptera, Ichneumonidae). Acta Arachnologica 2019 Dec. 68, 77-81. doi: not yet assigned

52. Nakada,T., Tsuchida,Y., Tomita,M. (2019) Improved taxon sampling and multigene phylogeny of unicellular chlamydomonads closely related to the colonial volvocalean lineage Tetrabaenaceae-Goniaceae-Volvocaceae (Volvocales, Chlorophyceae). Mol Phylogenet Evol. 130:1-8. doi: 10.1016/j.ympev.2018.09.013.

53. Nakada,T., Watanabe,S., Lewis,L.A., Tomita,M. (2019) Chlorococcum turfosum comb. nov. (Volvocales, Chlorophyceae) and visualization of chimeric sequences. Phycol Res. 67:239-243. doi: 10.1111/pre.12365.

54. Itaya, M., Sato, M., Watanabe, S., Yoshikawa, H., Tomita, M. and Sato, R. Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: Hub strains for giant DNA engineering. J Biochem. 2019 Sep 1;166(3):231-236. doi: 10.1093/jb/mvz031.

55. Harada, M., Ito, K., Nakajima, N., Yamamura, S., Tomita, M., Suzuki, H. and Amachi, S. Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation. G3 (Bethesda) 2019 May 7;9(5):1321-1329. doi: 10.1534/g3.118.200978.

56. Hamid, SS., Wakayama, M., Ichihara, K., Sakurai, K., Ashino, Y., Kadowaki, R., Soga, T. and Tomita, M. Metabolome profiling of various seaweed species discriminates between brown, red, and green algae. Planta. 2019 Jun;249(6):1921-1947. doi: 10.1007/s00425-019-03134-1.

57. Itaya, M., Nagasaku, M., Shimada, T., Ohtani, N., Shiwa, Y., Yoshikawa, H., Kaneko, S., Tomita, M. and Sato, M. Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids. FEMS Microbiol Lett. 2019 Feb 1;366(4). pii: fnz032. doi: 10.1093/femsle/fnz032.

58. Merino, N., Zhang, S., Tomita, M. and Suzuki, H. Comparative genomics of Bacteria commonly identified in the built environment. BMC Genomics. 2019 Jan 28;20(1):92. doi: 10.1186/s12864-018-5389-z.

59. Sasaki, K., Sagawa, H., Suzuki, M., Yamamoto, H., Tomita, M., Soga, T. and Ohashi, Y. Metabolomics Platform with Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Plasma Analysis. Anal Chem. 2019 Jan 15;91(2):1295-1301. doi: 10.1021/acs.analchem.8b02994.

60. Kawanishi, N., Hoshi, N., Masahiro, S., Enomoto, A., Ota, S., Kaneko, M., Soga, T., Tomita, M. and Kimoto, K. Effects of inter-day and intra-day variation on salivary metabolomic profiles. Clin Chim Acta. 2019 Feb;489:41-48. doi: 10.1016/j.cca.2018.11.030.

61. Yoshida Y, Sugiura K, Tomita M, Matsumoto M, Arakawa K. Comparison of the transcriptomes of two tardigrades with different hatching coordination. BMC Development Biology , 2019, 19(1):24. doi:10.1186/s12861-019-0205-9

62. Takahagi, W., Seo, K., Shibuya, T., Takano, Y., Fujishima, K., Saitoh, M., Shimamura, S., Matsui, Y., Tomita, M. and Takai, K. (2019) Peptide synthesis under the alkaline hydrothermal conditions on Enceladus. ACS Earth and Space Chemistry , 3, 2559-2568. doi:10.1021/acsearthspacechem.9b00108.

63. Suzuki, A., Onodera, K., Matsui, K., Seki, M., Esumi, H., Soga, T., Sugano, S., Kohno, T., Suzuki, Y., Tsuchihara, K., (2019) Characterization of cancer omics and drug perturbations in panels of lung cancer cells. Sci Rep. 9(1), 19529, doi:10.1038/s41598-019-55692-9, 2019.

64. Annan, D.A., Maishi, N., Soga T., Dawood, R. Li, C., Kikuchi, H., Hojo, T., Morimoto, M., Kitamura, T., Alam, M.T., Minowa, K., Shinohara, N., Nam, JM., Hida, Y., Hida, K., (2019) Carbonic anhydrase 2 (CAII) supports tumor blood endothelial cell survival under lactic acidosis in the tumor microenvironment. Cell Commun. Signal. 17(1), 169, doi: 10.1186/s12964-019-0478-4, 2019.

65. Fujiwara, H., Tateishi, K., Misumi, K., Hayashi, A., Igarashi, K, Kato, H., Nakatsuka, T., Suzuki, N., Yamamoto, K., Kudo, Y., Hayakawa, Y., Nakagawa, H., Tanaka, Y., Ijichi, H., Kogure, H, Nakai, Y, Isayama, H., Hasegawa, K., Fukayama, M., Soga, T., Koike, K., (2019) Mutant IDH1 confers resistance to energy stress in normal biliary cells through PFKP-induced aerobic glycolysis and AMPK activation.Sci. Rep. 9(1), 18859, doi: 10.1038/s41598-019-55211-w, 2019.

66. Nakagawa, M., Nakatani, F., Matsunaga H., Seki T., Endo M., Ogawara Y., Machida Y., Katsumoto T., Yamagata K., Hattori A., Fujita S., Aikawa Y., Ishikawa T., Soga T., Kawai A., Chuman H., Yokoyama N., Fukushima S., Yahiro K., Kimura A., Shimada E., Hirose T., Fujiwara T., Setsu N., Matsumoto Y., Iwamoto Y., Nakashima Y., *Kitabayashi I. (2019) Selective inhibition of mutant IDH1 by DS-1001b ameliorates aberrant histone modifications and impairs tumor activity in chondrosarcoma. Oncogene 38(42), 6835-6849, doi:10.1038/s41388-019-0929-9, 2019.

67. Osawa, T., Shimamura, T., Saito, K., Hasegawa, Y., Ishii, N., Nishida, M., Ando, R., Kondo, A., Anwar, M., Tsuchida, R., Hino, S., Sakamoto, A., Igarashi, K., Saitoh, K., Kato, K., Endo, K., Yamano, S., Kanki, Y., Matsumura, Y., Minami, T., Tanaka, T., Anai, M., Wada, Y., Wanibuchi, H., Hayashi, M., Hamada, A., Yoshida, M., Yachida, S., Nakao, M., Sakai, J., Aburatani, H., Shibuya, M., Hanada, K., Miyano, S., Soga, T., Kodama, T., (2019) Phosphoethanolamine Accumulation Protects Cancer Cells under Glutamine Starvation through Downregulation of PCYT2.Cell Rep. 29(1), 89-103. e7, doi:10.1016/j.celrep.2019.08.087, 2019.

68. Nishimura, T., Nakata, A., Chen, X., Nishi, K., Meguro-Horike, M., Sasaki, S., Kita, K., Horike, S., Saitoh, K., Kato, K., Igarashi, K., Murayama, T., Kohno, S., Takahashi, C., Mukaida, N., Yano, S., Soga, T., Tojo, A., Gotoh, N., (2019) Cancer stem-like properties and gefitinib resistance are dependent on purine synthetic metabolism mediated by the mitochondrial enzyme MTHFD2. Oncogene 38(14), 2464-2481, doi:10.1038/s41388-018-0589-1, 2019.

69. Nakai, G., Shimura, D., Uesugi, K., Kajimura, I., Jiao, Q., Kusakari, Y., Soga, T., Goda, N., Minamisawa, S., (2019) Pyruvate dehydrogenase activation precedes the down-regulation of fatty acid oxidation in monocrotaline-induced myocardial toxicity in mice. Heart Vessels. 34(3), 545-555, doi:10.1007/s00380-018-1293-3, 2019.

70. Maedera, S., Mizuno, T., Ishiguro, H., Ito, T., Soga, T., Kusuhara, H., (2019) GLUT6 is a lysosomal transporter that is regulated by inflammatory stimuli and modulates glycolysis in macrophages. FEBS Lett. 593(2), 195-208, doi:10.1002/1873-3468.13298, 2019.

70. Yoshino H, Yin G, Kawaguchi R, Popov KI, Temple B, Sasaki M, Kofuji S, Wolfe K, Kofuji K, Okumura K, Randhawa J, Malhotra A, Majd N, Ikeda Y, Shimada H, Kahoud ER, Haviv S, Iwase S, Asara JM, Campbell SL, Sasaki AT. Identification of lysine methylation in the core GTPase domain by GoMADScan. PLoS One. 2019 Aug 7;14(8):e0219436.

71. Kajiura D, Yamanaka-Okumura H, Hirayama A, Tatano H, Endo K, Honma M, Igarashi K, Syoji F, Ikeda S, Yamaguchi N, Katayama T, Morine Y, Imura S, Utsunomiya T, Soga T, Tomita M, Shimada M. Perioperative serum and urine metabolome analyses in patients with hepatocellular carcinoma undergoing partial hepatectomy. Nutrition 2019 Feb; 58:110-119. doi: 10.1016/j.nut.2018.06.002.

72. Ishiguro S, Mori H, Yachie N. DNA event recorders send past information of cells to the time of observation. Curr Opin Chem Biol 2019 Oct;52:54-62. doi: 10.1016/j.cbpa.2019.05.009.

73. Marchant A, Cisneros AF, Dubé AK, Gagnon-Arsenault I, Ascencio D, Jain H, Aubé S, Eberlein C, Evans-Yamamoto D, Yachie N, Landry CR. The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. Elife 2019 Aug 27;8:e46754. doi: 10.7554/eLife.46754.

74. Yano H., Shintani M., Tomita M., Suzuki H., Oshima T.(2019)Reconsidering plasmid maintenance factors for computational plasmid design. Comput Struct Biotechnol J. 17:70-81. doi: 10.1016/j.csbj.2018.12.001.

75. Asano M, Ishii T, Hirayama A, Mizuno M, Suzuki Y, Sakata F, Akiyama SI, Maruyama S, Soga T, Kinashi H, Katsuno T, Ito Y.(2019)Differences in peritoneal solute transport rates in peritoneal dialysis. Clin Exp Nephrol. 23(1):122-34.

2018

01. Tamaki, S., Tomita, M., Suzuki, H. and Kanai, A.(2018) Systematic analysis of the binding surfaces between tRNAs and their respective aminoacyl tRNA synthetase based on structural and evolutionary data. Front Genet. 8:227. doi: 10.3389/fgene.2017.00227. eCollection 2017.

02. Fujishima, K., K. M. Wang, J. A. Palmer, N. Abe, K. Nakahigashi, D. Endy, and L. J. Rothschild.(2018) Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes. Sci Rep. 8(1):1776. doi: 10.1038/s41598-018-19920-y.

03. Izuta, Y., Imada, T., Hisamura, R., Oonishi, E., Nakamura. S., Inagaki, E., Ito, M., Soga, T., Tsubota, K.(2018) Ketone body 3-hydroxybutyrate mimics calorie restriction via the Nrf2 activator, fumarate, in the retina. Aging Cell. 17(1). doi: 10.1111/acel.12699.

04. Stec, D., Arakawa, K., Michalczyk, Ł.(2018) An integrative description of Macrobiotus shonaicus sp. nov. (Tardigrada: Macrobiotidae) from Japan with notes on its phylogenetic position within the hufelandi group. PLoS One. 13(2):e0192210. doi: 10.1371/journal.pone.0192210.

05. Kim, S., Matsumoto, T., Kagawa, H., Nakamura, M., Hirohata, R., Ueno, A., Ohishi, M., Sakuma, T., Soga, T., Yamamoto, T., Woltjen, K.(2018) Microhomology-assisted scarless genome editing in human iPSCs. Nat Commun. 9(1):939. doi: 10.1038/s41467-018-03044-y.

06. Kaneko, S., Nakahama, M., Fukushima, H., Asano, S., Miyazaki, Y., Aizawa, Y., and Itaya, M.(2018) DNA synthesis by fragment assembly using extra-cellular DNA delivered by artificial controlled horizontal transfer. J. Biochem.2018 Apr 1;163(4):305-312. doi: 10.1093/jb/mvx085.

07. Itaya, M., Kusakabe, H., Sato, M., Tomita, M. and Sato, R.(2018) Efficient delivery of large DNA from Escherichia coli to Synechococcus elongatus PCC7942 by broad-host-range conjugal plasmid pUB307. J.Biochem.2018 Jul 1;164(1):15-20. doi: 10.1093/jb/mvy026.

08. Itaya, M., Hasegawa, M., Tomita, M., and Sato, M.(2018) The first high frequency of recombination-like conjugal transfer from an integrated origin of transfer sequence in Bacillus subtilis 168. Biosci. Biotechnol. Biochem. 82(2):356-362. doi: 10.1080/09168451.2017.1422970.

09. Oshima, K., Saiki, N., Tanaka, M., Imamura, H. Niwa, A., Tanimura, A., Nagahashi;, A., Hirayama, A., Okita, K., Hotta, A., Kitayama, S., Osawa, M., Kaneko, S., Watanabe, A., Asaka, I., Fujibuchi W., Imai, K., Yabe, H., Kamachi, Y., Hara J., Kojima, S., Tomita, M., Soga, T., Noma, T., Nonoyama, S., Nakahata, T., Saito, M.K.(2018) Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors. Biochem. Biophys. Res. Commun. 497(2):719-725. doi: 10.1016/j.bbrc.2018.02.139.

10. Takasuka K., Fritzé n N.R., Tanaka Y., Matsumoto R., Maeto K. & Shaw M.R.(2018) The changing use of the ovipositor in host shifts by ichneumonid ectoparasitoids of spiders (Hymenoptera, Ichneumonidae, Pimplinae). Parasite. 25:17. doi: 10.1051/parasite/2018011.

11. Tabata, S., Yamamoto, M., Goto, H., Hirayama, A., Ohishi, M., Kuramoto, T., Mitsuhashi, A., Ikeda, R., Haraguchi, M., Kawahara, K., Shinsato, Y., Minami, K., Saijo, A., Toyoda, Y., Hanibuchi, M., Nishioka, Y., Sone, S., Esumi, H., Tomita, M., Soga, T., Furukawa, T., Akiyama, SI.(2018) Thymidine catabolism promotes NADPH oxidase-derived reactive oxygen species (ROS) signalling in KB and yumoto cells. Sci Rep. 8(1):6760. doi: 10.1038/s41598-018-25189-y.

12. Nagata, Y., Hirayama, A., Ikeda, S., Shirahata, A., Shoji, F., Maruyama, M., Kayano, M., Bundo, M., Hattori, K., Yoshida, S., Goto, Y., Urakami, K., Soga, T., Ozaki, K., Niida, S.(2018) Comparative analysis of cerebrospinal fluid metabolites in Alzheimer's disease and idiopathic normal pressure hydrocephalus in a Japanese cohort. Biomark. Res. 6:5. doi: 10.1186/s40364-018-0119-x.

13. Saito, Y., Morine Y., Iwahashi, S., Ikemoto, T., Imura, S., Yamanaka-Okumura, H., Hirayama, A., Soga, T., Tomita, M., Shimada, M.(2018) Changes of Liver Metabolites following Hepatectomy with Ischemia Reperfusion towards Liver Regeneration. Ann. Gastroenterol. Surg. 2(3):204-211. doi: 10.1002/ags3.12058.

14. Asai, Y., Itoi, T., Sugimoto, M., Sofuni, A., Tsuchiya, T, Tanaka, R., Tonozuka, R., Honjo, M., Mukai, S., Fujita, M., Yamamoto, K., Matsunami, Y., Kurosawa, T., Nagakawa, Y., Kaneko, M., Ota, S., Kawachi, S., Shimazu, M., Soga, T., Tomita, M. and Sunamura., M.(2018) Elevated Polyamines in Saliva of Pancreatic Cancer. Cancers (Basel). 10(2). pii: E43. doi: 10.3390/cancers10020043.

15. Nakajima, T., Katsumata, K., Kuwabara, H., Soya, R., Enomoto, M., Ishizaki, T., Tsuchida, A., Mori, M., Hiwatari, K., Soga, T., Tomita, M., Sugimoto, M.(2018) Urinary Polyamine Biomarker Panels with Machine-Learning Differentiated Colorectal Cancers, Benign Disease, and Healthy Controls. Int. J. Mol. Sci. 19(3). pii: E756. doi: 10.3390/ijms19030756.

16. Morita, M., Sato, T., Nomura, M., Sakamoto, Y., Inoue, Y., Tanaka, R., Ito, S., Kurosawa, K., Yamaguchi, K., Sugiura, Y., Takizaki, H., Yamashita, Y., Katakura, R., Sato, I., Kawai, M., Okada, Y., Watanabe, H., Kondoh, G., Matsumoto, S., Kishimoto, A., Obata, M., Matsumoto, M., Fukuhara, T., Motohashi, H., Suematsu, M., Komatsu, M., Nakayama, KI., Watanabe, T., Soga, T., Shima, H., Maemondo, M., Tanuma. N.(2018) PKM1 confers metabolic advantages and promotes cell-autonomous tumor cell growth. Cancer Cell. 33(3):355-367.e7. doi: 10.1016/j.ccell.2018.02.004.

17. McCarthy, MT., Moncayo, G., Hiron, TK., Jakobsen, NA., Valli, A., Soga, T., Adam, J., O'Callaghan, CA.(2018) Purine nucleotide metabolism regulates expression of the human immune ligand MICA. J. Biol. Chem. 293(11):3913-3924. doi: 10.1074/jbc.M117.809459.

18. Hoshina, R. and Nakada, T.(2018) Carolibrandtia nom. nov. as a replacement name for BrandtiaHoshina (Chlorellaceae, Trebouxiophyceae). Phycol. Res. 66, 82-83. (2018)

19. Matsuda, J., Namba, T., Takabatake, Y., Kimura, T., Takahashi, A., Yamamoto, T., Minami, S., Sakai, S., Fujimura, R., Kaimori, J.Y., Matsui, I., Hamano, T., Fukushima, Y., Matsui, K., Soga, T., Isaka, Y.(2018) Antioxidant role of autophagy in maintaining the integrity of glomerular capillaries. Autophagy. 14(1):53-65. doi: 10.1080/15548627.2017.1391428.

20. Maeshima, K., Matsuda, T., Shindo, Y., Imamura, H., Tamura, S., Imai, R., Kawakami, S., Nagashima, R., Soga, T., Noji, H., Oka, K., Nagai, T.(2018) A Transient Rise in Free Mg2+ Ions Released from ATP-Mg Hydrolysis Contributes to Mitotic Chromosome Condensation. Curr. Biol. 28(3):444-451.e6. doi: 10.1016/j.cub.2017.12.035.

21. Aw W and Fukuda S. (2018) Understanding the role of the gut ecosystem in diabetes mellitus. J Diabetes Investig. 9(1):5-12. doi: 10.1111/jdi.12673.

22. Tahara, Y., Yamazaki, M., Sukigara, H., Motohashi, H., Sasaki, H., Miyakawa, H., Haraguchi, A., Ikeda, Y., Fukuda, S., Shibata, S.(2018) Gut microbiota-derived short-chain fatty acids induce circadian clock entrainment in mouse peripheral tissue. Sci. Rep. 8(1):1395. doi: 10.1038/s41598-018-19836-7.

23. Naganuma M, Sugimoto S, Mitsuyama K, Kobayashi T, Yoshimura N, Ohi H, Tanaka S, Andoh A, Ohmiya N, Saigusa K, Yamamoto T, Morohoshi Y, Ichikawa H, Matsuoka K, Hisamitsu T, Watanabe K, Mizuno S, Suda W, Hattori M, Fukuda S, Hirayama A, Abe T, Watanabe M, Hibi T, Suzuki Y, Kanai T, for the INDIGO STUDY GROUP.(2018) Efficacy of indigo naturalis in a multicenter randomized controlled trial of patients with ulcerative colitis. Gastroenterology. 154(4):935-947. doi: 10.1053/j.gastro.2017.11.024.

24. Furukawa T, Tabata S, Yamamoto M, Kawahara K, Shinsato Y, Minami K, Shimokawa M, Akiyama SI.(2018) Thymidine phosphorylase in cancer aggressiveness and chemoresistance. Pharmacol Res. 132:15-20. doi: 10.1016/j.phrs.2018.03.019.

25. Yasutomi, E., Hoshi, N., Adachi, S., Otsuka, T., Kong, L., Ku, Y., Yamairi, H., Inoue, J., Ishida, T., Watanabe, D., Ooi, M., Yoshida, M., Tsukimi, T., Fukuda, S., Azuma, T.(2018) Proton Pump Inhibitors Increase the Susceptibility of Mice to Oral Infection with Enteropathogenic Bacteria. Dig Dis Sci. 63(4):881-889. doi: 10.1007/s10620-017-4905-3.

26. Harada, S., Hirayama, A., Chan, Q., Kurihara, A., Fukai, K., Iida, M., Kato, S., Sugiyama, D., Kuwabara, K., Takeuchi, A., Akiyama, M., Okamura, T., Ebbels, TMD., Elliott, P., Tomita, M., Sato, A., Suzuki, C., Sugimoto, M., Soga, T., Takebayashi, T.(2018) Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry. PLoS ONE. 13(1):e0191230. doi: 10.1371/journal.pone.0191230.

27. Korenko, S., Hamouzová, K., Kysilková, K., Kolářová ,M., Kloss, T.G., Takasuka, K. & Pekár, S.(2018) Divergence in host utilisation by two spider ectoparasitoids within the genus Eriostethus (Ichneumonidae, Pimplinae). Zoologischer Anzeiger. 272,1-5.

28. Ohta, T., Kawashima, T., Shinozaki, NO., Dobashi, A., Hiraoka, S., Hoshino, T., Kanno, K., Kataoka, T., Kawashima, S., Matsui, M., Nemoto, W, Nishijima S, Suganuma N, Suzuki H, Taguchi Y, Takenaka Y, Tanigawa Y, Tsuneyoshi M, Yoshitake K., Sato, Y., Yamashita, R., Arakawa, K., Iwasaki, W.(2018) Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago. J Plant Res. 131(4):709-717. doi: 10.1007/s10265-018-1017-x.

29. Hirayama, A., Abe, H., Yamaguchi, N., Tabata, S., Tomita, T., Soga, T.(2018) Development of a sheathless CE‐ESI‐MS interface. Electrophoresis. 39(11):1382-1389. doi: 10.1002/elps.201800017.

30. Kumar, N., Hoque, A., and Sugimoto, M.(2018) Robust Volcano Plot: Identification of differential metabolites in the presence of outliers. BMC Bioinformatics. 19(1):128. doi: 10.1186/s12859-018-2117-2.

31. Mariscal, AM., Kakizawa, S., Hsu, JY., Tanaka, K., González-González, L., Broto, A., Querol, E., Lluch-Senar, M., Piñero-Lambea, C., Sun, L., Weyman, PD., Wise, KS., Merryman, C., Tse, G., Moore, AJ., Hutchison, CA 3rd., Smith, HO., Tomita, M., Venter, JC., Glass, JI., Piñol, J. and Suzuki, Y. (2018) Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells . ACS Synth Biol. 7(6):1538-1552. doi: 10.1021/acssynbio.8b00028.

32. Itaya M, Sato M, Hasegawa M, Kono N, Tomita M, Kaneko S.(2018) Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system. Sci Rep.Jun 8;8:8792. doi: 10.1038/s41598-018-26987-0.

33. Ishiguro S, Galipon J, Ishii R, Suzuki Y, Kondo S, Okada-Hatakeyama M, Tomita M, Ui-Tei K. (2018) Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2. RNA Biol.15:976-989. doi: 10.1080/15476286.2018.1486658.

34. Iuchi H, Sugimoto M, Tomita M.(2018) MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data. BMC Bioinformatics.Jun 28;19:249. 10.1186/s12859-018-2257-4.

35. Miyamoto T, Hirayama A, Sato Y, Koboyashi T, Katsuyama E, Kanagawa H, Fujie A, Morita M, Watanabe R, Tando T, Miyamoto K, Tsuji T, Funayama A, Soga T, Tomita M, Nakamura M, Matsumoto M.(2018) Metabolomics-based profiles predictive of low bone mass in menopausal women. Bone Rep.Dec;9:11-18. doi: 10.1016/j.bonr.2018.06.004.

36. Galipon J, Ishii R, Ishiguro S, Suzuki Y, Kondo S, Okada-Hatakeyama M, Tomita M, Ui-Tei K.(2018) High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA. Methods Mol Biol.1823:167-183. doi: 10.1007/978-1-4939-8624-8_13.

37. Yoshida Y, Konno S, Nishino R, Murai Y, Tomita M, Arakawa K.(2018) Ultralow Input Genome Sequencing Library Preparation from a Single Tardigrade Specimen. J Vis Exp.Jul 15;(137) doi: 10.3791/57615.

38. Tomita A, Mori M, Hiwatari K, Yamaguchi E, Itoi T, Sunamura M, Soga T, Tomita M, Sugimoto M.(2018) Effect of storage conditions on salivary polyamines quantified via liquid chromatography-mass spectrometry. Sci Rep.Aug 13;8:12075. doi: 10.1038/s41598-018-30482-x.

39. Yamamoto Y, Nakanishi Y, Murakami S, Aw W, Tsukimi T, Nozu R, Ueno M, Hioki K, Nakahigashi K, Hirayama A, Sugimoto M, Soga T, Ito M, Tomita M, Fukuda S.(2018) A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice. Microorganisms 6(4), 101, doi:10.3390/microorganisms6040101, 2018.

40. Nishihara T, Kuno S, Nonaka H, Tabata S, Saito N, Fukuda S, Tomita M, Sando S, Soga T.(2018) Beta-galactosidase-responsive synthetic biomarker for targeted tumor detection. Chem Commun (Camb).Oct 16;54:11745-11748. doi: 10.1039/c8cc06068a.

41. Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M, Yachie N.(2018) Fast and global detection of periodic sequence repeats in large genomic resources. Nucleic Acids Res.Oct 10; doi: 10.1093/nar/gky890.

42. Sato Y, Matsuda S, Maruyama A, Nakayama J, Miyashita T, Udagawa H, Umemura S, Yanagihara K, Ochiai A, Tomita M, Soga T, Tsuchihara K, Makinoshima H.(2018) Metabolic Characterization of Antifolate Responsiveness and Non-responsiveness in Malignant Pleural Mesothelioma Cells. Front Pharmacol.9:1129. doi: 10.3389/fphar.2018.01129.

43. Kono N, Tomita M, Arakawa K.(2018) Accelerated laboratory evolution reveals the influence of replication on the GC skew in Escherichia coli. Genome Biol Evol.Oct 29; doi: 10.1093/gbe/evy237.

44. Takasuka K.(2018) Cyclosa omonaga (Araneae: Araneidae), an alternative host of a spider-ectoparasitoid, Reclinervellus nielseni (Hymenoptera: Ichneumonidae), with notes on behavioural manipulation. Arachnology.17 406-409. doi: 10.13156/arac.2017.17.8.406

45. Arakawa K, Kono N, Ohtoshi R, Nakamura H, Tomita M.(2018) The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae). Mitochondrial DNA B Resour.2018, 3(2):812-813.

46. Arakawa K.(2018) The complete mitochondrial genome of Echiniscus testudo (Heterotardigrada: Echiniscidae). Mitochondrial DNA B Resour.2018, 3(2):810-811.

47. Sugiura K, Minato H, Suzuki AC, Arakawa K, Kunieda T, Matsumoto M.(2018) Comparison of sexual reproductive behavior in two species of Macrobiotidae (Tardigrada: Eutardigrada). Zool. Sci.

48. Ito K, Harada M, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S.(2018) Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan. J Genomics.2018; 6:122-126. doi:10.7150/jgen.27741

49. Fleming J, Kristensen R, Sørensen Martin, Park T, Arakawa K, Blaxter M, Rebecchi L, Guidetti R, Williams T, Roberts N, Vinther J, Pisani D.(2018) Molecular palaeontology illuminates evolution of ecdysozoan vision. Proceedings of the Royal Society B.

50. Doke T, Ishimoto T, Hayasaki T, Ikeda S, Hasebe M, Hirayama A, Soga T, Kato N, Kosugi T, Tsuboi N, Lanaspa MA, Johnson RJ, Kadomatsu K, Maruyama S.(2018) Lacking ketohexokinase-A exacerbates renal injury in streptozotocin-induced diabetic mice. Metabolism.Aug;85:161-170. doi:10.1016/j.metabol.2018.03.020.

51. Baba M, Endoh M, Ma W, Toyama H, Hirayama A, Nishikawa K, Takubo K, Hano H, Hasumi H, Umemoto T, Hashimoto M, Irie N, Esumi C, Kataoka M, Nakagata N, Soga T, Yao M, Kamba T, Minami T, Ishii M, Suda T.(2018) Folliculin Regulates Osteoclastogenesis Through Metabolic Regulation. J Bone Miner Res.Oct ;33:1785-1798. doi:10.1002/jbmr.3477.

52. Kawata K, Hatano A, Yugi K, Kubota H, Sano T, Fujii M, Tomizawa Y, Kokaji T, Tanaka KY, Uda S, Suzuki Y, Matsumoto M, Nakayama KI, Saitoh K, Kato K, Ueno A, Ohishi M, Hirayama A, Soga T, Kuroda S.(2018) Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks. iScience.Sep 28;7:212-229. doi:10.1016/j.isci.2018.07.022.

53. Hagiwara Y, Mori M, Kanazawa K, Ando A, Yabe Y, Koide M, Sekiguchi T, Itaya N, Tsuchiya M, Itoi E.(2018) Comparative proteome analysis of the capsule from patients with frozen shoulder. J Shoulder Elbow Surg.Oct;27:1770-1778. doi:10.1016/j.jse.2018.03.010.

54. Watanabe, S. & Nakada, T.(2018) Gymnomonas nepalensis gen. et sp. nov. for the naked flagellate strain 'Nepal', formerly identified as Dunaliella lateralis (Volvocales, Chlorophyceae). Phycol. Res.66,167-172

55.Nakada,T.,Takahashi,S.& M,Tomita.(2018) Microglena redcarensis sp. nov. (Volvocales, Chlorophyceae), a brackish water chlamydomonad with contractile vacuoles.Phycol. Res.66,310-317

56. Takahashi, S., Tomita, M. & Nakada, T.(2018) Morphology and phylogeny of a Japanese strain of Chlamydomonas augustae (Volvocales, Chlorophyceae). J. Jpn. Bot.93, 317-321

57. Hayakawa T, Nathan S, Stark DJ, Saldivar DAR, Sipangkui R, Goossens B, Tuuga A, Clauss M, Sawada A, Fukuda S, Imai H, Matsuda I.(2018) First report of foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes? Environ Microbiol Rep.Dec;10:655-662. 10.1111/1758-2229.12677.

58. Kisuse J, La-Ongkham O, Nakphaichit M, Therdtatha P, Momoda R, Tanaka M, Fukuda S, Popluechai S, Kespechara K, Sonomoto K, Lee YK, Nitisinprasert S, Nakayama J.(2018) Urban Diets Linked to Gut Microbiome and Metabolome Alterations in Children: A Comparative Cross-Sectional Study in Thailand. Front Microbiol.9:1345. 10.3389/fmicb.2018.01345.

59. Taniki N, Nakamoto N, Chu PS, Mikami Y, Amiya T, Teratani T, Suzuki T, Tsukimi T, Fukuda S, Yamaguchi A, Shiba S, Miyake R, Katayama T, Ebinuma H, Kanai T.(2018) Intestinal barrier regulates immune responses in the liver via IL-10-producing macrophages. JCI Insight.Jun 21;3:10.1172/jci.insight.91980.

60. Hayakawa T, Sawada A, Tanabe AS, Fukuda S, Kishida T, Kurihara Y, Matsushima K, Liu J, Akomo-Okoue EF, Gravena W, Kashima M, Suzuki M, Kadowaki K, Suzumura T, Inoue E, Sugiura H, Hanya G, Agata K.(2018) Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island. Primates.Sep;59:423-436. 10.1007/s10329-018-0671-x.

61. Sasaki M, Harada S, Kawasaki Y, Watanabe M, Ito H, Tanaka H, Takeuchi A, Tsubota K, Takebayashi T, Nishiwaki Y, Kawasaki R.(2018) Gender-specific association of early age-related macular degeneration with systemic and genetic factors in a Japanese population. Sci Rep.Jan 15;8:785. 10.1038/s41598-017-18487-4.

62. Mishima, E., Fukuda, S., Kanemitsu, Y., Saigusa, D., Mukawa, C., Asaji, K., Matsumoto, Y., Tsukamoto, H., Tachikawa, T., Tsukimi, T., Fukuda, N., Ho, HJ., Kikuchi, K. Suzuki, C., Nanto, F., Suzuki, T., Ito, S., Soga, T., Tomioka, Y., Abe, T.(2018) Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model. Am J Physiol Renal Physiol. 315(4), F824-F833, doi:10.1152/ajprenal.00314.2017, 2018.

63. Ikegami R, Shimizu I, Sato T, Yoshida Y, Hayashi Y, Suda M, Katsuumi G, Li J, Wakasugi T, Minokoshi Y, Okamoto S, Hinoi E, Nielsen S, Jespersen NZ, Scheele C, Soga T, Minamino T. (2018) Gamma-Aminobutyric Acid Signaling in Brown Adipose Tissue Promotes Systemic Metabolic Derangement in Obesity. Cell Rep.Sep 11;24:2827-2837 e2825. doi:10.1016/j.celrep.2018.08.024.

64. Kuranaga Y, Sugito N, Shinohara H, Tsujino T, Taniguchi K, Komura K, Ito Y, Soga T, Akao Y. (2018) SRSF3, a Splicer of the PKM Gene, Regulates Cell Growth and Maintenance of Cancer-Specific Energy Metabolism in Colon Cancer Cells. Int J Mol Sci.19(10), 3012,doi:10.3390/ijms19103012, 2018.

65. Ishii, C., Nakanishi, Y., Murakami, S., Nozu, R., Ueno, M., Hioki, K., Aw, W., Hirayama, A., Soga, T., Ito, M., Tomita, M., Fukuda, S. (2018) A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet. Int J Mol Sci. 19, pii: E4079. doi: 10.3390/ijms19124079, 2018.

66. Hamid, S.S., Wakayama, M., Soga, T., Tomita, M.,(2018) Drying and extraction effects on three edible brown seaweeds for metabolomics. J. Appl. Phycol., 30, 3335-3350, 2018. doi;10.1007/s10811-018-1614-z

67. Nishizawa S, Araki H, Ishikawa Y, Kitazawa S, Hata A, Soga T, Hara T. Low tumor glutathione level as a sensitivity marker for glutamate-cysteine ligase inhibitors. Oncol Lett 2018 Jun; 15(6):8735-8743. doi: 10.3892/ol.2018.8447.

68. Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H, Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science 2018 Sep 21;361(6408):1259-1262. doi: 10.1126/science.aas9129.

2017

01. Inaba, Y., Nakahigashi, K., Ito, T., & Tomita, M. (2017) Alteration of fatty acid chain length of Chlamydomonas reinhardtii by simultaneous expression of medium-chain-specific thioesterase and acyl carrier protein. Phycological Research. 2017,65(1), 94-99.

02. Sugimoto, M., Obiya, S., Kaneko, M., Enomoto, A., Honma, M., Wakayama, M., Soga, T. and Tomita, M.(2017)Metabolomic Profiling as a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams. J Agric Food Chem. 65(2):402-410. doi: 10.1021/acs.jafc.6b03844.

03. Nakada, T. and Tomita, M. (2017) Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae). J Phycol. 2017 Feb;53(1):108-117. doi: 10.1111/jpy.12484.

04. Nishihara, T., Inoue, J., Tabata, S., Murakami, S., Ishikawa, T., Saito, N., Fukuda, S., Tomita, M. and Soga, T.(2017) Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen. Chembiochem. doi: 10.1002/cbic.201700023.

05. Yuliana, T., Nakajima, N., Yamamura, S., Tomita, M., Suzuki, H., Amachi, S.(2017) Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan . J Genomics. 5:51-53. doi: 10.7150/jgen.19846.

06. Galipon, J., Ishii, R., Suzuki, Y., Tomita, M., and Ui-Tei, K.(2017) Differential binding of three major human ADAR isoforms to coding and long non-coding transcripts. Genes (Basel). 8(2). pii: E68. doi: 10.3390/genes8020068.

07. Noro, E., Mori, M., Makino, G., Takai, Y., Ohnuma, S., Sato, A., Tomita, M., Nakahigashi, K. and Kanai, A.(2017) Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. RNA Biol. 14(2):206-218. doi: 10.1080/15476286.2016.1270001.

08. Miyamoto, T., Hirayama, A., Sato, Y., Koboyashi, T., Katsuyama, E., Kanagawa, H., Miyamoto, H., Mori, T., Yoshida, S., Fujie, A., Morita, M., Watanabe, R., Tando, T., Miyamoto, K., Tsuji, T., Funayama, A., Nakamura, M., Matsumoto, M., Soga, T., Tomita, M. and Toyama, Y.(2017) A serum metabolomics-based profile in low bone mineral density postmenopausal women. Bone. 8(2). pii: E68. doi: 10.3390/genes8020068.

09. Jia, H., Hanate, M., Aw, W., Itoh, H., Saito, K., Kobayashi, S., Hachimura, S., Fukuda, S., Tomita, M., Hasebe, Y. and Kato, H. (2017) Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis. Sci Rep. 7:43993. doi: 10.1038/srep43993.

10. Itoi, T., Sugimoto, M., Umeda, J., Sofuni, A., Tsuchiya, T., Tsuji, S., Tanaka, R., Tonozuka, R., Honjo, M., Moriyasu, F., Kasuya, K., Nagakawa, Y., Abe, Y., Takano, K., Kawachi, S., Shimazu, M., Soga, T., Tomita, M., Sunamura, M.(2017) Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination. Int. J. Mol. Sci. 18(4). pii: E767. doi: 10.3390/ijms18040767.

11. Mishima, E., Fukuda, S., Mukawa, C., Yuri, A., Kanemitsu, Y., Matsumoto, Y., Akiyama, Y., Fukuda, NN., Tsukamoto, H., Asaji, K., Shima, H., Kikuchi, K., Suzuki, T., Tomioka, Y., Soga, T., Ito, S., Abe, T.(2017) Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS-based metabolomics approach. Kidney Int.92(3), 634-645, doi: 10.1016/j.kint.2017.02.011, 2017.

12.Aw, W. and Fukuda, S.(2017) Understanding the role of the gut ecosystem in diabetes mellitus. J Diabetes Investig. doi: 10.1111/jdi.12673.

13. Yachie, N., Robotic Biology Consortium and Natsume, T. < Collabolators> Takahashi, K., Katayama, T., Sakurada, T., Kanda, G. N., Takagi, E., Hirose, T., Katsura, T., Moriya, T., Kitano, H., Tsujii, J., Shiraki, T., Kariyazaki, H., Kamei, M., Abe, N., Fukuda, T., Sawada, Y., Hashiguchi, Y., Matsukuma, K., Murai, S., Sasaki, N., Ipposhi, T., Urabe, H., Kudo, T., Umeno, M., Ono, S., Miyauchi, K., Nakamura, M., Kizaki, T., Suyama, T., Hatta, T., Natsume, T., Ohta, T., Ozawa, Y., Ihara, S., Tamaki, S., Antezana, E., Garcia-Castro, A., Perret, J., L., Ishiguro, S., Mori, H., Evans-Yamamoto, D., Masuyama N, Tomita M, Katayama T, Matsumoto M, Nakayama H, Shirasawa A, Shimbo, K., Yamada, N., Nakayama, K., I., Shimizu, T., Saya, H., Yamashita, S., Matsushima, T., Asahara, H., Eguchi, H., Mikamori, M. and Mori, M. (2017) Robotic crowd biology with Maholo LabDroids. Nat Biotechnol. 35(4):310-312. doi: 10.1038/nbt.3758.

14. Sano, I., H., Toki, T., Naito, Y. and Tomita, M.(2017) Developmental changes in the balance of glycolytic ATP production and oxidative phosphorylation in ventricular cells: A simulation study. J Theor Biol. 419:269-277. doi: 10.1016/j.jtbi.2017.02.019.

15. Kim, YG., Sakamoto, K., Seo1, SU., Pickard, JM., Gillilland, M.G. 3rd, Pudlo, NA., Hoostal, M., Li, X., Feehley, T., Stefka, AT., Schmidt, TM., Martens, EC., Fukuda, S., Inohara, N., Nagler, CR., Núñez, G.(2017) Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens. Science. 356(6335):315-319. doi: 10.1126/science.aag2029.

16. Kitazawa, S., Ebara, S., Ando, A., Baba, Y., Satomi, Y., Soga, T., Hara, T.(2017) Succinate dehydrogenase B-deficient cancer cells are highly sensitive to bromodomain and extra-terminal inhibitors. Oncotarget. 8(17):28922-28938. doi: 10.18632/oncotarget.15959.

17. Sakata, F., Ito, Y., Mizuno, M., Sawai, A., Suzuki, Y., Tomita, T., Tawada, M., Tanaka, A., Hirayama, A., Sagara, A., Wada, T., Maruyama, S., Soga, T., Matsuo, S., Imai, E., Takei, Y.(2017) Sodium chloride promotes tissue inflammation via osmotic stimuli in subtotal-nephrectomized mice. Lab Invest. 97(4):432-446. doi: 10.1038/labinvest.2017.4.

18. Yoshitoshi-Uebayashi, E.Y., Toyoda, T., Yasuda, K., Kotaka, M., Nomoto, K., Okita, K., Yasuchika, K., Okamoto, S., Takubo, N., Nishikubo, T., Soga, T., Uemoto, S., Osafune, K.(2017) Modelling urea-cycle disorder citrullinemia type 1 with disease-specific iPSCs. Biochem Biophys Res Commun. 486(3):613-619. doi: 10.1016/j.bbrc.2017.03.037.

19. Tanaka, Y., Ogawa, T., Maruta, T., Yoshida, Y., Arakawa, K., Ishikawa, T.(2017) Glucan synthase-like 2 is indispensable for paramylon synthesis in Euglena gracilis. FEBS Lett. 591(10):1360-1370. doi: 10.1002/1873-3468.12659.

20. Tabata, S., Yamamoto, M., Goto, H., Hirayama, A., Ohishi, M., Kuramoto, T., Mitsuhashi, A., Ikeda, R., Haraguchi, M., Kawahara, K., Shinsato, Y., Minami, K., Atsuro Saijo, A., Hanibuchi, M., Nishioka, Y., Sone, S., Esumi, H., Tomita, M., Soga, T., Furukawa, T. and Akiyama, S.(2017) Thymidine Catabolism as a Metabolic Strategy for Cancer Survival. Cell Rep.19(7):1313-1321. doi: 10.1016/j.celrep.2017.04.061.

21. Kon, S., Ishibashi, K., Katoh, H., Kitamoto, S., Shirai, T., Tanaka, S., Kajita, M., Ishikawa, S., Yamauchi, H., Yako, Y., Kamasaki, T., Matsumoto, T., Watanabe, H., Egami, R., Sasaki, A., Nishikawa, A., Kameda, I., Maruyama, T., Narumi, R., Morita, T., Sasaki, Y., Enoki, R., Honma, S., Imamura, H., Oshima, M., Soga, T., Miyazaki, J., Duchen, MR.., Nam, J., Onodera, Y., Yoshioka, S., Kikuta, J., Ishii, M., Imajo, M., Nishida, E., Fujioka, Y., Ohba, Y., Sato, T., Fujita, Y.(2017) Cell competition with normal epithelial cells promotes apical extrusion of transformed cells through metabolic changes. Nat. Cell Biol. 19(5):530-541. doi: 10.1038/ncb3509.

22. Kitazawa, S., Nishizawa, S., Nakagawa, H., Funata, M., Nishimura, K., Soga, T., Hara, T.(2017) Cancer with low cathepsin D levels is susceptible to vacuolar (H+ )-ATPase inhibition. Cancer Sci. 108(6):1185-1193. doi: 10.1111/cas.13240.

23. Nozaki, T., Imai, R., Tanbo, M., Nagashima, R., Tamura, S., Tani, T., Joti, Y., Tomita, M., Hibino, K., Kanemaki, M.,T., Wendt, K.,S., Okada, Y., Nagai, T. and Maeshima, K.(2017) Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging. Mol Cell. 67(2):282-293.e7. doi: 10.1016/j.molcel.2017.06.018.

24. Yoshida, Y., Koutsovoulos, G., Laetsch, R., D., Stevens, L., Kumar, S., Horikawa, D., D., Ishino, K., Komine, S., Kunieda, T., Tomita, M., Blaxter, M. and Arakawa, K.(2017) Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLoS Biol. 15(7):e2002266. doi: 10.1371/journal.pbio.2002266.

25. Okuma, N., Saita M., Hoshi, N., Soga, T., Tomita, M., Sugimoto, M., Kimoto K.(2017) Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile. PLoS One. 12(8):e0183109. doi: 10.1371/journal.pone.0183109.

26. Satoh, K., Yachida, S., Sugimoto, M., Oshima, M., Nakagawa, T., Akamoto, S., Tabata, S., Saitoh, K., Kato, K., Sato, S., Igarashi, K., Aizawa, Y., Kajino-Sakamoto, R., Kojima, Y., Fujishita, T., Enomoto, A., Hirayama, A., Ishikawa, T., Taketo, M., M., Kushida, Y., Haba, R., Okano, K., Tomita, M., Suzuki, Y., Fukuda, S., Aoki, M., Soga, T.(2017) Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC. Proc Natl Acad Sci U S A. 114(37):E7697-E7706 doi: 10.1073/pnas.1710366114.

27. Kono, N., Tomita, M. and Arakawa, K.(2017) eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria. BMC Genomics. 18(1):784. doi: 10.1186/s12864-017-4162-z.


28. Nagata, S., Imai, J., Makino, G., Tomita, M. and Kanai, A.(2017) Evolutionary analysis of HIV-1 Pol proteins reveals representative residues for viral subtype differentiation. Front Microbiol. 8:2151. doi: 10.3389/fmicb.2017.02151.


29. Ikeda. Y., Okada, Y., Sato, A. Kanai, T., Tomita, M., Atomi, H. and Kanai, A.(2017) An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Sci Rep. 7(1):12674. doi: 10.1038/s41598-017-13062-3.

30. Suzuki H, Tomita M, Tsai PJ, Ko WC, Hung YP, Huang IH, Chen JW.(2017) Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan. Gut Pathog. 9:70. doi: 10.1186/s13099-017-0219-4.

31. Nijhuis, A., Thompson, H., Adam, J., Paker A., Gammmon, L., Lewis, A., Bundy, J.G., Soga, T., Jalaly, A., Propper, D., Jeffery, R., Suraweera, N., McDonald, S., Thaha, M.A., Feakins, R., Lowe, R., Bishop, C., Silver, A(2017) Remodelling of microRNAs in colorectal cancer by hypoxia alters metabolism profiles and 5-fluorouracil resistance. Hum Mol Genet.26(8):1552-1564. doi: 10.1093/hmg/ddx059.

32. Ishikawa, S., Sugimoto, M., Kitabatake, K., Tu, M., Sugano, A., Yamamori, I., Iba, A., Yusa, K., Kaneko, M., Ota, S., Hiwatari, K., Enomoto, A., Masaru, T., and Iino, M.(2017) Effect of timing of collection of salivary metabolomic biomarkers on oral cancer detection. Amino Acids.49(4):761-770. doi: 10.1007/s00726-017-2378-5.

33. Toyoda, Y., Kashikura, K., Soga, T., Tagawa, Y.(2017) Metabolomics of an in vitro liver model containing primary hepatocytes assembling around an endothelial cell network: comparative study on the metabolic stability and the effect of acetaminophen treatment. J. Toxicol. Sci.42(4):445-454. doi: 10.2131/jts.42.445.

34. Hayashi, Y., Otsuka, K., Ebina, M., Igarashi, K., Takehara, A., Matsumoto, M., Kanai, A., Igarashi, K., Soga, T. and Matsui, Y.(2017) Distinct requirements for energy metabolism in mouse primordial germ cells and their reprogramming to embryonic germ cells. Proc Natl Acad.114(31):8289-8294. doi: 10.1073/pnas.1620915114.

35. Krycer, JR., Yugi, K., Hirayama, A., Fazakerley, DJ., Quek, LE., Scalzo, R., Ohno, S., Hodson, MP. Ikeda, S., Shoji, F., Suzuki, K., Domanova, W., Parker, BL.,. Nelson, ME ., Humphrey, SJ., Turner, N., Hoehn, KL., Cooney, GJ., Soga, T., Kuroda, S., James, DE.(2017) Dynamic metabolomics reveals that insulin primes the adipocyte for glucose metabolism. Cell Rep. 21(12):3536-3547. doi: 10.1016/j.celrep.2017.11.085.

36. Nishihara, T., Kameyama, Y., Nonaka, H., Takakusagi, Y., Hyodo, F., Ichikawa, K., Sando, S.(2017) A Strategy to Design Hyperpolarized 13C Magnetic Resonance Probes Using [1-13C]α-Amino Acid as a Scaffold Structure. Chem. Asian J.12(9):949-953. doi: 10.1002/asia.201700098.

37. Tanada, Y., Okuda, J., Kato, T., Minamino-Muta, E., Murata, I., Soga, T., Shioi, T., Kimura, T.(2017)T he metabolic profile of a rat model of chronic kidney disease. Peer J. 5:e3352. doi: 10.7717/peerj.3352.

38. Adam, J., Ramracheya, R., Chibalina, M.V., Ternette, N., Hamilton, A., Tarasov, A.I., Zhang, Q., Rebelato, E., Rorsman, N.J.G., Martin-del-Rio, R., Lewis, A., Ozkan, G., Do, H.W., Spegal, P., Saitoh, K., Kato, K., Igarashi, K., Kessler, B.M., Pugh, C.W., Tamarit-Rodriques, J., Mulder, H., Clark, A., Fizzell, N., Soga, T., Ashcroft, F.M., Silver, A., Pollard, P.J., Rorsman, P.(2017) Fumarate hydratase deletion in pancreatic β cells leads to progressive diabetes. Cell Rep. 20(13):3135-3148. doi: 10.1016/j.celrep.2017.08.093.

39. Migita, T., Takayama, K., Urano, T., Obinata, D., Ikeda, K., Soga, T., Takahashi, S., Inoue, S.(2017) ACSL3 promotes intratumoral steroidogenesis in prostate cancer cells. Cancer Sci. 108(10):2011-2021. doi: 10.1111/cas.13339.

40. Suzuki, K., Yoshida, K., Nakanishi, Y., Fukuda, S.(2017) An equation-free method reveals the ecological interaction networks within complex microbial ecosystems. Methods Ecol Evol.8:1774-1785.

41. Takayasu, L., Suda, W., Watanabe, E., Fukuda, S., Takanashi, K., Ohno, H., Takayasu, M., Takayasu, H., Hattori, M.(2017) A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes. PLoS One. 12(8):e0180863. doi: 10.1371/journal.pone.0180863.

42. Hayashi, A., Mikami, Y., Miyamoto, K., Kamada, N., Sato, T., Mizuno, S., Naganuma, M., Teratani, T., Aoki, R., Fukuda, S., Suda, W., Hattori, M., Amagai, M., Ohyama, M., Kanai, T.(2017) Intestinal Dysbiosis and Biotin Deprivation Induce Alopecia through Overgrowth of Lactobacillus murinus in Mice. Cell Rep. 20(7):1513-1524. doi: 10.1016/j.celrep.2017.07.057.

43. Yang, JY., Lee, YS., Kim, Y., Lee, SH., Ryu, S., Fukuda, S., Hase, K., Yang, CS., Lim, HS., Kim, MS., Kim, HM., Ahn, SH., Kwon, BE., Ko, HJ., Kweon, MN.(2017) Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice. Mucosal Immunol. 10(1):104-116. doi: 10.1038/mi.2016.42.

44. Yanagihara, S., Kanaya, T., Fukuda, S., Nakato, G., Hanazato, M., Wu, XR., Yamamoto, N., Ohno, H.(2017) Uromodulin-SlpA binding dictates Lactobacillus acidophilus uptake by intestinal epithelial M cells. Int. Immunol. 29(8):357-363. doi: 10.1093/intimm/dxx043.

45. Date, Y., Ebisawa, M., Fukuda, S., Shima, H., Obata, Y., Takahashi, D., Kato, T., Hanazato, M., Nakato, G., Williams, IR., Hase, K., Ohno, H.(2017) NALT M cells are important for immune induction for the common mucosal immune system . Int. Immunol. 29(10):471-478. doi: 10.1093/intimm/dxx064.

46. Ikeda, K., Kang, Q., Yoneshiro, T., Camporez, J.P., Maki, H., Homma, M., Shinoda, K., Chen, Y., Lu, X., Maretich, P., Tajima, K., Ajuwon, K.M., Soga, T., Kajimura, S.(2017) UCP1-independent signaling involving SERCA2b-mediated calcium cycling regulates beige fat thermogenesis and systemic glucose homestasis. Nat. Med. 23(12):1454-1465. doi: 10.1038/nm.4429.

47. Hirata, Y., Sezaki, T., Tamura-Nakano, M., Oyama, C., Hagiwara, T., Ishikawa, T., Fukuda, S., Yamada, K., Higuchi, K., Dohi, T., Kawamura, YI.(2017) Fatty acids in a high-fat diet potentially induce gastric parietal-cell damage and metaplasia in mice. J. Gastroenterol. 52(8):889-903. doi: 10.1007/s00535-016-1291-0.

48. Sato, N., Sudo, K., Mori, M., Imai, C., Muramatsu, M., and Sugimoto, M.(2017) Early gestational maternal low-protein diet diminishes hepatic response to fasting in young adult male mice. Sci Rep. 7(1):9812. doi: 10.1038/s41598-017-10380-4.

49. Okada, T., Otsubo, T., Hagiwara, T., Inazuka, F., Koubayashi, E., Fukuda, S., Inoue, T., Higuchi, K., Kawamura, Y.I., Dohi, T.(2017) Intermittent fasting prompted recovery from dextran sulfate sodium-induced colitis in mice. J Clin Biochem Nutri. 61(2):100-107. doi: 10.3164/jcbn.17-9.

50. Takasuka, K., Korenko, S., Kysilková, K., Štefánik, M., Černecká, Ľ., Mihál, I., Dolejš, P. & Holý, K.(2017) Host utilization of koinobiont spider-ectoparasitoids (Ichneumonidae, Ephialtini, Polysphincta genus-group) associated with Cyclosa spp. (Araneae, Araneidae) across the Palaearctic.. Zoologischer Anzeiger.267, 8-14.

51. Akiyama, M, Abraham, C.(2017) Comparative cost-benefit analysis of tele-homecare for community-dwelling elderly in Japan: Non-Government versus Government Supported Funding Models. Int J Med Inform. 104:1-9. doi: 10.1016/j.ijmedinf.2017.04.017.

52. Malay A, Arakawa K, Numata K.(2017) Analysis of repetitive amino acid motifs reveals the essential features of spider dragline silk proteins. PLoS One. 12(8):e0183397. doi: 10.1371/journal.pone.0183397.

53. Jeelani, G., Sato, D., Soga, T., Nozaki, T.(2017) Genetic, metabolomic and transcriptomic analyses of the de novo L-cysteine biosynthetic pathway in the enteric protozoan parasite Entamoeba histolytica. Sci. Rep. 7(1):15649. doi: 10.1038/s41598-017-15923-3.

54. Sugito, N., Taniguchi, K., Kuranaga, Y., Ohishi, M., Soga, T., Ito, Y., Miyachi, M., Kikuchi, K., Hosoi, H., Akao, Y.(2017) Cancer-Specific Energy Metabolism in Rhabdomyosarcoma Cells Is Regulated by MicroRNA. Nucleic Acid Ther. 27(6):365-377. doi: 10.1089/nat.2017.0673.

55. Suda, M., Shimizu, I., Yoshida, Y., Hayashi, Y., Ikegami, R., Katsuumi, G., Wakasugi, T., Yoshida, Y., Okuda, S., Soga, T., Minamino, T., (2017) Inhibition of dipeptidyl peptidase-4 ameliorates cardiac ischemia and systolic dysfunction by up-regulating the FGF-2/EGR-1 pathway. PLoS One 12(8), e0182422, doi:10.1371/journal.pone.0182422, 2017.

2016

01. Shindo, Y., Iwamoto, K., Mouri, K., Hibino, K., Tomita, M., Kosako, H., Sako, Y. and Takahashi, K. (2016) Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signaling. Nat Commun. 2016 Jan 20;7:10485. doi: 10.1038/ncomms10485.

02. Harada, S., Takebayashi, T., Kurihara, A., Akiyama, M., Suzuki, A., Hatakeyama, Y., Sugiyama, D., Kuwabara, K., Takeuchi, A., Okamura, T., Nishiwaki, Y., Tanaka, T., Hirayama, A., Sugimoto, M., Soga, T. and Tomita, M.(2016) Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men.Environ Health Prev Med. 2016 Jan;21(1):18-26. doi: 10.1007/s12199-015-0494-y.

03. Akiyama M, Hirai K, Takebayashi T, Morita T, Miyashita M, Takeuchi A, Yamagishi A, Kinoshita H, Shirahige Y, and Eguchi K.(2016) The effects of community-wide dissemination of information on perceptions of palliative care, knowledge about opioids, and sense of security among cancer patients, their families, and the general public.Support Care Cancer. 2016 Jan;24(1):347-56. doi: 10.1007/s00520-015-2788-4.

04. Hamashima, K., Tomita, M. and Kanai, A. (2016) Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes. Mol Biol Evol. 2016 Feb;33(2):530-40. doi: 10.1093/molbev/msv253.

05. Yoshida, Y., Tomiyama, T., Maruta, T., Tomita, M., Ishikawa, T. and Arakawa, K. (2016) De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions. BMC Genomics.2016 Mar 3;17:182. doi: 10.1186/s12864-016-2540-6.

06. Galipon Josephine, 石黒宗, 冨田勝, 程久美子(2016) Detecting A-to-I RNA editing in RNA-Seq data. NGS Professional シリーズRNA-Seqマスターブック(羊土社) Review (2016)

07. Nakada, T., Tomita, M., Wu, J. T. and Nozaki, H. (2016) Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov. J. Phycol.2016 Apr;52(2):283-304. doi: 10.1111/jpy.12397.

08. Useh, N., Ngbede, E., Akange, N., Thomas, M., Foley, A., Keena, M., Nelson, E., Christopher-Hennings, J., Tomita, M., Suzuki, H. and Scaria, J. (2016) Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria. Genome Announc.2016 May 5;4(3). pii: e00315-16. doi: 10.1128/genomeA.00315-16.

09. Li, Q., Guo, S., Jiang, X., Bryk, J., Naumann, R., Enard, W., Tomita, M., Sugimoto, M., Khaitovich, P. and Pääbo, S. (2016) Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development. PNAS.2016 May 10;113(19):5358-63. doi: 10.1073/pnas.1519261113.

10. Kono, N., Nakamura, H., Ito, Y., Tomita, M. and Arakawa, K. (2016) Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. Mol Ecol Resour.2016 May;16(3):662-72. doi: 10.1038/srep31520.

11. Kimura, T., Yasuda, K., Yamamoto, R., Soga, T., Rakugi, H., Hayashi, T., Isaka, Y.(2016) Identification of biomarkers for development of end-stage kidney disease in chronic kidney disease by metabolomic profiling. Sci Rep.2016 May 18;6:26138. doi: 10.1038/srep26138.

12. Munakata, H., Nakada, T., Nakahigashi, K., Nozaki, H. and Tomita, M.(2016) Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis (Volvocales, Chlorophyceae), among Unicellular Algae. Eukaryot Microbiol. 2016 May;63(3):340-8. doi: 10.1111/jeu.12283.

13. Arakawa, K.(2016) No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. PNAS.2016 May 31;113(22):E3057. doi: 10.1073/pnas.1602711113.

14. Nakada, T. & Ota, S.(2016) What is the correct name for the type species of Haematococcus Flot. (Volvocales, Chlorophyceae)? Taxon.65(2):343-348,May 2016

15. Tando, T., Hirayama, A., Furukawa, M., Sato, Y., Kobayashi, T., Funayama, A., Kanaji, A., Hao, W., Watanabe, R., Morita, M., Oike, T., Miyamoto, K., Soga, T., Nomura, M., Yoshimura, A., Tomita, M., Matsumoto, M., Nakamura, M., Yoshiaki Toyama. Y. and Miyamoto, T. (2016) Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy. J Biol Chem. 2016 Jun 3;291(23):12184-94.doi: 10.1074/jbc.M115.680579.

16. Saito, T., Ichimura, Y., Taguchi, K., Suzuki, T., Mizushima, T., Takagi, K., Hirose, Y., Nagahashi, M., Iso, T., Fukutomi, T., Ohishi, M., Endo, K., Uemura, T., Nishito, Y., Okuda, S., Obata, M., Kouno, T., Imamura, R., Tada, Y., Obata, R., Yasuda, D., Takahashi, K., Fujimura, T., Pi, J., Lee, MS., Ueno, T., Ohe, T., Mashino, T., Wakai, T., Kojima, H., Okabe, T., Nagano, T., Motohashi, H., Waguri, S., Soga, T., *Yamamoto, M., *Tanaka, K., *Komatsu, M.(2016) p62/Sqstm1 promotes malignancy of HCV-positive hepatocellular carcinoma through Nrf2-dependent metabolic reprogramming. Nat Commun. 2016 Jun 27;7:12030. doi: 10.1038/ncomms12030.

17. Saito, T., Sugimoto, M., Okumoto, K., Haga, H., Katsumi, T., Mizuno, K., Nishina, T., Sato, S., Igarashi, K., Maki, H., Tomita, M., Ueno, Y., Soga, T.(2016) Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C. World J. Gastroenterol. 2016 Jul 21;22(27):6224-34. doi: 10.3748/wjg.v22.i27.6224.

18. Yamanaka, R., Tabata, S., Shindo, Y., Hotta, K., Suzuki, K., Soga, T., Oka, K.(2016) Mitochondrial Mg2+ homeostasis decides cellular energy metabolism and vulnerability to stress. Sci Rep. 2016 Jul 26;6:30027. doi: 10.1038/srep30027.

19. Iida, M., Harada, S., Kurihara, A., Fukai, K., Kuwabara, K., Sugiyama, D., Takeuchi, A., Okamura, T., Akiyama, M., Nishiwaki, Y., Suzuki, A., Hirayama, A., Sugimoto, M., Soga, T., Tomita, M., Banno, K., Aoki, D. and Takebayashi, T. (2016) Profiling of plasma metabolites in postmenopausal women with metabolic syndrome. Menopause.2016 Jul;23(7):749-58. doi: 10.1097/GME.0000000000000630.

20. Akiyama M, Abraham C.(2016) A Systematic Review of the Economic Evaluation of Telemedicine in Japan. J Prev Med Public Health.2016 Jul;49(4):183-96. doi: 10.3961/jpmph.16.043.

21. Karigane, D., Kobayashi, H., Morikawa, T., Ootomo, Y., Sakai, M., Nagamatsu, G., Kubota, Y., Goda, N., Matsumoto, M., Nishimura, E. K., Soga, T., Otsu, K., Suematsu, M., Okamoto, S., Suda, T., Takubo, K.(2016) p38α activates purine metabolism to initiate hematopoietic stem/progenitor cell cycling in response to stress. Cell Stem Cell. 2016 Aug 19;6:31520. doi: 10.1038/srep31520.

22. Ishikawa, S., Sugimoto, M., Kitabatake, K., Sugano, A., Nakamura, M., Kaneko, M., Ota, S., Hiwatari, K., Enomoto, A., Soga, T., Tomita, M. and Iino, M.(2016) Identification of salivary metabolomic biomarkers for oral cancer screening. Sci Rep. 2016 Aug 19;6:31520. doi: 10.1038/srep31520.

23. Arakawa, K., Yoshida, Y., Tomita, M.(2016) Genome sequencing of a single tardigrade Hypsibius dujardini individual. Sci Data. 2016 Aug 16;3:160063. doi: 10.1038/sdata.2016.63.

24. Hashimoto T, Horikawa DD, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, Minakuchi Y, Ohishi K, Motoyama A, Aizu T, Enomoto A, Kondo K, Tanaka S, Hara Y, Yoshikawa S, Sagara H, Miura T, Yokobori S, Miyazawa K, Suzuki Y, Kubo T, Oyama M, Kohara Y, Fujiyama A, Arakawa K, Katayama T, Toyoda A, and Kunieda T.(2016) Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nat Commun. 2016 Sep 20;7:12808. doi: 10.1038/ncomms12808.

25. Bardella C, Al-Dalahmah O, Krell D, Brazauskas P, Al-Qahtani K, Tomkova M, Adam J, Serres S, Lockstone H, Freeman-Mills L, Pfeffer I, Sibson N, Goldin R, Schuster-Böeckler B, Pollard, PJ, Soga T, McCullagh JS, Schofield CJ, Mulholland P, Ansorge O, Kriaucionis S, Ratcliffe PJ, Szele, FG, Tomlinson I.(2016) Expression of Idh1R132H in the murine subventricular zone stem cell niche recapitulates features of early gliomagenesis. Cancer Cell. 2016 Oct 10;30(4):578-594. doi: 10.1016/j.ccell.2016.08.017.

26. Ito,K., Nakajima, N., Yamamura, S., Tomita, M., Suzuki, H. and Amachi, S. (2016) Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment. Genome Announc. 2016 Oct 13;4(5). pii: e01155-16. doi:10.1128/genomeA.01155-16.

27. Fukai, K., Harada, S., Iida, M., Kurihara, A.,Takeuchi, A., Kuwabara, K., Sugiyama, D., Okamura, T., Akiyama, M.,Nishiwaki, Y., Oguma, Y., Suzuki, A., Suzuki, C., Hirayama, A., Sugimoto,M., Soga, T., Tomita, M. and Takebayashi, T. (2016) Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men. PLoS ONE. 2016 Oct 14;11(10):e0164877. doi: 10.1371/journal.pone.0164877. eCollection 2016.

28. Ogawa, T., Tsubakiyama, R., Kanai, M., Koyama , T., Fujii, T., Iefuji, H., Soga, T., Kume, K., Miyakawa, T., Hirata, D., Mizunuma, M.(2016) Stimulating S-adenosyl-L-methionine synthesis extends lifespan via activation of AMPK. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11913-11918.

29. Sugimoto, M., Obiya, S., Kaneko, M., Enomoto, A., Honma, M., Wakayama, M., and Tomita, M. (2016) Simultaneous analysis of consumer variables, acceptability and sensory characteristics of dry-cured ham. Meat Sci. 2016 Nov;121:210-5. doi: 10.1016/j.meatsci.2016.06.015.

30. Iwai,H., Horikawa, D., Arakawa, K., Tomita, M., Komatsu, T. and Maruyama, M.(2016) Rearing and observation of immature stages of the hoverfly Microdon katsurai (Diptera, Syrphidae). Biodivers Data J. 2016 Dec 9;(4):e10185. doi: 10.3897/BDJ.4.e10185. eCollection 2016.

31. Watanabe, S., Nozaki, H., Nakada, T. & Lewis, L. A.(2016) Comparative ultrastructural analysis of Chloromonas and Gloeomonas (Chlorophyceae): tracing the origin of Gloeomonas-specific basal apparatus traits. Phycologia. 55, 585-601

32. Kuwabara K, Harada S, Sugiyama D, Kurihara A, Kubota Y, Higashiyama A, Hirata T, Nishida Y, Kawasaki M, Takebayashi T, Okamura T.(2016) Relationship between Non-High-Density Lipoprotein Cholesterol and Low-Density Lipoprotein Cholesterol in the General Population. J Atheroscler Thromb.23:477-490. 10.5551/jat.33100.

33. Yamano Y, Sugimoto M, Hirayama A, Kume S, Yamato M, Jin G, Tajima S, Goda N, Iwai K, Fukuda S, Yamaguti K, Kuratsune H, Soga T, Watanabe Y, Kataoka Y. Index markers of chronic fatigue syndrome with dysfunction of TCA and urea cycles. Sci Rep 2016 Oct 11; 6:34990. doi: 10.1038/srep34990.

34. Hegazy AM, Yamada D, Kobayashi M, Kohno S, Ueno M, Ali MA, Ohta K, Tadokoro Y, Ino, Y, Todo T, Soga T, Takahashi C, Hirao A. Therapeutic Strategy for Targeting Aggressive Malignant Gliomas by Disrupting Their Energy Balance. J Biol Chem 2016 Oct 7; 291(41):21496-21509. doi: 10.1074/jbc.M116.734756.

35. Kemppainen E, George J, Garipler G, Tuomela T, Kiviranta E, Soga T, Dunn CD, Jacobs HT. Mitochondrial Dysfunction Plus High-Sugar Diet Provokes a Metabolic Crisis That Inhibits Growth. PLoS One 2016 Jan 26; 11(1):e0145836. doi: 10.1371/journal.pone.0145836.

36. Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Mol Syst Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660.

2015

01. Tsuge K, Sato Y, Kobayashi Y, Gondo M, Hasebe M, Togashi T, Tomita M, Itaya M. (2015) Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments. Sci Rep, 5, 10655.

02. Simeoni O, Piras V, Tomita M, Selvarajoo K. (2015) Tracking global gene expression responses in T cell differentiation. Gene, 569, 259-266.

03. Selvarajoo K .(2015) Measuring merit: take the risk. Science, 347, 139-140.
Pubmed

04. Piras V, Selvarajoo K. (2015) The reduction of gene expression variability from single cells to populations follows simple statistical laws. Genomics, 105, 137-144.
Pubmed

05. Ogawara Y, Katsumoto T, Aikawa Y, Shima Y, Kagiyama Y, Soga T, Matsunaga H, Seki T, Araki K, Kitabayashi I .(2015) IDH2 and NPM1 Mutations Cooperate to Activate Hoxa9/Meis1 and Hypoxia Pathways in Acute Myeloid Leukemia.Cancer Res, 75, 2005-2016.
Pubmed

06. Mishima E, Fukuda S, Shima H, Hirayama A, Akiyama Y, Takeuchi Y, Fukuda NN, Suzuki T, Suzuki C, Yuri A, Kikuchi K, Tomioka Y, Ito S, Soga T, Abe T. (2015) Alteration of the Intestinal Environment by Lubiprostone Is Associated with Amelioration of Adenine-Induced CKD. J Am Soc Nephrol, 26, 1787-1794.
Pubmed

07. Matsumura T, Sugawara Y, Yutani M, Amatsu S, Yagita H, Kohda T, Fukuoka S, Nakamura Y, Fukuda S, Hase K, Ohno H, Fujinaga Y. (2015) Botulinum toxin A complex exploits intestinal M cells to enter the host and exert neurotoxicity. Nat Commun, 6, 6255.
Pubmed

08. Kume S, Yamato M, Tamura Y, Jin G, Nakano M, Miyashige Y, Eguchi A, Ogata Y, Goda N, Iwai K, Yamano E, Watanabe Y, Soga T, Kataoka Y.(2015) Potential biomarkers of fatigue identified by plasma metabolome analysis in rats. PLoS One, 10, e0120106.
Pubmed

09. Kobayashi S, Sato M, Kasakoshi T, Tsutsui T, Sugimoto M, Osaki M, Okada F, Igarashi K, Hiratake J, Homma T, Conrad M, Fujii J, Soga T, Bannai S, Sato H.(2015) Cystathionine is a novel substrate of cystine/glutamate transporter: implications for immune function. J Biol Chem, 290, 8778-8788.
Pubmed

10. Kishikawa T, Otsuka M, Tan PS, Ohno M, Sun X, Yoshikawa T, Shibata C, Takata A, Kojima K, Takehana K, Ohishi M, Ota S, Noyama T, Kondo Y, Sato M, Soga T, Hoshida Y, Koike K.(2015) Decreased miR122 in hepatocellular carcinoma leads to chemoresistance with increased arginine. Oncotarget, 6, 8339-8352.
Pubmed

11. Ikeda KT, Hirose Y, Hiraoka K, Noro E, Fujishima K, Tomita M, Kanai A.(2015) Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA, 21, 230-242.
Pubmed

12. Hirayama A, Sugimoto M, Suzuki A, Hatakeyama Y, Enomoto A, Harada S, Soga T, Tomita M, Takebayashi T.(2015) Effects of processing and storage conditions on charged metabolomic profiles in blood. Electrophoresis, Pubmed

13.Hamashima K, Mori M, Andachi Y, Tomita M, Kohara Y, Kanai A.(2015) Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs. PLoS One, 10, e0116981.
Pubmed

14.Garcia-Contreras R, Sugimoto M, Umemura N, Kaneko M, Hatakeyama Y, Soga T, Tomita M, Scougall-Vilchis RJ, Contreras-Bulnes R, Nakajima H, Sakagami H.(2015) Alteration of metabolomic profiles by titanium dioxide nanoparticles in human gingivitis model.Biomaterials, 57, 33-40.
Pubmed

15. Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Paabo S, Sherwood CC, Hof PR, Ely JJ, Li Y, Steinhauser D, Willmitzer L, Giavalisco P, Khaitovich P.(2015) Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues.Neuron, 85, 695-702.
Pubmed

16. Aw W, Fukuda S.(2015) Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach. Semin Immunopathol, 37, 5-16.
Pubmed

17. Takahashi, K., Itaya, K., Nakamura, M., Koizumi, M., Arakawa, N., Tomita, M. and Yamakawa, H. (2015) A Generic Software Platform for Brain-Inspired Cognitive Computing. Procedia Computer Science, 71: 31-37.

18. Murakami, S., Goto, Y., Ito, K., Hayasaka, S., Kurihara, S., Soga, T., Tomita, M. and Fukuda, S. (2015) The consumption of bicarbonate-rich mineral water improves glycemic control. Evidence-Based Complementary and Alternative Medicine 2015:10.

19. Tsurumaki, M., Kotake, M., Iwasaki, M., Saito, M., Tanaka, K., Aw, W., and Fukuda, S. and Tomita, M. (2015) The application of omics technologies in the functional evaluation of inulin and inulin-containing prebiotics dietary supplementation. Nutr Diabetes. 5:e185.

20. Sakagami, H., Shimada, C., Kanda, Y., Amano, O., Sugimoto, M., Ota, S., Soga, T., Tomita, M., Sato, A., Tanuma, S., Takao, K., and Sugita, Y.(2015) Effects of 3-styrylchromones on metabolic profiles and cell death in oral squamous cell carcinoma cells. Toxicology Reports, 2:1281-1290.

21. Kawasaki, Y., Nakada, T. and Tomita, M.(2015) Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives. J. Phycol. 51: 1000-1016.

22. Uetaki, M., Tabata, S., Nakasuka, F., Soga, T. and Tomita, M. (2015) Metabolomic alterations in human cancer cells by vitamin C-induced oxidative stress. Scientific Reports 5:13896.

23. Murakami, S., Baba, F., Fukuda, S., Soga, T., Fujishima, H. and Tomita, M. (2015) Comprehensive analysis of microbes and metabolites in human tear fluids. KEIO SFC JOURNAL, 15(1):382-400.

24. Hirose, Y., Ikeda, T., K., Noro, E., Hiraoka, K., Tomita, M. and Kanai, A. (2015) Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp). BMC Genetics, 16:83.

25. Shimo, H., Arjunan, S., N., V., Machiyama, H., Nishino, T., Suematsu, M., Fujita, H., Tomita, M., and Takahashi, K. (2015) Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.PLoS Comput Biol 11(6):e1004210.

26. Nakada, T., Matsuzaki, R., Krienitz, L., Tomita, M. and Nozaki, H. (2015) Taxonomic reassessment of strains formerly classified as Chloromonas insignis (Volvocales, Chlorophyceae), and description of Gloeomonas anomalipyrenoides sp. nov. Acta phytotaxonomica et geobotanica,66(1):23-33.

27. Ohtani, N., Tomita, M. and Itaya, M. (2015) Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain. Appl Environ Microbiol. 2015 Dec 28;82(5):1537-48. doi: 10.1128/AEM.03603-15.

28. Nakano T, Saiki Y, Kudo C, Hirayama A, Mizuguchi Y, Fujiwara S, Soga T, Sunamura M, Matsumura N, Motoi F, Unno M, Horii A. Acquisition of chemoresistance to gemcitabine is induced by a loss-of-function missense mutation of DCK. Biochem Biophys Res Commun. 2015 Sep 4; 464(4):1084-1089. doi: 10.1016/j.bbrc.2015.07.080.

29. Watanabe S, Ohbayashi R, Kanesaki Y, Saito N, Chibazakura T, Soga T, Yoshikawa H. Intensive DNA Replication and Metabolism during the Lag Phase in Cyanobacteria. PLoS One 2015 Sep 2; 10(9):e0136800. doi: 10.1371/journal.pone.0136800.

30. Valli A, Rodriguez M, Moutsianas L, Fischer R, Fedele V, Huang HL, Van Stiphout R, Jones D, Mccarthy M, Vinaxia M, Igarashi K, Sato M, Soga T, Buffa F, Mccullagh J, Yanes O, Harris A, Kessler B. Hypoxia Induces a Lipogenic Cancer Cell Phenotype via HIF1α-Dependent and -Independent Pathways. Oncotarget 2015 Feb 10; 6(4):1920-1941. doi: 10.18632/oncotarget.3058.

2014

01. Sakagami, H., Sugimoto, M., Tanaka, S., Onuma, H., Ota, S., Kaneko, M., Soga, T. and Tomita, M. (2014) Metabolomic profiling of sodium fluoride-induced cytotoxicity in an oral squamous cell carcinoma cell line. Metabolomics. 10: 270-9.

02. Sugimoto M, Takada M, Toi M. (2014) Development of Web tools to predict axillary lymph node metastasis and pathological response to neoadjuvant chemotherapy in breast cancer patients. Int J Biol Markers, doi: 10.5301/jbm.5000103.

03. Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Pieszek R, Sherwood CC, Hof PR, Ely JJ, Steinhauser D, Willmitzer L, Bangsbo J, Hansson O, Call J, Giavalisco P, Khaitovich P. (2014) Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biol., 12(5):e1001871.

04. Sato D, Sugimoto M, Akashi H, Tomita M, Soga T. (2014) Comparative metabolite profiling of foxglove aphids (Aulacorthum solani Kaltenbach) on leaves of resistant and susceptible soybean strains. Mol Biosyst., 10(4):909-15.

05. Kono N, Arakawa K, Sato M, Yoshikawa H, Tomita M, Itaya M. (2014) Undesigned selection for replication termination of bacterial chromosomes. J Mol Biol.,426(16):2918-27.

06. Amariei C, Tomita M, Murray DB. (2014) Quantifying periodicity in omics data. Front Cell Dev Biol.,2:40. doi: 10.3389/fcell.2014.00040.

07. Nakahigashi K, Takai Y, Shiwa Y, Wada M, Honma M, Yoshikawa H, Tomita M, Kanai A and Mori H. (2014) Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo. BMC Genomics,15:1115 DOI: 10.1186/1471-2164-15-1115.

08. Hayashi K, Tabata S, Piras V, Tomita M and Selvarajoo K. (2014) Systems Biology Strategy Reveals PKC-delta is Key for SensitizingTRAIL-Resistant Human Fibrosarcoma. Front. Immunol. 5:659.doi:10.3389/fimmu.2014.00659.

09. Piras V, Tomita M, and Selvarajoo K. (2014) Transcriptome-wide Variability in Single Embryonic Development Cells. Sci Rep, 4, 7137 doi:10.1038/srep07137.

10. Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M. (2014) Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nat Commun, 2014 Jan 31; 5:3233. doi: 10.1038/ncomms4233.

11. Hirayama A, Wakayama M, Soga T. (2014) Metabolome analysis based on capillary electrophoresis-mass spectrometry. Trend Anal Chem, Oct ; 61, 215-222, doi:10.1016/j.trac.2014.05.005.

12. Nakada, T. and Tomita, M. (2014) Light microscopy and phylogenetic analyses of Chlamydomonas species (Volvocales, Chlorophyceae). II. Molecular phylogeny, 
secondary structure of ITS-2, cell morphology, and nomenclature of Microglena 
opisthopyren, and M. media, comb. nov. Acta Phytotax. Geobot. 65, 67-73.

13. Nakada T, Tsuchida Y, Arakawa K, Ito T and Tomita M. (2014) Hybridization between Japanese and North American Chlamydomonas reinhardtii (Volvocales, Chlorophyceae). Phycol. Res. 62, 232-236.

14. Sano, I., H., Toki, T., Naito, Y. and Tomita, M. (2014) Contribution of developmental changes in energy metabolism to excitation-contraction coupling of a ventricular cell: a simulation study. 41: 73-76.

15. Jia, H., Aw, W., Hanate, M., Takahashi, S., Kenji, S., Tanaka, H., Tomita, M. and Kato, H. (2014) Multi-faceted integrated omics analysis revealed Parsley (Petroselinum crispum) as a novel dietary intervention in dextran sodium sulphate induced colitic mice. J. Funct. Food 11:438-448.

16. Arakawa, K. and Tomita, M. (2014) Genome Analysis Workshop: a Personal Genomics class at Keio SFC.14:158-197.

17. Hirayama, A., Igarashi, K., Tomita, M. and Soga, T. (2014) Development of quantitative method for determination of <GAMMA>-glutamyl peptides by capillary electrophoresis tandem massspectrometry: an efficient approach avoiding matrix effect . J. Chromatogr. A 1369, 161-169.

18. Oshita K, Tomita M and Arakawa K. (2014) G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved].F1000Research 2015 3:285.

19. Tabata S, Ikeda R, Yamamoto M, Shimaoka S, Mukaida N, Takeda Y, Yamada K, Soga T, Furukawa T, Akiyama S. Thymidine phosphorylase activates NFκB and stimulates the expression of angiogenic and metastatic factors in human cancer cells. Oncotarget 2014 Nov 15; 5(21):10473-10485. doi: 10.18632/oncotarget.2242.

20. Jeelani G, Sato D, Soga T, Watanabe H, Nozaki T. Mass spectrometric analysis of L-cysteine metabolism: physiological role and fate of L-cysteine in the enteric protozoan parasite Entamoeba histolytica. mBio 2014 Nov 4; 5(6):e01995. doi: 10.1128/mBio.01995-14.

21. Xu F, Sudo Y, Sanechika S, Yamashita J, Shimaguchi S, Honda S, Sumi-Ichinose C, Mori-Kojima M, Nakata R, Furuta T, Sakurai M, Sugimoto M, Soga T, Kondo K, Ichinose H. Disturbed biopterin and folate metabolism in the Qdpr-deficient mouse. FEBS Lett 2014 Nov 3;588(21):3924-3931. doi: 10.1016/j.febslet.2014.09.004.

22. Mishima E, Inoue C, Saigusa D, Inoue R, Ito K, Suzuki Y, Jinno D, Tsukui Y, Akamatsu Y, Araki M, Araki K, Shimizu R, Shinke H, Suzuki T, Takeuchi Y, Shima H, Akiyama Y, Toyohara T, Suzuki C, Saiki Y, Tominaga T, Miyagi S, Kawagisihi N, Soga T, Ohkubo T, Yamamura K, Imai Y, Masuda S, Sabbisetti V, Ichimura T, Mount DB, Bonventre JV, Ito S, Tomioka Y, Itoh K, Abe T. Conformational Change in Transfer RNA Is an Early Indicator of Acute Cellular Damage. J Am Soc Nephrol. 2014 Oct; 25(10):2316-2326. doi: 10.1681/ASN.2013091001.

23. Yang M, Su H, Soga T, Kranc KR, Pollard PJ. Prolyl hydroxylase domain enzymes: important regulators of cancer metabolism. Hypoxia 2014 Aug 30; 2:127-142. doi: 10.2147/HP.S47968.

24. Takeuchi K, Ohishi M, Endo K, Suzumura K, Naraoka H, Ohata T, Seki J, Miyamae Y, Honma M, Soga T. Metabolomic Analysis of the Effects of Omeprazole and Famotidine on Aspirin-induced Gastric Injury. Metabolomics 2014 Oct.; 10(5), 995-1004, doi: 10.1007/s11306-014-0627-0.

25. Nishimura T, Higuchi K, Sai Y, Sugita Y, Yoshida Y, Tomi M, Wada M, Wakayama T, Tamura A, Tsukita S, Soga T, Nakashima E. Fetal Growth Retardation and Lack of Hypotaurine in Ezrin Knockout Mice. PLoS One 2014 Aug 21; 9(8):e105423. doi: 10.1371/journal.pone.0105423.

26. Yugi K, Kubota H, Toyoshima Y, Noguchi R, Kawata K, Komori Y, Uda S, Kunida K, Tomizawa Y, Funato Y, Miki H, Matsumoto M, Nakayama KI, Kashikura K, Endo K, Ikeda K, Soga T, Kuroda S. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep 2014 Aug 21; 8(4):1171-1183. doi: 10.1016/j.celrep.2014.07.021.

27. Takeuchi K, Ohishi M, Endo K, Suzumura K, Naraoka H, Ohata T, Seki J, Miyamae Y, Honma M, Soga T. Hydroxyproline, a Serum Biomarker Candidate for Gastric Ulcer in Rats: A Comparison Study of Metabolic Analysis of Gastric Ulcer Models Induced by Ethanol, Stress, and Aspirin. Biomark Insights 2014 Jul 27; 9:61-66. doi: 10.4137/BMI.S15918.

28. Migita T, Okabe S, Ikeda K, Igarashi S, Sugawara S, Tomida A, Soga T, Taguchi R, Seimiya H. Inhibition of ATP citrate lyase induces triglyceride accumulation with altered fatty acid composition in cancer cells. Int J Cancer 2014 Jul 1; 135(1):37-47. doi: 10.1002/ijc.28652.

29. Ohka F, Ito M, Ranjit M, Senga T, Motomura A, Motomura K, Saito K, Kato K, Kato Y, Wakabayashi T, Soga T, Natsume A. Quantitative metabolome analysis profiles activation of glutaminolysis in glioma with IDH1 mutation. Tumour Biol 2014 Jun; 35(6):5911-5920. doi: 10.1007/s13277-014-1784-5.

30. Adam J, Yang M, Soga T, Pollard PJ. Rare insights into cancer biology. Oncogene 2014 May 15; 33(20):2547-2556. doi: 10.1038/onc.2013.222.

31. Obata F, Kuranaga E, Tomioka K, Ming M, Takeishi A, Chen C, Soga T, Miura M. Necrosis-driven systemic immune response alters SAM metabolism through the FOXO-GNMT axis. Cell Rep 2014 May 8; 7(3):821-833. doi: 10.1016/j.celrep.2014.03.046.

32. Yamatani H, Takahashi K, Yoshida T, Soga T, Kurachi H. Differences in the fatty acid metabolism of visceral adipose tissue in postmenopausal women. Menopause 2014 Feb; 21(2):170-176. doi: 10.1097/GME.0b013e318296431a.

2013

01. Martínez, P., Gálvez, S., Ohtsuka, N., Budinich, M., Paz Corté s, M., Serpell, C., Nakahigashi, K.., Hirayama, A., Tomita, M., Soga. T., Martínez, S., Maass, A. and Parada, P. (2013) Metabolomic study of of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licananta. Metabolomics. 9: 247-57.
PubmedPublisher

02. Matsui, M., Tomita, M. and Kanai, A. (2013) Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks. Genome Biol Evol.5: 267-82.
PubmedPublisher

03. Selvarajoo K. and Tomita M. (2013) Physical laws shape biology. Science. 339: 6120-646.
PubmedPublisher

04. Soga, T. (2013) Cancer metabolism: key players in metabolic reprogramming. Cancer Sci. 104: 275-81.
PubmedPublisher

05. Takubo, K., Nagamatsu, G., Kobayashi, C. I, Nakamura-Ishizu, A., Kobayashi, H., Ikeda, E., Goda, N., Johnson, R. S, Rahimi, Y., Soga, T., Hirao, A., Suematsu, M., and Suda, T. (2013) Regulation of Glycolysis by Pdk Functions as a Metabolic Checkpoint for Cell Cycle Quiescence in Hematopoietic Stem Cells. Cell Stem Cell. 12: 49-61.
PubmedPublisher

06. Maekawa, K., Hirayama, A., Iwata Y., Tajima Y., Nishimaki-Mogami T., Sugawara S., Ueno, N., Abe, H., Ishikawa M., Murayama M., Matsuzawa Y., Nakanishi H., Ikeda K., Arita M., Taguchi, R., Minamino N., Wakabayashi, S., Soga T., and Saito, Y. (2013) Global metabolomic analysis of heart tissue in a hamster model for dilated cardiomyopathy. J. Mol. Cell. Cardiol. 59: 76-85.
PubmedPublisher

07. Takeuchi, K., Ohishi, M., Ota, S., Suzumura, K., Naraoka, H., Ohata, T., Seki, J., Miyamae, Y., Honma, M., and Soga, T. (2013) Metabolic Profiling to Identify Potential Serum Biomarkers for gastric ulceration induced by non-steroid anti-inflammatory drugs. J. Proteome Res.12, 1399-407.
PubmedPublisher

08. Hisano, Y., Ota, S., Arakawa, K., Muraki, M., Kono, N., Oshita, K., Sakuma, T., Tomita, M., Yamamoto, T., Okada, Y., and Kawahara, A. (2013) Quantitative assay for TALEN activity at endogenous genomic loci. Biology Open. 363-7.
PubmedPublisher

09. Shindo, Y., Nozaki, T., Saito, R., Tomita M. (2013) Computational analysis of associations between alternative splicing and histone modifications. FEBS LETTERS. 587: 516-21.
PubmedPublisher

10. Iwasaki, W., Y., Kiga, K., Kayo, H., Fukuda-Yuzawa, Y., Weise, J., Inada, T., Tomita, M., Ishihama, Y. and Fukao, T. (2013) Global MicroRNA Elevation by Inducible Exportin 5 Regulates Cell Cycle Entry. RNA. 490-7.
PubmedPublisher

11. Sugimoto, M., Saruta, J., Matsuki, C., To, M., Onuma, H., Kaneko, M., Soga, T., Tomita, M. and Tsukinoki, K. (2013) Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles. Metabolomics. 454-63.
Publisher

12. Kami, K., Fujimori, T., Sato, H., Sato, M., Yamamoto, H., Ohashi, Y., Sugiyama, N., Ishihama, Y., Onozuka, H., Kinoshita, T., Saito, N., Ochiai, A., Esumi, H., Soga, T. and Tomita, M. (2013) Metabolomic Profiling of Lung and Prostate Tumor Tissues by Capillary Electrophoresis Time-of-flight Mass Spectrometry. Metabolomics. 444-53.
Publisher

13. Ito, T., Tanaka, M., Shinkawa, H., Nakada, T., Ano, Y., Kurano, N., Soga, T. and Tomita, M. (2013) Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions. Metabolomics. 9: 178-87.
PubmedPublisher

14. Tsuruoka, M., Hara, J., Hirayama, A., Sugimoto, M., Soga, T., Shankle, W.R., Tomita, M. (2013) Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis. 34: 2865-72.
PubmedPublisher

15. Okubo, C., Sano, HI., Naito, Y., Tomita, M. (2013) Contribution of quantitative changes in individual ionic current systems to the embryonic development of ventricular myocytes: a simulation study. J Physiol Sci. 63: 355-67.
PubmedPublisher

16. Itaya, H., Oshita, K., Arakawa, K. and Tomita, M. (2013) GEMBASSY: an EMBOSS Associated Software Package for Comprehensive Genome Analyses. Source Code Biol Med.8: 17.
PubmedPublisher

17. Ito, T., Sugimoto, M., Toya, Y., Ano, Y., Kurano N, Soga., T, Tomita, M. (2013) Time-resolved metabolomics of a novel trebouxiophycean alga using 13CO2 feeding. J Biosci Bioeng. 116: 408-15.
PubmedPublisher

18. Nishino. T., Yachie-Kinoshita.A., Hirayama, A., Soga, T., Suematsu, M. and Tomita, M. (2013) Dynamic simulation and metabolome analysis of long-term erythrocyte storage in adenine-guanosine solution. PLOS ONE. 144: 212-23.
Publisher

19. Migita, T., Okabe, S., Ikeda, K., Igarashi, S., Sugawara, S., Tomida, A., Taguchi, R., Soga, T., and Seimiya, H. (2013) Inhibition of ATP citrate lyase induces an anticancer effect via reactive oxygen species: AMPK as a predictive biomarker for therapeutic impact. Am J Pathol. 182: 1800-10.
PubmedPublisher

20. Adam, J., Yang, M., Bauerschmidt, C., Kitagawa, M., O'Flaherty, L., Maheswaran, P., O¨ zkan, G., Sahgal, N., Baban, D., Kato, K., Saito, K., Iino, K., Igarashi, K., Stratford, M., Pugh, C., Tenant, D., Ludwig, C., Davies, B., Ratcliffe, P. J., El-Bahrawy, M., Ashrafian, H., Soga, T., and Pollard, P. J. (2013) A Role for Cytosolic Fumarate Hydratase in Urea Cycle Metabolism and Renal Neoplasia. Cell Rep. 3: 1440-48.
PubmedPublisher

21. Ternette N., Yang M., Laroyia M., Kitagawa M., O'Flaherty L., Wolhulter K., Igarashi K., Saito K., Kato K., Fischer R., Berquand A., Kessler B.M., Lappin T., Frizzell N., Soga T., Adam J, Pollard P.J. (2013) Inhibition of Mitochondrial Aconitase by Succination in Fumarate Hydratase Deficiency. Cell Rep. 3: 689-700.
PubmedPublisher

22. Furusawa, Y., Obata, Y., Fukuda, S., Endo, T., A., Nakato, G., Takahashi, D., Nakanishi, Y., Uetake, C., Kato, K., Kato, T., Takahashi, M., Fukuda, N., N., Murakami, S., Miyauchi, E., Hino, S., Atarashi, K., Onawa, S., Fujimura, Y., Lockett, T., Clarke, J., M., Topping, D., L., Tomita, M., Hori, S., Ohara, O., Morita, T., Koseki, H., Kikuchi, J., Honda, K., Hase, K. and Ohno, H. (2013) Commensal microbe-derived butyrate
induces the Differentiation of colonic regulatory T cells.
Nature. 504: 446-50.
PubmedPublisher

23. Hayashi, K., Piras, V., Tabata, S., Tomita, M., and Selvarajoo, K. (2013) Systems Biology Approach to Suppress TNF-induced Proinflammatory Gene Expressions. Cell Communication and Signaling. 11: 84.
Pubmed
Publisher

24. Karasawa T., Saito T., Ueno .Y., Sugimoto M., Soga T. (2013) Metabolome analysis of erythrocytes from patients with chronic hepatitis C reveals the etiology of ribavirin-induced hemolysis. International Journal of Medical Sciences,10 ,1575-1577.
Pubmed
Publisher

25. Saito T., Sugimoto M., Igarashi K., Saito K., Shao L., Katsumi T., Tomita K., Sato C., Aso R., Okumoto K., Nishise Y., Watanabe H., Tomita M., Ueno Y., Soga T. (2013) Dynamics of serum metabolites in patients with chronic hepatitis C receiving pegylated interferon plus ribavirin: A metabolomics analysis, Metabolism, 62, 1577-1586.
Pubmed
Publisher

26. Sato D., Akashi H., Sugimoto M., Tomita M., Soga T. (2013) Metabolomic profiling of the response of susceptible and resistant soybean strains to foxglove aphid, Aulacorthum solani Kaltenbach, Journal of Chromatography B, 925(5): 95-103.
Publisher

27. Koh T., Murakami Y., Machino M., Onuma H., Kaneko M., Sugimoto M., Soga T., Tomita M. (2013) Changes of Metabolic Profiles in an Oral Squamous Cell Carcinoma Cell Line Induced by Eugenol, In Vivo, 27(2): 233-243.
Pubmed
Publisher

28. Atarashi, K., Tanoue, T., Suda, W., Oshima, K., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., Kim, S.W., Fritz, J.V., Wilmes, P., Ueha, S., Matsushima, K., Ohno, H., Olle, B., Sakaguchi, S., Taniguchi, T., Morita, H., Hattori, M., Honda, K. (2013) Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota, Nature 500: 232-236.
Pubmed
Publisher

29. Amariei C, Machné R, Sasidharan K, Gottstein W, Tomita M, Soga T, Lloyd D, Murray DB. (2013) The dynamics of cellular energetics during continuous yeast culture, Conf Proc IEEE Eng Med Biol Soc. 2708-2711. doi: 10.1109/EMBC.2013.6610099
Pubmed
Publisher

30. Soma, A., Sugahara, J., Onodera, A., Yachie, N., Kanai, A., Watanabe, S., Yoshikawa, H., Ohnuma, M., Kuroiwa, H., Kuroiwa, T. and Sekine, Y. (2013) Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Sci Rep. 3:2321. doi: 10.1038/srep02321

31. Okuda, J., Niizuma, S., Shioi, T., Kato, T., Inuzuka, Y., Kawashima, T., Tamaki, Y., Kawamoto, A., Tanada, Y., Iwanaga, Y., Narazaki, M., Matsuda, T., Adachi, S., Soga, T., Takemura, G., Kondoh, H., Kita, T., Kimura, T. (2013) Persistent overexpression of phosphoglycerate mutase, a glycolytic enzyme, modifies energy metabolism and reduces stress resistance of heart in mice. PLoS ONE. 8(8):e72173.
doi:10.1371/journal.pone.0072173

32. Uema, N., Ooshio, T., Harada, K., Naito, M., Naka, K., Hoshii, T., Tadokoro, Y., Ohta, K., Ali, MA., Katano, M., Soga, T., Nakanuma, Y., Okuda, A., Hirao, A. (2013) Abundant nucleostemin expression supports the undifferentiated properties of germ cell tumors. Am J Pathol. 183(2):592-603. doi:10.1016/j.ajpath.2013.04.018

33. Yang, M., Soga, T., and Pollard, P. J. (2013) Oncometabolites: Linking Altered Metabolism with Cancer? J. Clin. Invest. 123(9):3652-3658. doi:10.1172/JCI67228

34. Kimura T, Takahashi A, Takabatake Y, Namba T, Yamamoto T, Kaimori J, Matsui I, Kitamura H, Niimura F, Matsusaka T, Soga T, Rakugi H, Isaka Y. Autophagy protects kidney proximal tubule epithelial cells from mitochondrial metabolic stress. Autophagy 2013 Nov 1; 9(11):1876-1886. doi: 10.4161/auto.25418.

35. Shimura D, Nakai G, Jiao Q, Osanai K, Kashikura K, Endo K, Soga T, Goda N, Minamisawa S. Metabolomic profiling analysis reveals chamber-dependent metabolite patterns in the mouse heart. Am J Physiol Heart Circ Physiol 2013 Aug 15; 305(4):H494-505. doi: 10.1152/ajpheart.00867.2012.

36. Oyama-Okubo N, Sakai T, Ando T, Nakayama M, Soga T. Metabolome profiling of floral scent production in Petunia axillaris. Phytochemistry 2013 Jun; 90:37-42. doi: 10.1016/j.phytochem.2013.03.006.

37. Noguchi R, Kubota H, Yugi K, Toyoshima Y, Komori Y, Soga T, Kuroda S. The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns. Mol Syst Biol 2013 May 14; 9:664. doi: 10.1038/msb.2013.19.

38. Jeelani G, Husain A, Sato D, Soga T, Suematsu M, Nozaki T. Biochemical and functional characterization of novel NADH kinase in the enteric protozoan parasite Entamoeba histolytica. Biochimie. 2013 Feb; 95(2):309-319. doi: 10.1016/j.biochi.2012.09.034.

39. Ohtani N, Tomita M, Itaya M. (2013) Identification of a replication initiation protein of the pvv8 plasmid from Thermus thermophilus HB8. Extremophiles. 17(1):15-28.

40. Arakawa K, Tomita M. (2013) Merging multiple omics datasets in silico: statistical analyses and data interpretation. Methods Mol Biol. 985:459-70.

2012

01. Selvarajoo, K. (2012) The recognition of chaos in host-pathogen response. Front. Physio. 3:7.
PubmedPublisher

02. Murakami, S., Fujishima, K., Tomita, M. and Kanai, A. (2012) Metatranscriptomic analysis of microbes in an ocean-front deep subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Applied and Environmental Microbiology. 78(4): 1015-1022.
PubmedPublisher

03. Sugimoto, M., Sakagami, H., Yokote, Y., Onuma, H., Kaneko, M., Mori, H., Sakaguchi, Y., Soga, T., and Tomita, M. (2012) Non-targeted metabolite profiling in activated macrophage secretion. Metabolomics. 8: 624-33.
Publisher

04. Sugimoto, M., Kaneko, M., Onuma, H., Sakaguchi, Y., Mori, M., Abe, S., Soga, T., and Tomita, M. (2012) Changes in the Charged Metabolite and Sugar Profiles of Pasteurized and Unpasteurized Japanese Sake with Storage. J. Agric. Food Chem. 60 (10): 2586-2593.
PubmedPublisher

05. Sugahara, J., Fujishima, K., Nunoura, T., Takaki, Y., Takami, H., Takai, K., Tomita M., and Kanai, A. (2012) Genomic Heterogeneity in a Natural Archaeal Population Suggests a Model of tRNA Gene Disruption. PLoS ONE. 7(3):e32504.
PubmedPublisher

06. Arakawa, K. and Tomita, M. (2012) Measures of Compositional Strand Bias Related to Replication Machinery and its Applications. Current Genomics. 13(1):4-15.
Publisher

07. Tomita, M. and Kami, K. (2012) Systems Biology, Metabolomics, and Cancer Metabolism. Science. 336:990-991.
Publisher

08. Selvarajoo K., and Giuliani A. (2012) Finding Self-organization from the Dynamic Gene Expressions of Innate Immune Responses. Front. Physiol. 3:192.
PubmedPublisher

09. Selvarajoo K. (2012) Understanding multimodal biological decisions from single cell and population dynamics. Wiley Interdiscip Rev Syst Biol Med.4(4) 385-99.
PubmedPublisher

10. Kono, N., Arakawa, K., and Tomita, M. (2012) Validation of bacterial replication termination models using simulation of genomic mutations. PLoS One.7(4):e34526.
PubmedPublisher

11. Hamashima, K., Fujishima, K., Masuda, T., Sugahara, J., Tomita, M., and Kanai, A.(2012) Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic Acids Res. 40: 3653-3662.
PubmedPublisher

12. Sugimoto, M., Kawakami, M., Robert, M., Soga, T. and Tomita, M. (2012) Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis. Current Bioinformatics. 7: 96-108.
PubmedPublisher

13. Helmy, M., Tomita, M. and Ishihama, Y.(2012) Peptide Identification by Searching Large-Scale Tandem Mass Spectra against Large Databases: Bioinformatics Methods in Proteogenomics. Genes Genomes Genomics. 6: 76-85.
PubmedPublisher

14. Helmy, M., Sugiyama, N., Tomita, M. and Ishihama, Y. (2012)Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics.Genesto Cells Manuscript.(2012). 17: 633-44.
PubmedPublisher

15. Fujishima, H., Okada, N., Dogru, M., Baba, F., Tomita, M., Abe, J., Matsumoto, K., and Saito, H. (2012)The role of Staphylococcal enterotoxin in atopic keratoconjunctivitis and corneal ulceration.Allergy. 67: 799-803.
PubmedPublisher

16. Sasidharan, K., Amariei, C., Tomita, M., and Murray, D.B. (2012)Rapid DNA, RNA and protein extraction protocols optimised for slow continuously growing yeast cultures.Yeast Journal. 29:311-322.
PubmedPublisher

17. Piras, V., Tomita, M., and Selvarajoo, K. (2012) Is central dogma a global property of cellular information flow? Front. Physiol.3,439.
PubmedPublisher

18. Hirayama, A., Nakashima, E., Sugimoto, M., Akiyama, S., Sato, W., Maruyama, S., Matsuo, S., Tomita, M., Yuzawa, Y. and Soga, T. (2012) Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy. Anal Bioanal Chem. 404:3101-9.
PubmedPublisher

19. Iino, K., Sugimoto, M., Soga, T. and Tomita, M. (2012) Metabolomics: A New Omics Technology for Traditional Herbal Medicine Analysis. Chinese Medicine: Acupuncture, Herbal Medicine and Therapies. 45-55.                        

20. Tanaka, S., Taga, H., Maehara, K., Kaneshima, A., Machino, M., Onuma, H., Kaneko, M., Sakagami, H., Sugimoto, M., Soga, T. and Tomita, M. (2012) Pilot Study of Changes in Salivary Metabolic Profiles Induced by Template Therapy. In Vivo. 26:1015-20.
PubmedPublisher

21. Hirayama, A., Tomita, M. and Soga, T. (2012) Sheathless capillary electrophoresis-mass spectrometry with a high- sensitivity porous sprayer for cationic metabolome analysis. Analyst. 137:5026-5033.
PubmedPublisher

22. Imami, K., Sugiyama, N., Imamura, H., Wakabayashi, M., Tomita, M., Taniguchi, M., Ueno, T., Toi, M. and Ishihama, Y. (2012) Temporal profiling of lapatinib-suppressed phosphorylation signals inEGFR/HER2 pathways. Mol Cell Proteomics. 12:1741-57.
PubmedPublisher

23. Sasidharan, K., Soga, T., Tomita, M. and Murray, D., B. (2012) A Yeast Metabolite Extraction Protocol Optimised for Time-Series Analyses. PLoS ONE. 7:e44283.
PubmedPublisher

24. Piras, V., Hayashi, K., Tomita, M. and Selvarajoo, K. (2012) Investigation of stochasticity in TRAIL signaling cancer model. IEEE/ICME Com. Med. Eng. 609-614.
Publisher

25. Takada, M., Sugimoto, M., Ohno, S., Kuroi, K., N. Sato , H., Bando, H., Masuda, N., Iwata, H., Kondo, M., Sasano, H., Chow, L., W., C., Inamoto, T., Naito, Y., Tomita, M. and Toi, M. (2012) Predictions of the pathological response to neoadjuvant chemotherapy in patients with primary breast cancer using a data mining technique. Breast Cancer Res Treat. 134:661-70.
Pubmed Publisher

26. Sasidharan, K., Tomita, M., Aon, M., Lloyd, D. and Murray, D, B.(2012) Time-structure of the yeast metabolism in vivo. Adv Exp Med Biol. 736:359-79.
Pubmed Publisher

27. Takada, M., Sugimoto, M., Naito, Y., Moon, H., G., Han, W., Noh, D., Y., Kondo, M., Kuroi, K., Sasano, H., Inamoto, T., Tomita, M., and Toi, M. (2012) Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model. BMC Med Inform Decis Mak 12:54.
Pubmed Publisher

28. Ohtani., N., Tomita, M. and Itaya, M. (2012) The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination.Extremophiles. 16:237-44.
PubmedPublisher

29. Helmy, M., Sugiyama, N., Tomita, M. and Ishihama, Y. (2012) The rice proteogenomics database OryzaPG-DB: development, expansion and new features. Front. Plant Sci. 3:65.
Pubmed Publisher

30. Jeelani G., Sato D., Husain A., Cadiz A.E., Sugimoto M., Soga T., Suematsu M., Nozaki T.(2012) Metabolic Profiling of the Protozoan Parasite Entamoeba invadens Revealed Activation of Unpredicted Pathway during Encystation, Plos One, 7(5), e37740.
PubmedPublisher

31. Sugimoto, M., Ikeda, S., Niigata, K., Tomita, M., Sato, H. and Soga, T. (2012) MMMDB: Mouse Multiple Tissue Metabolome Database. Nucleic Acids Res. 40: D809-D814.
Pubmed Publisher

32. Itaya,M., Kawata, Y., Sato. M., Tomita. M. and Nakahigashi. K. (2012) A simple method to provide a shuttling plasmid for delivery to other host ascertained by prolonged stability of extracellular plasmid DNA released from Escherichia coli K12 endA mutant, deficient in major endonuclease. J. Biochem. 152:501-504.
PubmedPublisher

33. Toya, Y., Nakahigashi, K., Tomita, M., and Shimizu, K. (2012) Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. Molecular BioSystems. 8: 2593-604.
PubmedPublisher

34. Yamada, M., Takanashi, K., Hamatani, T., Hirayama, A., Akutsu, H., Fukunaga, T., Ogawa, S., Sugawara, K., Shinoda, K., Soga, T., Umezawa, A., Kuji, N., Yoshimura, Y. and Tomita, M. (2012) A medium-chain fatty acid as an alternative energy source in mouse preimplantation development. Scientific Reports. 2.
Pubmed Publisher

35. Hoshi, T., Tadokoro, Y., Naka, K., Ooshio, T., Muraguchi, T., Sugiyama, N., Soga, T., Araki, K., Yamamura, K., and Hirao, A. (2012) mTORC1 is Essential for Leukemia Propagation but Not Stem Cell Self- renewal. J. Clin. Invest. 122, 2114-29.
PubmedPublisher

36. Kasukawa, T., Sugimoto, M., Hida, A., Minami, Y., Mori, M., Honma, S., Honma, K., Mishima, K., Soga, T., and Ueda, H.R. (2012) Human blood metabolite timetable indicates internal body time. Proc. Natl. Acad. Sci. USA. 109, 15036-141.
PubmedPublisher

37. Imaizumi, Y., Okada, Y., Akamatsu, W., Koike, M., Kuzumaki, N., Hayakawa, H., Nihira, T., Kobayashi, T., Ohyama, M., ,Sato, S., Takanashi, M., Funayama, M., Hirayama, A., Soga, T., Hishiki, T., Suematsu, M., Yagi, T., Ito, D., Kosakai, A., Hayashi, K., Shouji, M., Nakanishi, A., Suzuki, N., Mizuno, Y., Mizushima, N., Amagai, M., Uchiyama, Y., Mochizuki, H., Hattori, N., and Okano H. (2012) Mitochondrial dysfunction associated with increased oxidative stress and α-synuclein accumulation in PARK2 iPSC-derived neurons and postmortem brain tissue. Mol Brain. 5: 35.
PubmedPublisher

38. Takahashi, M., Miyata, S., Fujii, J., Inai, Y., Ueyama, S., Araki, M., Soga, T., Fujinawa, R., Nishitani C., Ariki S., Shimizu T., Abe T., Ihara Y., Nishikimi, M., Kozutsumi Y., Taniguchi N., and Kuroki, Y. (2012) In vivo role of aldehyde reductase. Biochim. Biophys. Acta. 1820: 1787-96.
PubmedPublisher

39. Akiyama, Y., Takeuchi, Y., Kikuchi, K., Mishima, E., Yamamoto, Y., Suzuki, C., Toyohara, T., Suzuki, T., Hozawa, A., Ito, S., Soga, T., and Abe, T.(2012) A Metabolomic approach for clarifying the effect of AST-120 on 5/6 nephrectomized rats by Capillary Electrophoresis with Mass Spectrometry(CE-MS). Toxins. 4: 1309-22.
PubmedPublisher

40. Omori, Y., Ohtani, T., Sakata, Y., Mano, T., Takeda, Y., Tamaki, S., Tsukamoto. Y., Kamimura, D., Aizawa, Y., Miwa, T., Komuro, I., Soga, T., and Yamamoto, K. (2012) L-Carnitine Prevents the Development of Ventricular Fibrosis and Heart Failure with Preserved Ejection Fraction in Hypertensive Heart Disease . J. Hypertens. 30: 1834-44.
PubmedPublisher

41. Yang, M., Soga, T., Pollard, P.J., and Adam, J. (2012) The emerging role of fumarate as an oncometabolite. Front. Oncol. 2: 85.
PubmedPublisher

42. Hirata, Y., Ikeda, K., Sudoh, M., Tokunaga, Y., Suzuki, A., Weng, L., Ohta, M., Tobita, Y., Okano, K., Ozeki, K., Kawasaki, K., Tsukuda, T., Katsume, A., Aoki, Y., Umehara, T., Sekiguchi, S., Toyoda, T., Shimotohno, K., Soga, T., Nishijima, M., Taguchi, R., and Kohara, M.(2012) Self-enhancement of hepatitis C virus replication by promotion of specific sphingolipid biosynthesis. PLoS Pathog. 8.
PubmedPublisher

43. Husain, A., Sato, D., Jeelani, G., Soga, T., and Nozaki, T. (2012) Dramatic Increase in Glycerol Biosynthesis upon Oxidative Stress in the Anaerobic Protozoan Parasite Entamoeba histolytica. PLoS Negl. Trop. Dis. 6.
PubmedPublisher

44. Liu, C., Kurakane, S., Takita, J., Itano R., Soga, T., Oikawa A., and Igarashi, K. (2012) Antihypertensive Effects of Unripe Persimmon (Diospyros kaki L.cv. Hiratanenashi) Fruit and Its Component in Spontaneously Hypertensive Rats. Food Sci. Technol. Res. 18, 391-8.
Publisher

45. Deguchi, K., Sato, D., Sugimoto, M., Hara, H., Kawasaki, Y., Demura, S., Watanabe, T., Denholme, S. J., Okazaki, H., Ozaki, T., Yamaguchi, T., Takeya, H., Soga, T., Tomita, M., and Takano, Y. (2012) Clarification as to why alcoholic beverages have the ability to induce superconductivity in Fe1+dTe1−xSx. Supercond. Sci. Technol. 25(8), 084025.
Publisher

46. Nakada T, Nozaki H, Tomita M. (2012) Light microscopy and phylogenetic analyses of 
Chlamydomonas species (Volvocales, Chlorophyceae). I. Chlamydomonas pseudomacrostigma and Chlamydomonas media. Acta Phytotaxonomica et Geobotanica, 62, 69-78

47. Yamamotoya T, Dose H, Tian Z, Fauré A, Toya Y, Honma M, Igarashi K, Nakahigash, K, Soga T, Mori H, Matsuno H. Glycogen is the primary source of glucose during the lag phase of E. coli proliferation. Biochim Biophys Acta 2012 Dec; 1824(12):1442-8. doi: 10.1016/j.bbapap.2012.06.010.

48. Kato T, Niizuma S, Inuzuka Y, Kawashima T, Okuda J, Kawamoto A, Tamai Y, Iwanaga Y, Soga T, Kita T, Kimura T, Shioi T. Analysis of Liver Metabolism in a Rat Model of Heart Failure. Int J Cardiol 2012 Nov 29; 161(3):130-136. doi: 10.1016/j.ijcard.2011.07.056.

49. Kami K, Fujita Y, Igarashi S, Koike S, Sugawara S, Ikeda S, Sato N, Ito M, Tanaka M, Tomita M, Soga T. Metabolomic Profiling Rationalized Pyruvate Efficacy in Cybrid Cells Harboring MELAS Mitochondrial DNA Mutations. Mitochondrion 2012 Nov; 12(6):644-653. doi: 10.1016/j.mito.2012.07.113.

50. Toyoda Y, Tamai M, Kashikura K, Kobayashi S, Fujiyama Y, Soga T, Tagawa Y. Acetaminophen-induced Hepatotoxicity in a Liver Tissue Model Consisting of Primary Hepatocytes Assembling Around an Endothelial Cell Network. Drug Metab Dispos 2012 Jan; 40(1):169-77. doi: 10.1124/dmd.111.041137.

51. Ohtani N, Hasegawa M, Sato M, Tomita M, Kaneko S, Itaya M. (2012) Serial assembly of Thermus megaplasmid DNA in the genome of Bacillus subtilis 168: a BAC-based domino method applied to DNA with a high GC content. Biotechnol J. 7(7):867-76.

2011

01. Yachie, N., Saito, R., Sugiyama, N., Tomita, M. and Ishihama, Y. (2011) Integrative features of the yeast phosphoproteome and protein-protein interaction map. PLoS Comput. Biol., 7(1), e1001064.
PubmedPublisher

02. Kono, N., Arakawa, K. and Tomita, M. (2011) Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC Genomics, 12(1), 19.
PubmedPublisher

03. Yoshida, S., Imoto, J., Minato, T., Oouchi, R., Kamada, Y., Tomita, M., Soga, T. and Yoshimoto, H. (2011)A novel mechanism regulates H(2) S and SO(2) production in Saccharomyces cerevisiae. Yeast, 28(2), 109-21.
PubmedPublisher

04. Hayashi, K., Sasamura, H., Hishiki, T., Suematsu, M., Ikeda, S., Soga, T., and Itoh, H.(2011) Use of Serum and Urine Metabolome Analysis for the Detection of Metabolic Changes in Patients with Stage 1-2 Chronic Kidney Disease. Nephro-Urol. Mon. 3: 164-71.
Publisher

05. Nozaki, T., Yachie, N., Ogawa, R., Saito, R. and Tomita, M. (2011) Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA. Gene, 476(1-2), 10-4.
PubmedPublisher

06. Ogawa, Y., Koike, N., Kurosawa, G., Soga, T., Tomita, M. and Tei, H. (2011) Positive Autoregulation Delays the Expression Phase of Mammalian Clock Gene Per2. PLoS ONE, 6(4), e18663.
PubmedPublisher

07. Selvarajoo, K. (2011) Macroscopic law of conservation revealed in the population dynamics of Toll-like receptor signaling. Cell Communication and Signaling, 9(9).
PubmedPublisher

08. Nakada, T. and Tomita, M. (2011) Chlamydomonas neoplanoconvexa nom. nov. and its unique phylogenetic position within Volvocales (Chlorophyceae). Phycological Research, 59(3), 194-9.
Publisher

09. Murray, B.D., Haynes, K. and Tomita, M. (2011) Redox Regulation in Respiring Saccharomyces cerevisiae. Biochim Biophys Acta. 1810(10), 945-58.
PubmedPublisher

10. Ooga, T., Sato, H., Nagashima, A., Sasaki, K., Tomita, M., Soga T. and Ohashi, Y. (2011) Metabolomic Anatomy of Animal Model Revealing Homeostatic Imbalances in Dyslipidemia. Y. Mol. BioSyst.,7, 1217-23.
PubmedPublisher

11. Oshita,K., Arakawa, K., and Tomita, M. (2011) KBWS: an EMBOSS associated package for accessing bioinformatics webservices. Source Code Biol. Med., 6, 8.
PubmedPublisher

12. Komasa, M., Fujishima, K., Hiraoka, K., Shinhara, A., Lee, Baek-Seok., Tomita, M. and Kanai, A. (2011) A screening system for artificial small RNAs that inhibit the growth of Escherichia coli. J. Biochem., 150(3), 289-94.
PubmedPublisher

13. Helmy, M., Tomita, M., Ishihama, Y. (2011) OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol., 11, 13.
PubmedPublisher

14. Saito, R., Kohno, K., Okada, Y., Osada, Y., Numata, K., Kohama, C., Watanabe, K., Nakaoka, H., Yamamoto, N., Kanai, A., Yasue, H., Murata, S., Abe, K., Tomita, M., Ohkohchi, N. and Kiyosawa, H. (2011) Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. BMC Med Genomics., 4, 42.
PubmedPublisher

15. Toya, Y., Kono, N., Arakawa, K., Tomita, M. (2011) Metabolic flux analysis and visualization. J. Proteome Res., 10(8), 3313-23.
PubmedPublisher

16. Takane, K., Kanai, A. (2011) Vertebrate Virus-Encoded MicroRNAs and Their Sequence Conservation. Jpn. J. Infect. Dis., 64(5), 357-66.
PubmedPublisher

17. Nozaki, T., Yachie, N., Ogawa, R., Kratz, A., Saito, R., Tomita, M. (2011) Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC Genomics, 12, 416.
PubmedPublisher

18. Shinhara, A., Matsui, M., Hiraoka, K., Nomura, W., Hirano, R., Nakahigashi, K., Tomita, M., Mori, H., Kanai, A. (2011) Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics, 12, 428.
PubmedPublisher

19. Soga, T., Sugimoto, M., Honma, M., Mori, M., Igarashi, K., Kashikura, K., Ikeda, S., Hirayama, A., Yamamoto, T., Yoshida, H., Otsuka, M., Tsuji, S., Yatomi, Y., Sakuragawa, T., Watanabe, H., Nihei, K., Saito, T., Kawata, S., Suzuki, H., Tomita, M., Suematsu, M. (2011) Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease. J. Hepatol., 55(4), 896-905.
PubmedPublisher

20. Piras, V., Hayashi, K., Tomita, M., Selvarajoo, K. (2011) Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules. Sci. Rep., 1,144.
PubmedPublisher

21. Sato, A., Soga, T., Igarashi, K., Takesue, K., Tomita, M., Kanai, A. (2011) GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes Cells, 16(12), 1190-1199.
PubmedPublisher

22. Adam, J., Hatipoglu, E., O'Flaherty, L., Ternette, N., Sahgal, N., Lockstone, H., Baban D., Nye, E., Stamp, G.W., Wolhuter, K., Stevens, M., Fischer, R., Carmeliet, P., Maxwell, P.H., Pugh, C.W., Frizzell, N., Soga, T., Kessler, B.M., El-Bahrawy, M., Ratcliffe, P.J., Pollard, P.J. (2011) Renal Cyst Formation in Fh1-Deficient Mice Is Independent of the Hif/Phd Pathway: Roles for Fumarate in KEAP1 Succination and Nrf2 Signaling, Cancer Cell, 20, 524-537.
PubmedPublisher

23. Deng, L., Shoji, I., Ogawa, W., Kaneda, S., Soga, T., Jiang, D., Ide, Y., Hotta, H. (2011)Hepatitis C Virus Infection Promotes Hepatic Gluconeogenesis through an NS5A-Mediated, FoxO1-Dependent Pathway, J. Virol. 85, 8556-8568.
PubmedPublisher

24. Ochiai, D., Goda, N., Hishiki, T., Kanai, M., Senoo-Matsuda, N., Soga, T., Johnson, R.S., Yoshimura, Y., Suematsu, M. (2011) Disruption of HIF-1α in Hepatocytes Impairs Glucose Metabolism in Diet-induced Obesity Mice, Biochem. Biophys. Res. Commun, 415(3):445-9
PubmedPublisher

25. Suzuki, T., Toyohara, T., Akiyama, Y., Takeuchi, Y., Mishima, E., Suzuki, C., Ito, S., Soga, T., Abe, T.(2011), Transcriptional Regulation of Organic Anion Transporting Polypeptide SLCO4C1 as a New Therapeutic Modality to Prevent Chronic Kidney Disease, J. Pharm. Sci., 100, 3696-3707.
PubmedPublisher

26. Gustavsson, C., Soga, T., Wahlström, E, Vesterlund, M, Azimi, A., Norstedt, G., Tollet-Egnell, P.(2011) Sex-dependent Hepatic Transcripts and Metabolites in the Development of Glucose Intolerance and Insulin Resistance in Zucker Diabetic Fatty Rats, J. Mol. Endcrinol. 47, 129-143.
PubmedPublisher

27. Kimura, T., Takabatake, Y., Takahashi, A., Kaimori, J., Matsui, I., Namba, T., Kitamura, H., Niimura, F., Matsusaka, T., Soga, T., Rakugi, H., Isaka, Y.(2011) Autophagy Protects the Proximal Tubule from Degeneration and Acute Ischemic Injury, J. Am. Soc. Nephrol. 22, 902-913.
PubmedPublisher

28. Masuda, T., Sugiyama, N., Tomita, M., Ishihama, Y. (2011) Microscale Phosphoproteome Analysis of 10 000 Cells from Human Cancer Cell Lines. Anal. Chem. 83:7698-703.
PubmedPublisher

29. Fujishima, K., Sugahara, J., Miller, CS., Baker, BJ., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, JF., Kanai, A. (2011) A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res. 39:9695-9704.
PubmedPublisher

30. Seike M, Saitou T, Kouchi Y, Ohara T, Matsuhisa M, Sakaguchi K, Tomita K, Kosugi K, Kashiwagi A, Kasuga M, Tomita M, Naito Y, Nakajima H. (2011) Computational assessment of insulin secretion and insulin sensitivity from 2-h oral glucose tolerance tests for clinical use for type 2 diabetes. J Physiol Sci. 61(4):321-30.

31. Shimo H, Nishino T, Tomita M. (2011) Predicting the Kinetic Properties Associated with Redox Imbalance after Oxidative Crisis in G6PD-Deficient Erythrocytes: A Simulation Study. Adv Hematol. 2011:398945.

2010

01. Kitamura, S., Fujishima, K., Sato, A., Tsuchiya, D., Tomita, M. and Kanai, A. (2010) Characterization of RNase HII substrate recognition using RNase HII-Argonaute chimeric enzymes from Pyrococcus furiosus. Biochem. J., 426(3), 337-44.
PubmedPublisher

02. Arjunan, S.N.V. and Tomita, M. (2010) A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Syst. Synth. Biol., 4(1), 35-53.
PubmedPublisher

03. Takane, K., Fujishima, K., Watanabe, Y., Sato, A., Saito, N., Tomita, M. and Kanai, A., (2010) Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC Genomics, 11(1), 101.
PubmedPublisher

04. Imami, K., Sugiyama, N., Tomita, M. and Ishihama, Y. (2010) Quantitative Proteome and Phosphoproteome Analysis of Cultured Cells Based on SILAC Labeling without Requirement of Serum Dialysis, Mol Biosyst., 6(3), 594-602.
PubmedPublisher

05. Shinoda, K., Tomita, M. and Ishihama, Y. (2010) emPAI Calc -- for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics, 26(4), 576-7.
PubmedPublisher

06. Ogawa, R., Kitagawa, N., Ashida, H., Saito, R. and Tomita, M. (2010) Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences. FEBS Lett.,584(8), 1498-1502.
PubmedPublisher

07. Iwasaki, M., Miwa, S., Ikegami, T., Tomita, M., Tanaka, N. and Ishihama, Y. (2010) One-Dimensional Capillary Liquid Chromatographic Separation Coupled with Tandem Mass Spectrometry Unveils the Escherichia coli Proteome on a Microarray Scale. Anal. Chem., 82(7), 2616-2620.
PubmedPublisher

08. Sato, D., Kobayashi, S., Yasui, H., Shibata, N., Toru, T., Yamamoto, M., Tokoro, G., Ali, V., Soga, T., Takeuchi, T., Suematsu, M., Nozaki, T. (2010) Cytotoxic Effect of Amide Derivatives of Trifluoromethionine against The Enteric Protozoan Parasite Entamoeba histolytica. Int. J. Antimicrob. Agents., 35(1), 56-61.[Erratum in: Int. J. Antimicrob. Agents., 35(4) 417.]
PubmedPublisher

09. Nakada, T., Shinkawa, H., Ito, T. and Tomita, M. (2010) Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan. J. Plant Res., 123(1), 67-78.
PubmedPublisher

10. Nakada, T., Soga, T. and Tomita, M. (2010) Phylogenetic position of a rare loricated green alga, Cephalomonas granulata N. L. Higinb. (Volvocales, Chiorophyceae). Phycol. Res., 58(1), 62-68.
Publisher

11. Nakada, T. (2010) Nomenclatural notes on some ambiregnal generic names (comments to Özdikmen, 2009). Mun. Ent. Zool., 5(1), 204-208.
Publisher

12. Kato, T., Niizuma, S., Inuzuka, Y., Kawashima, T., Okuda, J., Tamaki, Y., Iwanaga, Y., Narazaki, M., Matsuda, T., Soga, T., Kita, T., Kimura, T. and Shioi, T. (2010) Analysis of Metabolic Remodeling in Compensated Left Ventricular Hypertrophy and Heart Failure. Circ. Heart Fail., ePub.3(3), 420-30.
PubmedPublisher

13. Nakada, T., Soga, T., Tomita, M. and Nozaki, H. (2010) Chlorogonium complexum sp. nov. (Volvocales, Chlorophyceae), and morphological evolution of Chlorogonium. Eur. J. Phycol., 45(1), 97-107.
Publisher

14. Nozaki, H., Nakada, T. and Watanabe, S. (2010) Evolutionary origin of Gloeomonas (Volvocales, Chlorophyceae), based on ultrastructure of chloroplasts and molecular phylogeny. J. Phycol., 46(1), 195-201.
Publisher

15. Maruyama, S., Sugahara, J., Kanai, A. and Nozaki, H. (2010) Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Mol Biol Evol., 27(5), 1070-1076.
PubmedPublisher

16. Imamura, H., Yachie, N., Saito, R., Ishihama, Y. and Tomita, M. (2010) Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics, 11:232.
PubmedPublisher

17. Fujishima, K., Sugahara, J., Tomita, M., Kanai, A. (2010) Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Mol Biol Evol. 27(10), 2233-2243.
PubmedPublisher

18. Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language genome analysis environment with REST and SOAP web service interfaces. Nucleic Acids Research, 38, W700-W705.
PubmedPublisher

19 Kim, H., Lee, B.S., Tomita, M., Kanai, A. (2010) Transcription-Associated Mutagenesis Increases Protein Sequence Diversity More Effectively than Does Random Mutagenesis in Escherichia coli. PLoS One, 5(5), e10567
PubmedPublisher

20. Saito, N., Ohashi, Y., Soga, T. and Tomita, M. (2010) Unveiling cellular biochemical reactions via metabolomics-driven approaches. Curr Opin Microbiol., 13, 358-362.
PubmedPublisher

21. Fujiwara, K., Ishihama, Y., Nakahigashi, K., Soga, T. and Taguchi, H. (2010) A Systematic Survey of in vivo Obligate Shaperonin-dependent Substrates. EMBO J., 29, 1552 - 1564.
PubmedPublisher

22. Kato, Y., Kubo, Y., Iwata, D., Kato, S., Sudo, T., Sugiura, T., Kagaya, T., Wakayama, T., Hirayama, A., Sugimoto, M., Sugihara, K., Kaneko, S., Soga, T., Asano, M., Tomita, M., Matsui, T., Wada, M. and Tsuji, A. (2010) Gene knockout and metabolome analysis of carnitine/organic cation transporter OCTN1. Pharm. Res., 27(5), 832-404.
PubmedPublisher

23. Kratz, A., Arner, E., Saito, R., Kubosaki, A., Kawai, J., Suzuki, H., Carninci, P., Arakawa, T., Tomita, M., Hayashizaki, Y. and Daub, C.O. (2010) Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. BMC Genomics, 11, 257.
PubmedPublisher

24. Nakada, T., Nozaki, H., and Tomita, M. (2010) Another Origin of Coloniality in Volvocaleans: The Phylogenetic Position of Pyrobotrys Arnoldi (Spondylomoraceae, Volvocales). J. Eukaryot. Microbiol., 57(4):379-82.
PubmedPublisher

25. Ozawa Y., Saito R., Fujimori S., Kashima H., Ishizaka M., Yanagawa H., Miyamoto-Sato E. and Tomita M. (2010) Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. BMC Bioinformatics.,11,350.
PubmedPublisher

26. Kyono Y., Sugiyama N., Tomita M., Ishihama Y.(2010) Chemical dephosphorylation for identification of multiply phosphorylated peptides and phosphorylation site determination. Rapid communications in mass spectrometry.,24(15), 2277-82.
PubmedPublisher

27. Sugimoto M., Hirayama A., Robert M., Abe S., Soga T., Tomita M.(2010) Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS data. ELECTROPHORESIS,31(14), 2311-18.
PubmedPublisher

28. Tsuchiya M., Piras V., Giuliani A., Tomita M., Selvarajoo K.(2010) Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed. PLoS One,5(8), e12116.
PubmedPublisher

29. Katayama T., Arakawa K., Nakao M., Ono K., Aoki-Kinoshita F K., Yamamoto Y., Yamaguchi A., Kawashima S., Chun H., Aerts J., et al.(2010) The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semantics,1(1)8.
PubmedPublisher

30. Nakada, T. (2010) (138) A proposal on the designation of cultures of fungi and algae as types. Taxon, 59(3), 983.
Publisher

31. Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M. and Sakakibara, Y. (2010) Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics, 11, 243.
PubmedPublisher

32. Kaneko, S. and Itaya, M. (2010) Designed horizontal transfer of stable giant DNA released from Escherichia coli. J. Biochem., 147(6), 819-822.
PubmedPublisher

33. Itaya, M. and Kaneko, S. (2010) Integration of stable extra-cellular DNA released from Escherichia coli into the Bacillus subtilis genome vector by culture mix method. Nucleic Acids Res., 38(8), 2551-2557.
PubmedPublisher

34. Sakuragawa, T., Hishiki, T., Ueno, Y., Ikeda, S., Soga, T., Yachie, A.K., Kajimura, M. and Suematsu, M. (2010) Hypotaurine is an Energy-Saving Hepatoprotective Compound against Ischemia-Reperfusion Injury of Rat Liver. J. Clin. Biochem. Nutr., 46(2), 126-134.
PubmedPublisher

35. Hayama, H., Nakada, T., Hamaji, T. and Nozaki, H. (2010) Morphology, molecular phylogeny and taxonomy of Gonium maiaprilis sp. nov. (Goniaceae, Chlorophyta) from Japan. Phycologia,49(3), 221-234.
Publisher

36. Matsuzaki, R., Nakada, T., Hara, Y. and Nozaki, H. (2010) Light and electron microscopy and molecular phylogenetic analyses of Chloromonas pseudoplatyrhyncha (Volvocales, Chlorophyceae). Phycol. Res., 58(3) 202-209.
Publisher

37. Toya, Y., Ishii, N., Nakahigashi, K., Hirasawa, T., Soga, T., Tomita, M. and Shimizu, K. (2010) 13C-metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol. Prog., 26(4):975-992.
PubmedPublisher

38. Kitagawa, M., Ikeda, S., Tashiro, E., Soga, T., Imoto, M. (2010) Metabolomic Identification of the Target of the Filopodia Protrusion Iinhibitor Glucopiericidin A. Chem Biol. 17(9):989-998.
PubmedPublisher

39. Jeelani, G., Husain, A., Sato, D., Ali, V., Suematsu, M., Soga, T., Nozaki, T.(2010) Two Atypical L-cysteine-regulated NADPH-dependent Oxidoreductases Involved in Redox Maintenance, L-cystine and Iron Reduction, and Metronidazole Activation in the Enteric Protozoon Entamoeba Histolytica, J. Biol. Chem., 285, 26889-26899.
Publisher

40. Miyamoto-Sato, E., Fujimori, S., Ishizaka, M., Hirai1, N., Masuoka1, K., Saito, R., Ozawa, Y., Hino, K., Washio, T., Tomita, M., Yamashita, T., Oshikubo, T., Akasaka, H., Sugiyama, J., Matsumoto, Y. and Yanagawa, H. (2010) A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks. Electrophoresis,5(2):e9289.
PubmedPublisher

41. Aono, E., Baba, T., Ara, T., Nishi, T., Nakamichi, T., Inamoto, E., Toyonaga, H., Hasegawa, M., Takai, Y., Okumura,Y., Baba, M., Tomita, M., Kato, C., Oshima, T., Nakasone, K. and Mori, H. (2010)Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments. Mol. Biosyst., 6(7):1216-26.
PubmedPublisher

42. Nakagami, H., Sugiyama, N., Mochida, K., Daudi, A., Yoshida, Y., Toyoda, T., Tomita, M., Ishihama, Y. and Shirasu, K. (2010)Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol., 153(3):1161-74.
PubmedPublisher

43. Sugimoto, M., Goto, H., Otomo, K., Ito, M., Onuma, H., Suzuki, A., Sugawara, M., Abe, S., Tomita, M. and Soga, T. (2010)Metabolomic Profiles and Sensory Attributes of Edamame under Various Storage Duration and Temperature Conditions. J. Agric. Food Chem., 58(14):8418-25.
PubmedPublisher

44. Yachie, A. K., Nishino, T., Shimo, H., Suematsu, M., and Tomita, M. (2010)A Metabolic Model of Human Erythrocytes: Practical Application of the E-Cell Simulation Environment.J. Biomed. Biotechnol., 2010,642420.
PubmedPublisher

45. Nakada, T., Tomita, M. and Nozaki, H. (2010)Volvulina compacta ( Volvocaceae, Chlorophyceae ), new to Japan, and its phylogenetic position.J. Jpn. Bot., 85, 364-369.
Publisher

46. Horiguchi, K., Toi, M., Horiguchi, S., Sugimoto, M., Naito, Y., Hayashi, Y., Ueno, T., Ohno, S., Funata, N., Kuroi, K., Tomita, M. and Eishi, Y. (2010) Predictive value of CD24 and CD44 for neoadjuvant chemotherapy response and prognosis in primary breast cancer patients. J. Med. Dent. Sci., 57(2), 165-75.
PubmedPublisher

47. Sugimoto, M., Wong, D. T., Hirayama, A., Soga, T. and Tomita, M. (2010) Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics, 6, 78-95.
Publisher

48. Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., Oda, Y., Kakazu, Y., Kusano, M., Tohge, T., Matsuda, F., Sawada, Y., Hirai, Y. M., Nakanishi, H., Ikeda, K., Akimoto, N., Maoka, T., Takahashi, H., Ara, T., Sakurai, N., Suzuki, H., Shibata, D., Neumann, S., Iida, T., Tanaka, K., Funatsu, K., Matsuura, F., Soga, T., Taguchi, R., Saito, K., Nishioka, T. (2010) MassBank: A Public Repository for Sharing Mass Spectral Data for Life Sciences. J. Mass Spectro. 45, 703-714.
PubmedPublisher

49. Sugimoto, M., Koseki, T., Hirayama, A., Abe, S., Sano, T., Tomita, M. and Soga, T. (2010) Correlation between Sensory Evaluation Scores of Japanese Sake and Metabolome Profiles, J. Agric. Food Chem., 58, 374-383.
PubmedPublisher

50. Sugimoto, M., Hirayama, A., Ihiskawa, T., Robert, M., Baran, R., Uehara, K., Kawai, K., Soga, T., Tomita, M. (2010) Differential Metabolomics Software for Capillary Electrophoresis-Mass Spectrometry Data Analysis, Metabolomics, 6, 27-41.
PubmedPublisher

51. Husain, A., Sato, D., Jeelani, G., Suematsu, M., Soga, T., Nozaki, T.(2010) Metabolome Analysis Revealed Increase in S-methylcysteine and Phosphatidylisopropanolamine Synthesis upon L-cysteine Deprivation in The Anaerobic Protozoan Parasite Entamoeba Histolytica, J. Biol. Chem., 285, 39160-39170.
PubmedPublisher

52. Toyohara, T., Akiyama, Y., Suzuki, T., Takeuchi, Y., Mishima, E., Tanemoto, M., Momose, A., Toki, N., Sato, H., Nakayama, M., Hozawa, A., Tsuji, I., Ito, S., Soga, T. and Abe. T (2010) Metabolomic profiling of uremic solutes in CKD patients, Hypertens. Res. 33, 944-952.
PubmedPublisher

53. Sugiura, T., Kato, S., Shimizu, T., Wakayama, T., Nakamichi, N., Kubo, Y., Iwata, D., Suzuki, K., Soga, T., Asano, M., Iseki, S., Tamai, I., Tsuji, A., and Kato, Y. (2010) Functional Expression of Carnitine/Organic Cation Transporter OCTN1/SLC22A4 in Mouse Small Intestine and Liver. Drug Metab Dispos. 38: 1665-72.
PubmedPublisher

54. Ohtani N, Tomita M, Itaya M. (2010)An extreme thermophile, Thermus thermophilus, is a polyploid bacterium. J Bacteriol. 192(20):5499-505.

2009

01. Yachie N, Saito R, Sugahara J, Tomita M, Ishihama Y (2009) In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution, Mol Cell Proteomics, 8, 1061-1071
Pubmed

02. Tsuchiya M, Selvarajoo K, Piras V, Tomita M, Giuliani A (2009) Local and global responses in complex gene regulation networks, Physica A: Statistical Mechanics and its Applications, 388, 1738-1746
Pubmed

03. Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, Giuliani A, Selvarajoo K (2009) Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages, PLoS One, 4, e4905
Pubmed

04. Toyohara T, Suzuki T, Morimoto R, Akiyama Y, Souma T, Shiwaku HO, Takeuchi Y, Mishima E, Abe M, Tanemoto M, Masuda S, Kawano H, Maemura K, Nakayama M, Sato H, Mikkaichi T, Yamaguchi H, Fukui S, Fukumoto Y, Shimokawa H, Inui K, Terasaki T, Goto J, Ito S, Hishinuma T, Rubera I, Tauc M, Fujii-Kuriyama Y, Yabuuchi H, Moriyama Y, Soga T, Abe T (2009) SLCO4C1 transporter eliminates uremic toxins and attenuates hypertension and renal inflammation, J Am Soc Nephrol, 20, 2546-2555
Pubmed

05. Tajima T, Goda N, Fujiki N, Hishiki T, Nishiyama Y, Senoo-Matsuda N, Shimazu M, Soga T, Yoshimura Y, Johnson RS, Suematsu M (2009) HIF-1alpha is necessary to support gluconeogenesis during liver regeneration, Biochem Biophys Res Commun, 387, 789-794
Pubmed

06. Suzuki H, Saito R, Tomita M (2009) Measure of synonymous codon usage diversity among genes in bacteria, BMC Bioinformatics, 10, 167
Pubmed

07. Sugahara J, Fujishima K, Morita K, Tomita M, Kanai A (2009) Disrupted tRNA gene diversity and possible evolutionary scenarios, J Mol Evol, 69, 497-504
Pubmed

08. Soga T, Igarashi K, Ito C, Mizobuchi K, Zimmermann HP, Tomita M (2009) Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry, Anal Chem, 81, 6165-6174
Pubmed

09. Shintani T, Iwabuchi T, Soga T, Kato Y, Yamamoto T, Takano N, Hishiki T, Ueno Y, Ikeda S, Sakuragawa T, Ishikawa K, Goda N, Kitagawa Y, Kajimura M, Matsumoto K, Suematsu M (2009) Cystathionine beta-synthase as a carbon monoxide-sensitive regulator of bile excretion, Hepatology, 49, 141-150
Pubmed

10. Selvarajoo K, Tomita M, Tsuchiya M (2009) Can complex cellular processes be governed by simple linear rules?, J Bioinform Comput Biol, 7, 243-268
Pubmed

11. Sato D, Nozaki T (2009) Methionine gamma-lyase: the unique reaction mechanism, physiological roles, and therapeutic applications against infectious diseases and cancers, IUBMB Life, 61, 1019-1028
Pubmed

12. Saito N, Robert M, Kochi H, Matsuo G, Kakazu Y, Soga T, Tomita M (2009) Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli, J Biol Chem, 284, 16442-16451
Pubmed

13. Ravichandran A, Sugiyama N, Tomita M, Swarup S, Ishihama Y (2009) Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species, Proteomics, 9, 2764-2775
Pubmed

14. Ooga T, Ohashi Y, Kuramitsu S, Koyama Y, Tomita M, Soga T, Masui R (2009) Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus, J Biol Chem, 284, 15549-15556
Pubmed

15. Numata K, Osada Y, Okada Y, Saito R, Hiraiwa N, Nakaoka H, Yamamoto N, Watanabe K, Okubo K, Kohama C, Kanai A, Abe K, Kiyosawa H (2009) Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes, BMC Genomics, 10, 392
Pubmed

16. Nock A, Ascano JM, Jones T, Barrero MJ, Sugiyama N, Tomita M, Ishihama Y, Malik S (2009) Identification of DNA-dependent protein kinase as a cofactor for the forkhead transcription factor FoxA2, J Biol Chem, 284, 19915-19926
Pubmed

17. Nishino T, Yachie-Kinoshita A, Hirayama A, Soga T, Suematsu M, Tomita M (2009) In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods, J Biotechnol, 144, 212-223
Pubmed

18. Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M (2009) Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism, Mol Syst Biol, 5, 306
Pubmed

19. Minami Y, Kasukawa T, Kakazu Y, Iigo M, Sugimoto M, Ikeda S, Yasui A, van der Horst GT, Soga T, Ueda HR (2009) Measurement of internal body time by blood metabolomics, Proc Natl Acad Sci U S A, 106, 9890-9895
Pubmed

20. Masuda T, Saito N, Tomita M, Ishihama Y (2009) Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants, Mol Cell Proteomics, 8, 2770-2777
Pubmed

21. Kuramori C, Hase Y, Hoshikawa K, Watanabe K, Nishi T, Hishiki T, Soga T, Nashimoto A, Kabe Y, Yamaguchi Y, Watanabe H, Kataoka K, Suematsu M, Handa H (2009) Mono-(2-ethylhexyl) phthalate targets glycogen debranching enzyme and affects glycogen metabolism in rat testis, Toxicol Sci, 109, 143-151
Pubmed

22. Kosugi S, Hasebe M, Tomita M, Yanagawa H (2009) Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs, Proc Natl Acad Sci U S A, 106, 10171-10176
Pubmed

23. Kosugi S, Hasebe M, Matsumura N, Takashima H, Miyamoto-Sato E, Tomita M, Yanagawa H (2009) Six classes of nuclear localization signals specific to different binding grooves of importin alpha, J Biol Chem, 284, 478-485
Pubmed

24. Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M (2009) Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API, PLoS One, 4, e7710
Pubmed

25. Kaneko S, Takeuchi T, Itaya M (2009) Genetic connection of two contiguous bacterial artificial chromosomes using homologous recombination in Bacillus subtilis genome vector, J Biotechnol, 139, 211-213
Pubmed

26. Kanai A, Sato A, Fukuda Y, Okada K, Matsuda T, Sakamoto T, Muto Y, Yokoyama S, Kawai G, Tomita M (2009) Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus, RNA, 15, 420-431
Pubmed

27. Iwasaki M, Masuda T, Tomita M, Ishihama Y (2009) Chemical cleavage-assisted tryptic digestion for membrane proteome analysis, J Proteome Res, 8, 3169-3175
Pubmed

28. Iuchi Y, Okada F, Takamiya R, Kibe N, Tsunoda S, Nakajima O, Toyoda K, Nagae R, Suematsu M, Soga T, Uchida K, Fujii J (2009) Rescue of anaemia and autoimmune responses in SOD1-deficient mice by transgenic expression of human SOD1 in erythrocytes, Biochem J, 422, 313-320
Pubmed

29. Hirayama A, Kami K, Sugimoto M, Sugawara M, Toki N, Onozuka H, Kinoshita T, Saito N, Ochiai A, Tomita M, Esumi H, Soga T (2009) Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry, Cancer Res, 69, 4918-4925
Pubmed

30. Helmy M, Gohda J, Inoue J, Tomita M, Tsuchiya M, Selvarajoo K (2009) Predicting novel features of toll-like receptor 3 signaling in macrophages, PLoS One, 4, e4661
Pubmed

31. Fujishima K, Sugahara J, Kikuta K, Hirano R, Sato A, Tomita M, Kanai A (2009) Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea, Proc Natl Acad Sci U S A, 106, 2683-2687
Pubmed

32. Asai N, Nishioka T, Takabayashi J, Furuichi T (2009) Plant volatiles regulate the activities of Ca2+ -permeable channels and promote cytoplasmic calcium transients in Arabidopsis leaf cells, Plant Signal Behav, 4, 294-300
Pubmed

33. Arjunan SNaT, M (2009) Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System, International Journal of Computer Science and Information Security,, 211-216, />

34. Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M (2009) Genome Projector: zoomable genome map with multiple views, BMC Bioinformatics, 10, 31
Pubmed

35. Arakawa K, Suzuki H, Tomita M (2009) Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index, BMC Genomics, 10, 640
Pubmed

36. Arakawa K, Oshita K, Tomita M (2009) A web server for interactive and zoomable Chaos Game Representation images, Source Code Biol Med, 4, 6
Pubmed

37. Tsuchiya D, Shimizu N, Tomita M. (2009) Cooperativity of two active sites in bacterial homodimeric aconitases. Biochem Biophys Res Commun. 379(2):485-8.

38. Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol. 5:335.

39. Yanashima R, Kitagawa N, Matsubara Y, Weatheritt R, Oka K, Kikuchi S, Tomita M, Ishizaki S. (2009) Network Features and Pathway Analyses of a Signal Transduction Cascade. Front Neuroinform. 3:13.

2008

01. Yoshida S, Imoto J, Minato T, Oouchi R, Sugihara M, Imai T, Ishiguro T, Mizutani S, Tomita M, Soga T, Yoshimoto H (2008) Development of bottom-fermenting saccharomyces strains that produce high SO2 levels, using integrated metabolome and transcriptome analysis, Appl Environ Microbiol, 74, 2787-2796
Pubmed

02. Yachie N, Ohashi Y, Tomita M (2008) Stabilizing synthetic data in the DNA of living organisms, Syst Synth Biol, 2, 19-25
Pubmed

03. Watanabe Y, Tomita, M. and Kanai, A. (2008) Perspective in the Evolution of Human MicroRNAs : Copy Number Expansion and Acquisition of Target Gene Speciallization., Progress of Theoretical Physics, Supplement No.173, 219-228

04. Tsuchiya D, Shimizu N, Tomita M (2008) Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase, Biochim Biophys Acta, 1784, 1847-1856
Pubmed

05. Sugiyama N, Nakagami H, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y (2008) Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis, Mol Syst Biol, 4, 193
Pubmed

06. Sugahara J, Kikuta K, Fujishima K, Yachie N, Tomita M, Kanai A (2008) Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales, Mol Biol Evol, 25, 2709-2716
Pubmed

07. Shinoda K, Tomita M, Ishihama Y (2008) Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments, Bioinformatics, 24, 1590-1595
Pubmed

08. Shinoda K, Sugimoto M, Tomita M, Ishihama Y (2008) Informatics for peptide retention properties in proteomic LC-MS, Proteomics, 8, 787-798
Pubmed

09. Selvarajoo K, Takada Y, Gohda J, Helmy M, Akira S, Tomita M, Tsuchiya M, Inoue J, Matsuo K (2008) Signaling flux redistribution at toll-like receptor pathway junctions, PLoS One, 3, e3430
Pubmed

10. Sato S, Arita M, Soga T, Nishioka T, Tomita M (2008) Time-resolved metabolomics reveals metabolic modulation in rice foliage, BMC Syst Biol, 2, 51
Pubmed

11. Sato D, Yamagata W, Harada S, Nozaki T (2008) Kinetic characterization of methionine gamma-lyases from the enteric protozoan parasite Entamoeba histolytica against physiological substrates and trifluoromethionine, a promising lead compound against amoebiasis, FEBS J, 275, 548-560
Pubmed

12. Sato D, Karaki T, Shimizu A, Kamei K, Harada S, Nozaki T (2008) Crystallization and preliminary X-ray analysis of L-methionine gamma-lyase 1 from Entamoeba histolytica, Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 697-699
Pubmed

13. Sagane K, Ishihama Y, Sugimoto H (2008) LGI1 and LGI4 bind to ADAM22, ADAM23 and ADAM11, Int J Biol Sci, 4, 387-396
Pubmed

14. Okada Y, Tashiro C, Numata K, Watanabe K, Nakaoka H, Yamamoto N, Okubo K, Ikeda R, Saito R, Kanai A, Abe K, Tomita M, Kiyosawa H (2008) Comparative expression analysis uncovers novel features of endogenous antisense transcription, Hum Mol Genet, 17, 1631-1640
Pubmed

15. Ohtani N, Tomita M, Itaya M (2008) Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex, Biochem J, 412, 517-526
Pubmed

16. Ohtani N, Tomita M, Itaya M (2008) Junction ribonuclease activity specified in RNases HII/2, FEBS J, 275, 5444-5455
Pubmed

17. Ohtani N, Sato M, Tomita M, Itaya M (2008) Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168, Biosci Biotechnol Biochem, 72, 2472-2475
Pubmed

18. Ohno H, Naito Y, Nakajima H, Tomita M (2008) Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule, Artif Life, 14, 3-28
Pubmed

19. Ohashi Y, Hirayama A, Ishikawa T, Nakamura S, Shimizu K, Ueno Y, Tomita M, Soga T (2008) Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS, Mol Biosyst, 4, 135-147
Pubmed

20. Ogawa Y, Arakawa K, Kaizu K, Miyoshi F, Nakayama Y, Tomita M (2008) Comparative study of circadian oscillatory network models of Drosophila, Artif Life, 14, 29-48
Pubmed

21. Miyamoto K, Hara T, Kobayashi H, Morisaka H, Tokuda D, Horie K, Koduki K, Makino S, Nunez O, Yang C, Kawabe T, Ikegami T, Takubo H, Ishihama Y, Tanaka N (2008) High-efficiency liquid chromatographic separation utilizing long monolithic silica capillary columns, Anal Chem, 80, 8741-8750
Pubmed

22. Matsubara Y, Kikuchi S, Sugimoto M, Oka K, Tomita M (2008) Algebraic method for the analysis of signaling crosstalk, Artif Life, 14, 81-94
Pubmed

23. Masuda T, Tomita M, Ishihama Y (2008) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis, J Proteome Res, 7, 731-740
Pubmed

24. Laborde T, Tomita M, Krishnan A (2008) GANDivAWeb: a web server for detecting early folding units ("foldons") from protein 3D structures, BMC Struct Biol, 8, 15
Pubmed

25. Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y (2008) Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography, J Proteome Res, 7, 4585-4593
Pubmed

26. Kuroki A, Toda T, Matsui K, Uotsu-Tomita R, Tomita M, Itaya M (2008) Reshuffling of the Bacillus subtilis 168 genome by multifold inversion, J Biochem, 143, 97-105
Pubmed

27. Krishnan A, Zbilut JP, Tomita M, Giuliani A (2008) Proteins as networks: usefulness of graph theory in protein science, Curr Protein Pept Sci, 9, 28-38
Pubmed

28. Krishnan A, Tomita M, Giuliani A (2008) Evolution of gene regulatory networks: Robustness as an emergent property of evolution, Physica A: Statistical Mechanics and its Applications, 387, 2170-2186
Pubmed

29. Krishnan A, Giuliani A, Zbilut JP, Tomita M (2008) Implications from a network-based topological analysis of ubiquitin unfolding simulations, PLoS One, 3, e2149
Pubmed

30. Kratz A, Tomita M, Krishnan A (2008) GeNESiS: gene network evolution simulation software, BMC Bioinformatics, 9, 541
Pubmed

31. Kosugi S, Hasebe M, Tomita M, Yanagawa H (2008) Nuclear export signal consensus sequences defined using a localization-based yeast selection system, Traffic, 9, 2053-2062
Pubmed

32. Kosugi S, Hasebe M, Entani T, Takayama S, Tomita M, Yanagawa H (2008) Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling, Chem Biol, 15, 940-949
Pubmed

33. Itaya M, Fujita K, Kuroki A, Tsuge K (2008) Bottom-up genome assembly using the Bacillus subtilis genome vector, Nat Methods, 5, 41-43
Pubmed

34. Ishii K, Nakamura S, Morohashi M, Sugimoto M, Ohashi Y, Kikuchi S, Tomita M (2008) Comparison of metabolite production capability indices generated by network analysis methods, Biosystems, 91, 166-170
Pubmed

35. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008) Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics, 9, 102
Pubmed

36. Ishihama Y (2008) NanoLC-MS systems in proteomics., Chromatography, 29, 25-31
Pubmed

37. Ishihama Y (2008) Molecular dynamics in cellular signal transduction systems, The Japan Society of Mechanical Engineers, 111, 578-581

38. Imami K, Sugiyama N, Kyono Y, Tomita M, Ishihama Y (2008) Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column, Anal Sci, 24, 161-166
Pubmed

39. Imami K, Ishihama Y, Terabe S (2008) On-line selective enrichment and ion-pair reaction for structural determination of sulfated glycopeptides by capillary electrophoresis-mass spectrometry, J Chromatogr A, 1194, 237-242
Pubmed

40. Horai HaN, T (2008) Automatic Generation of Structure of Phospholipids, Journal of Computer Aided Chemistry, 55-61, />

41. Fujishima K, Sugahara J, Tomita M, Kanai A (2008) Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves, PLoS One, 3, e1622
Pubmed

42. Fujishima K, Komasa, M., Kitamura, S., Tomita, M. and Kanai, A. (2008) Comparison and Characterization of Proteomes in the Three Domains of Life Using 2D Correlation Analysis, Progress of Theoretical Physics, Supplement No.173, 206-218

43. Asti KG. B-FJ, Cini M., De Ninno A., Del Giudice E., Drago A, Elia V., Farina L., Gagliasso E., Germano R., Giuliani A., Krishnan A., Levy Leblond JM., Licata I., Modonesi C., Rossi PA., Selvarajoo K., Silvestrini V., Tamino G., Tomita M., Tsuchiya M., Verma C., Vitiello G., Webber CL. and Zbilut JP. (2008) Web era Theatrum Mundi: Another Big Chill in Science?, Alliage, 61, 41-46

44. Arakawa. K, Suzuki. H, Tomita. M (2008) Computational Genome Analysis Using The G-language System., Genes, Genomes and Genomics, 2, 1-13

45. Arakawa K, Yachie, N. and Tomita, M (2008) Visualizing Conplex Omics Information - Scientific Visualization for Genomics and Systems Biology., BIOforum Europe, 6, 27-29

46. Aon MA, Roussel MR, Cortassa S, O'Rourke B, Murray DB, Beckmann M, Lloyd D (2008) The scale-free dynamics of eukaryotic cells, PLoS One, 3, e3624
Pubmed

2007

01. Zbilut JP, Chua GH, Krishnan A, Bossa C, Rother K, Webber CL, Jr., Giuliani A (2007) A topologically related singularity suggests a maximum preferred size for protein domains, Proteins, 66, 621-629
Pubmed

02. Yeo ZX, Wong ST, Arjunan SN, Piras V, Tomita M, Selvarajoo K, Giuliani A, Tsuchiya M (2007) Sequential logic model deciphers dynamic transcriptional control of gene expressions, PLoS One, 2, e776
Pubmed

03. Yachie N, Sekiyama K, Sugahara J, Ohashi Y, Tomita M (2007) Alignment-based approach for durable data storage into living organisms, Biotechnol Prog, 23, 501-505
Pubmed

04. Watanabe Y, Tomita M, Kanai A (2007) Computational methods for microRNA target prediction, Methods Enzymol, 427, 65-86
Pubmed

05. Watanabe Y, Kishi A, Yachie N, Kanai A, Tomita M (2007) Computational analysis of microRNA-mediated antiviral defense in humans, FEBS Lett, 581, 4603-4610
Pubmed

06. Tsuchiya M, Wong ST, Yeo ZX, Colosimo A, Palumbo MC, Farina L, Crescenzi M, Mazzola A, Negri R, Bianchi MM, Selvarajoo K, Tomita M, Giuliani A (2007) Gene expression waves. Cell cycle independent collective dynamics in cultured cells, FEBS J, 274, 2878-2886
Pubmed

07. Toya Y, Ishii N, Hirasawa T, Naba M, Hirai K, Sugawara K, Igarashi S, Shimizu K, Tomita M, Soga T (2007) Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis, J Chromatogr A, 1159, 134-141
Pubmed

08. Tamaki S, Arakawa K, Kono N, Tomita M (2007) Restauro-G: a rapid genome re-annotation system for comparative genomics, Genomics Proteomics Bioinformatics, 5, 53-58
Pubmed

09. Suzuki H, Saito R, Tomita M (2007) Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria, EURASIP Journal on Bioinformatics and Systems Biology, 2007, 61374
Pubmed

10. Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y (2007) Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications, Mol Cell Proteomics, 6, 1103-1109
Pubmed

11. Sugahara J, Yachie N, Arakawa K, Tomita M (2007) In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs, RNA, 13, 671-681
Pubmed

12. Soma A, Onodera A, Sugahara J, Kanai A, Yachie N, Tomita M, Kawamura F, Sekine Y (2007) Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae, Science, 318, 450-453
Pubmed

13. Soga T, Ishikawa T, Igarashi S, Sugawara K, Kakazu Y, Tomita M (2007) Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique, J Chromatogr A, 1159, 125-133
Pubmed

14. Sato T, Ishihama Y, Oda Y (2007) Quantitative proteomics of mouse brain and specific protein-interaction studies using stable isotope labeling, Methods Mol Biol, 359, 53-70
Pubmed

15. Robert M, Soga T, Tomita M (2007) E. coli metabolomics: capturing the complexity of a "simple" model., Metabolomics. Topics in Current Genetics., 18, 189-234
Pubmed

16. Rappsilber J, Mann M, Ishihama Y (2007) Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips, Nat Protoc, 2, 1896-1906
Pubmed

17. Piras V, Selvarajpp, K., Fujikawa, N., Choi, S., Tomita, M., Giuliani, A. and Tsuchiya M. (2007) Statistical Analysis of Gene Expression in Innate Immune Responses Dynamic Interactions between MicroRNA and Signaling Molecules., Genomics and Informatics, 5, 107-112

18. Ogawa T, Mori H, Tomita M, Yoshino M (2007) Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli, Res Microbiol, 158, 159-163
Pubmed

19. Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, Tomita M (2007) Comparative analysis of cis-encoded antisense RNAs in eukaryotes, Gene, 392, 134-141
Pubmed

20. Murray DB, Lloyd D (2007) A tuneable attractor underlies yeast respiratory dynamics, Biosystems, 90, 287-294
Pubmed

21. Murray DB, Beckmann M, Kitano H (2007) Regulation of yeast oscillatory dynamics, Proc Natl Acad Sci U S A, 104, 2241-2246
Pubmed

22. Morohashi M, Shimizu K, Ohashi Y, Abe J, Mori H, Tomita M, Soga T (2007) P-BOSS: a new filtering method for treasure hunting in metabolomics, J Chromatogr A, 1159, 142-148
Pubmed

23. Morohashi M, Ohashi Y, Tani S, Ishii K, Itaya M, Nanamiya H, Kawamura F, Tomita M, Soga T (2007) Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilis, J Biochem, 142, 183-191
Pubmed

24. Mori K, Saito R, Kikuchi S, Tomita M (2007) Inferring rules of Escherichia coli translational efficiency using an artificial neural network, Biosystems, 90, 414-420
Pubmed

25. Monton MR, Tomita M, Soga T, Ishihama Y (2007) Polymer entrapment in polymerized silicate for preparing highly stable capillary coatings for CE and CE-MS, Anal Chem, 79, 7838-7844
Pubmed

26. Monton MR, Soga T (2007) Metabolome analysis by capillary electrophoresis-mass spectrometry, J Chromatogr A, 1168, 237-246; discussion 236
Pubmed

27. Miyoshi F, Nakayama Y, Kaizu K, Iwasaki H, Tomita M (2007) A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria, J Biol Rhythms, 22, 69-80
Pubmed

28. Matsuzaki Y, Kikuchi S, Tomita M (2007) Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis, Artif Intell Med, 41, 145-150
Pubmed

29. Matsui M, Yachie N, Okada Y, Saito R, Tomita M (2007) Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse, FEBS Lett, 581, 4184-4188
Pubmed

30. Lloyd D, Murray DB (2007) Redox rhythmicity: clocks at the core of temporal coherence, Bioessays, 29, 465-473
Pubmed

31. Lee HJ, Chua GH, Krishnan A, Lane DP, Verma CS (2007) Substrate specificity of cyclins determined by electrostatics, Cell Cycle, 6, 2219-2226
Pubmed

32. Kuroki A, Ohtani N, Tsuge K, Tomita M, Itaya M (2007) Conjugational transfer system to shuttle giant DNA cloned by Bacillus subtilis genome (BGM) vector, Gene, 399, 72-80
Pubmed

33. Krishnan J, Selvarajoo, K., Tsuchiya, M., Lee, G. and Choi, S. (2007) Toll-like receptor signal transduction, Exp Mol Med, 39, 421-438

34. Krishnan A, Giuliani A, Zbilut JP, Tomita M (2007) Network scaling invariants help to elucidate basic topological principles of proteins, J Proteome Res, 6, 3924-3934
Pubmed

35. Krishnan A, Giuliani A, Tomita M (2007) Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity, PLoS One, 2, e562
Pubmed

36. Kotake Y, Sagane K, Owa T, Mimori-Kiyosue Y, Shimizu H, Uesugi M, Ishihama Y, Iwata M, Mizui Y (2007) Splicing factor SF3b as a target of the antitumor natural product pladienolide, Nat Chem Biol, 3, 570-575
Pubmed

37. Kochiwa H, Tomita M, Kanai A (2007) Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes, BMC Evol Biol, 7, 128
Pubmed

38. Kinoshita A, Tsukada K, Soga T, Hishiki T, Ueno Y, Nakayama Y, Tomita M, Suematsu M (2007) Roles of hemoglobin Allostery in hypoxia-induced metabolic alterations in erythrocytes: simulation and its verification by metabolome analysis, J Biol Chem, 282, 10731-10741
Pubmed

39. Kinoshita A, Nakayama Y, Kitayama T, Tomita M (2007) Simulation study of methemoglobin reduction in erythrocytes. Differential contributions of two pathways to tolerance to oxidative stress, FEBS J, 274, 1449-1458
Pubmed

40. Itoh H, Naito Y, Tomita M (2007) Simulation of developmental changes in action potentials with ventricular cell models, Syst Synth Biol, 1, 11-23
Pubmed

41. Ishii N, Suga Y, Hagiya A, Watanabe H, Mori H, Yoshino M, Tomita M (2007) Dynamic simulation of an in vitro multi-enzyme system, FEBS Lett, 581, 413-420
Pubmed

42. Ishii N, Nakayama Y, Tomita M (2007) Distinguishing enzymes using metabolome data for the hybrid dynamic/static method, Theor Biol Med Model, 4, 19
Pubmed

43. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations, Science, 316, 593-597
Pubmed

44. Ishihama Y, Wei FY, Aoshima K, Sato T, Kuromitsu J, Oda Y (2007) Enhancement of the efficiency of phosphoproteomic identification by removing phosphates after phosphopeptide enrichment, J Proteome Res, 6, 1139-1144
Pubmed

45. Ishihama Y (2007) Optimization of Nano-Liquid Chromatography Coupled with Mass Spectrometry for Proteomics, J Mass Spectrom Soc Jpn, 55, 157-164

46. Imami K, Monton MR, Ishihama Y, Terabe S (2007) Simple on-line sample preconcentration technique for peptides based on dynamic pH junction in capillary electrophoresis-mass spectrometry, J Chromatogr A, 1148, 250-255
Pubmed

47. Hu B, Tomita M (2007) The Hsp70 chaperone system maintains high concentrations of active proteins and suppresses ATP consumption during heat shock, Syst Synth Biol, 1, 47-58
Pubmed

48. Hashimoto M, Ishihama Y, Tomita M, Soga T (2007) Microelectrospray interface with coaxial sheath flow for high-resolution capillary electrophoresis/mass spectrometry separation, Rapid Commun Mass Spectrom, 21, 3579-3584
Pubmed

49. Fujishima K, Komasa M, Kitamura S, Suzuki H, Tomita M, Kanai A (2007) Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus, DNA Res, 14, 91-102
Pubmed

50. Baran R, Robert M, Suematsu M, Soga T, Tomita M (2007) Visualization of three-way comparisons of omics data, BMC Bioinformatics, 8, 72
Pubmed

51. Arakawa K, Uno R, Nakayama Y, Tomita M (2007) Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli, Gene, 392, 239-246
Pubmed

52. Arakawa K, Tomita M (2007) Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes, Evol Bioinform Online, 3, 279-286
Pubmed

53. Arakawa K, Tomita M (2007) The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection, Evol Bioinform Online, 3, 159-168
Pubmed

54. Arakawa K, Saito R, Tomita M (2007) Noise-reduction filtering for accurate detection of replication termini in bacterial genomes, FEBS Lett, 581, 253-258
Pubmed

55. Negishi Y, Nakamura H, Yachie N, Saito R, Tomita M. (2007) eXpanda: an integrated platform for network analysis and visualization. In Silico Biol. 7(2):141-4.

2006

01. Zbilut JP, Chua GH, Krishnan A, Bossa C, Colafranceschi M, Giuliani A (2006) Entropic criteria for protein folding derived from recurrences: six residues patch as the basic protein word, FEBS Lett, 580, 4861-4864
Pubmed

02. Yachie N, Numata K, Saito R, Kanai A, Tomita M (2006) Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model, Gene, 372, 171-181
Pubmed

03. Yachie N, Arakawa K, Tomita M (2006) On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli, FEBS Lett, 580, 6909-6914
Pubmed

04. Watanabe Y, Yachie N, Numata K, Saito R, Kanai A, Tomita M (2006) Computational analysis of microRNA targets in Caenorhabditis elegans, Gene, 365, 2-10
Pubmed

05. Wakabayashi Y, Kobayashi M, Akashi-Takamura S, Tanimura N, Konno K, Takahashi K, Ishii T, Mizutani T, Iba H, Kouro T, Takaki S, Takatsu K, Oda Y, Ishihama Y, Saitoh S, Miyake K (2006) A protein associated with toll-like receptor 4 (PRAT4A) regulates cell surface expression of TLR4, J Immunol, 177, 1772-1779
Pubmed

06. Uno R, Nakayama Y, Tomita M (2006) Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12, Gene, 380, 30-37
Pubmed

07. Takahashi H, Hayashi M, Goto F, Sato S, Soga T, Nishioka T, Tomita M, Kawai-Yamada M, Uchimiya H (2006) Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase, Ann Bot, 98, 819-825
Pubmed

08. Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, Kanai A (2006) SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level, In Silico Biol, 6, 411-418
Pubmed

09. Soga T, Baran R, Suematsu M, Ueno Y, Ikeda S, Sakurakawa T, Kakazu Y, Ishikawa T, Robert M, Nishioka T, Tomita M (2006) Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption, J Biol Chem, 281, 16768-16776
Pubmed

10. Shinoda K, Yachie N, Masuda T, Sugiyama N, Sugimoto M, Soga T, Tomita M (2006) HybGFS: a hybrid method for genome-fingerprint scanning, BMC Bioinformatics, 7, 479
Pubmed

11. Shinoda K, Sugimoto M, Yachie N, Sugiyama N, Masuda T, Robert M, Soga T, Tomita M (2006) Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks, J Proteome Res, 5, 3312-3317
Pubmed

12. Sakaya N, Kaneko S, Matsunaga S, Itaya M (2006) Experimental basis for a stable plasmid, pLS30, to shuttle between Bacillus subtilis species by conjugational transfer, J Biochem, 139, 557-561
Pubmed

13. Saito N, Robert M, Kitamura S, Baran R, Soga T, Mori H, Nishioka T, Tomita M (2006) Metabolomics approach for enzyme discovery, J Proteome Res, 5, 1979-1987
Pubmed

14. Saito H, Oda Y, Sato T, Kuromitsu J, Ishihama Y (2006) Multiplexed Two-Dimensional Liquid Chromatography for MALDI and Nanoelectrospray Ionization Mass Spectrometry in Proteomics, Journal of Proteome Research, 5, 1803-1807
Pubmed

15. Osada Y, Saito R, Tomita M (2006) Comparative analysis of base correlations in 5' untranslated regions of various species, Gene, 375, 80-86
Pubmed

16. Okada K, Takahashi M, Sakamoto T, Kawai G, Nakamura K, Kanai A (2006) Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus, Nucleosides Nucleotides Nucleic Acids, 25, 383-395
Pubmed

17. Okada K, Matsuda T, Sakamoto T, Muto Y, Yokoyama S, Kanai A, Kawai G (2006) 1H, 13C and 15N resonance assignments of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus, J Biomol NMR, 36 Suppl 1, 16
Pubmed

18. Murata K, Mano N, Asakawa N, Ishihama Y (2006) Simplified gradient generator for micro- and nano-liquid chromatography, J Chromatogr A, 1123, 47-52
Pubmed

19. Monton MR, Terabe S (2006) Sample enrichment techniques in capillary electrophoresis: focus on peptides and proteins, J Chromatogr B Analyt Technol Biomed Life Sci, 841, 88-95
Pubmed

20. Matsubara Y, Kikuchi S, Sugimoto M, Tomita M (2006) Parameter estimation for stiff equations of biosystems using radial basis function networks, BMC Bioinformatics, 7, 230
Pubmed

21. Kono N, Arakawa K, Tomita M (2006) MEGU: pathway mapping web-service based on KEGG and SVG, In Silico Biol, 6, 621-625
Pubmed

22. Kochiwa H, Itaya M, Tomita M, Kanai A (2006) Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements, FEBS J, 273, 420-429
Pubmed

23. Kitayama T, Kinoshita A, Sugimoto M, Nakayama Y, Tomita M (2006) A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles, Theor Biol Med Model, 3, 24
Pubmed

24. Kanai A, Sato A, Imoto J, Tomita M (2006) Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein, Biochem J, 393, 373-379
Pubmed

25. Kanai A (2006) Importance of systematic identification of RNA-binding proteins in a hyperthermophilic archaeon., Viva Origino, 34, 144-147

26. Itaya M, Sakaya N, Matsunaga S, Fujita K, Kaneko S (2006) Conjugational transfer kinetics of pLS20 between Bacillus subtilis in liquid medium, Biosci Biotechnol Biochem, 70, 740-742
Pubmed

27. Ishii K, Washio T, Uechi T, Yoshihama M, Kenmochi N, Tomita M (2006) Characteristics and clustering of human ribosomal protein genes, BMC Genomics, 7, 37
Pubmed

28. Ishihama Y, Rappsilber J, Mann M (2006) Modular stop and go extraction tips with stacked disks for parallel and multidimensional Peptide fractionation in proteomics, J Proteome Res, 5, 988-994
Pubmed

29. Hu B, Mayer MP, Tomita M (2006) Modeling Hsp70-mediated protein folding, Biophys J, 91, 496-507
Pubmed

30. Fujita H, Samejima H, Kitagawa N, Mitsuhashi T, Washio T, Yonemoto J, Tomita M, Takahashi T, Kosaki K (2006) Genome-wide screening of dioxin-responsive genes in fetal brain: bioinformatic and experimental approaches, Congenit Anom (Kyoto), 46, 135-143
Pubmed

31. Chua GH, Krishnan A, Li KB, Tomita M (2006) Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar proteins, J Bioinform Comput Biol, 4, 1245-1267
Pubmed

32. Baran R, Kochi H, Saito N, Suematsu M, Soga T, Nishioka T, Robert M, Tomita M (2006) MathDAMP: a package for differential analysis of metabolite profiles, BMC Bioinformatics, 7, 530
Pubmed

33. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol Syst Biol, 2, 2006 0008
Pubmed

34. Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12, Genome Res, 16, 686-691
Pubmed

35. Arakawa KaT, M (2006) Large-scale Modeling for Systems Biology, BIOforum Europe, 10, 54-55

36. Arakawa K TM (2006) G-langage System as a platform for large-scale analysis of high-throughput omics data, Journal of Pesticide Science, 31, 282-288

37. Arakawa K, Yamada Y, Shinoda K, Nakayama Y, Tomita M (2006) GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes, BMC Bioinformatics, 7, 168
Pubmed

38. Arakawa K, Nakayama Y, Tomita M (2006) GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness, In Silico Biol, 6, 49-60
Pubmed

2005

01. Yugi K, Nakayama Y, Kojima S, Kitayama T, Tomita M (2005) A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks, BMC Bioinformatics, 6, 299
Pubmed

02. Yugi K, Nakayama Y, Kinoshita A, Tomita M (2005) Hybrid dynamic/static method for large-scale simulation of metabolism, Theor Biol Med Model, 2, 42
Pubmed

03. Takahashi K, Arjunan SN, Tomita M (2005) Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico, FEBS Lett, 579, 1783-1788
Pubmed

04. Suzuki H, Saito R, Tomita M (2005) A problem in multivariate analysis of codon usage data and a possible solution, FEBS Lett, 579, 6499-6504
Pubmed

05. Sugimoto M, Kikuchi S, Arita M, Soga T, Nishioka T, Tomita M. Large-Scale Prediction of Cationic Metabolites Identity and Migration Time in Capillary Electrophoresis Mass Spectrometry using Artificial Neural Networks. Anal Chem 2005 Jan 1; 77(1):78-84. doi: 10.1021/ac048950g.
Pubmed

06. Sugimoto M, Kikuchi S, Tomita M (2005) Reverse engineering of biochemical equations from time-course data by means of genetic programming, Biosystems, 80, 155-164
Pubmed

07. Ohtani N, Saito N, Tomita M, Itaya M, Itoh A (2005) The SCO2299 gene from Streptomyces coelicolor A3(2) encodes a bifunctional enzyme consisting of an RNase H domain and an acid phosphatase domain, FEBS J, 272, 2828-2837
Pubmed

08. Ohashi Y, Yamashiro A, Washio T, Ishii N, Ohshima H, Michishita T, Tomita M, Itaya M (2005) In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations, Gene, 347, 11-19
Pubmed

09. Nakayama Y, Kinoshita A, Tomita M (2005) Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition, Theor Biol Med Model, 2, 18
Pubmed

10. Kitagawa N, Washio T, Kosugi S, Yamashita T, Higashi K, Yanagawa H, Higo K, Satoh K, Ohtomo Y, Sunako T, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2005) Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa), Bioinformatics, 21, 1758-1763
Pubmed

11. Jaros M, Soga T, van de Goor T, Gas B (2005) Conductivity detection in capillary zone electrophoresis: inspection by PeakMaster, Electrophoresis, 26, 1948-1953
Pubmed

12. Ishihama Y (2005) Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry, J Chromatogr A, 1067, 73-83
Pubmed

13. Inagaki S, Numata K, Kondo T, Tomita M, Yasuda K, Kanai A, Kageyama Y (2005) Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila, Genes Cells, 10, 1163-1173
Pubmed

14. Hoque MA, Ushiyama H, Tomita M, Shimizu K (2005) Dynamic responses of the intracellular metabolite concentrations of the wild type and pykA mutant Escherichia coli against pulse addition of glucose or NH3 under those limiting continuous cultures, Biochemical Engineering Journal, 26, 38-49
Pubmed

15. Fujimori S, Washio T, Tomita M (2005) GC-compositional strand bias around transcription start sites in plants and fungi, BMC Genomics, 6, 26
Pubmed

16. Arita M, Robert M, Tomita M (2005) All systems go: launching cell simulation fueled by integrated experimental biology data, Curr Opin Biotechnol, 16, 344-349
Pubmed

17. Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M (2005) A comprehensive software suite for the analysis of cDNAs, Genomics Proteomics Bioinformatics, 3, 179-188
Pubmed

18. Arakawa K, Kono N, Yamada Y, Mori H, Tomita M (2005) KEGG-based pathway visualization tool for complex omics data, In Silico Biol, 5, 419-423
Pubmed

19. Ishii N, Soga T, Nishioka T, Tomita M. Metabolome Analysis and Metabolic Simulation. Metabolomics 2005 Mar; 1(1), 29-37, doi: 10.1007/s11306-005-1105-5.

2004

01. Zhao J, Baba T, Mori H, Shimizu K (2004) Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities, Appl Microbiol Biotechnol, 64, 91-98
Pubmed

02. Zhao J, Baba T, Mori H, Shimizu K (2004) Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate, Metab Eng, 6, 164-174
Pubmed

03. Yugi K, Tomita M (2004) A general computational model of mitochondrial metabolism in a whole organelle scale, Bioinformatics, 20, 1795-1796
Pubmed

04. Yano Y, Saito R, Yoshida N, Yoshiki A, Wynshaw-Boris A, Tomita M, Hirotsune S (2004) A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene, J Mol Med (Berl), 82, 414-422
Pubmed

05. Yahagi N, Kosaki R, Ito T, Mitsuhashi T, Shimada H, Tomita M, Takahashi T, Kosaki K (2004) Position-specific expression of Hox genes along the gastrointestinal tract, Congenit Anom (Kyoto), 44, 18-26
Pubmed

06. Takahashi K, Kaizu K, Hu B, Tomita M (2004) A multi-algorithm, multi-timescale method for cell simulation, Bioinformatics, 20, 538-546
Pubmed

07. Suzuki H, Saito R, Tomita M (2004) The 'weighted sum of relative entropy': a new index for synonymous codon usage bias, Gene, 335, 19-23
Pubmed

08. Soga T, Kakazu Y, Robert M, Tomita M, Nishioka T (2004) Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry, Electrophoresis, 25, 1964-1972
Pubmed

09. Sato S, Soga T, Nishioka T, Tomita M (2004) Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection, Plant J, 40, 151-163
Pubmed

10. Qiu D, Mao L, Kikuchi S, Tomita M (2004) Sustained MAPK activation is dependent on continual NGF receptor regeneration, Dev Growth Differ, 46, 393-403
Pubmed

11. Qiu D, Fujita K, Sakuma Y, Tanaka T, Ohashi Y, Ohshima H, Tomita M, Itaya M (2004) Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes, Appl Environ Microbiol, 70, 6247-6256
Pubmed

12. Ohtani N, Yanagawa H, Tomita M, Itaya M (2004) Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction, Biochem J, 381, 795-802
Pubmed

13. Ohtani N, Yanagawa H, Tomita M, Itaya M (2004) Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7, Nucleic Acids Res, 32, 5809-5819
Pubmed

14. Melnick J, Lis E, Park JH, Kinsland C, Mori H, Baba T, Perkins J, Schyns G, Vassieva O, Osterman A, Begley TP (2004) Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase, J Bacteriol, 186, 3660-3662
Pubmed

15. Kitamura-Abe S, Itoh H, Washio T, Tsutsumi A, Tomita M (2004) Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs, J Bioinform Comput Biol, 2, 309-331
Pubmed

16. Itoh H, Washio T, Tomita M (2004) Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes, RNA, 10, 1005-1018
Pubmed

17. Itoh A, Ohashi Y, Soga T, Mori H, Nishioka T, Tomita M (2004) Application of capillary electrophoresis-mass spectrometry to synthetic in vitro glycolysis studies, Electrophoresis, 25, 1996-2002
Pubmed

18. Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M (2004) Toward large-scale modeling of the microbial cell for computer simulation, J Biotechnol, 113, 281-294
Pubmed

19. Hua Q, Yang C, Oshima T, Mori H, Shimizu K (2004) Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures, Appl Environ Microbiol, 70, 2354-2366
Pubmed

20. Hoque MA, Siddiquee KAZ, Shimizu K (2004) Metabolic control analysis of gene-knockout Escherichia coli based on the inverse flux analysis with experimental verification, Biochemical Engineering Journal, 19, 53-59
Pubmed

21. Arita M, Ohashi Y (2004) Secret signatures inside genomic DNA, Biotechnol Prog, 20, 1605-1607
Pubmed

2003

01. Zhao J, Shimizu K (2003) Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method, J Biotechnol, 101, 101-117

02. Yang C, Hua Q, Baba T, Mori H, Shimizu K (2003) Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout, Biotechnol Bioeng, 84, 129-144

03. Takahashi K, Ishikawa N, Sadamoto Y, Sasamoto H, Ohta S, Shiozawa A, Miyoshi F, Naito Y, Nakayama Y, Tomita M (2003) E-Cell 2: multi-platform E-Cell simulation system, Bioinformatics, 19, 1727-1729

04. Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T (2003) Quantitative metabolome analysis using capillary electrophoresis mass spectrometry, J Proteome Res, 2, 488-494

05. Sato M, Umeki H, Saito R, Kanai A, Tomita M (2003) Computational analysis of stop codon readthrough in D.melanogaster, Bioinformatics, 19, 1371-1380

06. Sato A, Kanai A, Itaya M, Tomita M (2003) Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus, Biochem Biophys Res Commun, 309, 247-252

07. Ozawa Y, Saito R, Washio T, Tomita M (2003) Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes, J Mol Evol, 56, 665-672

08. Ohashi Y, Ohshima H, Tsuge K, Itaya M (2003) Far different levels of gene expression provided by an oriented cloning system in Bacillus subtilis and Escherichia coli, FEMS Microbiol Lett, 221, 125-130

09. Ohashi Y, Inaoka T, Kasai K, Ito Y, Okamoto S, Satsu H, Tozawa Y, Kawamura F, Ochi K (2003) Expression profiling of translation-associated genes in sporulating Bacillus subtilis and consequence of sporulation by gene inactivation, Biosci Biotechnol Biochem, 67, 2245-2253

10. Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M, Group RG, Members GSL (2003) Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection, Genome Res, 13, 1301-1306

11. Miyoshi F, Nakayama Y, Tomita M (2003) [E-Cell simulation system and its application to the modeling of circadian rhythm], Seikagaku, 75, 5-16

12. Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system, Bioinformatics, 19, 643-650

13. Kikuchi S, Fujimoto K, Kitagawa N, Fuchikawa T, Abe M, Oka K, Takei K, Tomita M (2003) Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A, Neural Netw, 16, 1389-1398

14. Kanai A, Oida H, Matsuura N, Doi H (2003) Expression cloning and characterization of a novel gene that encodes the RNA-binding protein FAU-1 from Pyrococcus furiosus, Biochem J, 372, 253-261

15. Jiao Z, Baba T, Mori H, Shimizu K (2003) Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurement, FEMS Microbiol Lett, 220, 295-301

16. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin, II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J, Forum S (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, 19, 524-531

17. Hua Q, Yang C, Baba T, Mori H, Shimizu K (2003) Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts, J Bacteriol, 185, 7053-7067

18. Fukuda Y, Nakayama Y, Tomita M (2003) On dynamics of overlapping genes in bacterial genomes, Gene, 323, 181-187

19. Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription, FEBS Lett, 554, 17-22

20. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, Tomita M (2003) G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining, Bioinformatics, 19, 305-306

2002

01. Takahashi. K, Yugi. K, Hashimoto. K, Yamada. Y, Pickett. CJF, Tomita M (2002) Computational Challenges in Cell Simulation: A Software Engineering Approach, IEEE Intelligent Systems , 17, 64-71

02. Soga T, Ueno Y, Naraoka H, Ohashi Y, Tomita M, Nishioka T (2002) Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry, Anal Chem, 74, 2233-2239

03. Soga T, Ueno Y, Naraoka H, Matsuda K, Tomita M, Nishioka T (2002) Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions, Anal Chem, 74, 6224-6229

04. Sakurai A, Fujimori S, Kochiwa H, Kitamura-Abe S, Washio T, Saito R, Carninci P, Hayashizaki Y, Tomita M (2002) On biased distribution of introns in various eukaryotes, Gene, 300, 89-95

05. Ozawa Y, Hanaoka S, Saito R, Washio T, Nakano S, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M (2002) Comprehensive sequence analysis of translation termination sites in various eukaryotes, Gene, 300, 79-87

06. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, Consortium F, I RGERGP, Team II (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, 420, 563-573

07. Kosaki K, Kosaki R, Suzuki T, Yoshihashi H, Takahashi T, Sasaki K, Tomita M, McGinnis W, Matsuo N (2002) Complete mutation analysis panel of the 39 human HOX genes, Teratology, 65, 50-62

08. Kochiwa H, Suzuki R, Washio T, Saito R, Bono H, Carninci P, Okazaki Y, Miki R, Hayashizaki Y, Tomita M, Team RGERGPI (2002) Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data, Genome Res, 12, 1286-1293

09. Hashimoto K, Seno S, Dhar P, Tomita M (2002) Integrative modeling of gene expression and metabolism with E-CELL System, Artificial Life and Robotics, 6, 99-107

10. Fujita H, Kosaki R, Yoshihashi H, Ogata T, Tomita M, Hasegawa T, Takahashi T, Matsuo N, Kosaki K (2002) Characterization of the aryl hydrocarbon receptor repressor gene and association of its Pro185Ala polymorphism with micropenis, Teratology, 65, 10-18

11. Matsuda K, Yamaguchi H, Ueno Y, Soga T, Fujita Y, Nishioka T. Combined Metabolome and Transcriptome Analysis of Bacillus subtilis Cells Cultured on Different Carbon Sources. Genomic Informatics 2002; 13, 593-594, doi:10.11234/gi1990.13.593. [J-stage]:

2001

01. Tomita M (2001) Whole-cell simulation: a grand challenge of the 21st century, Trends Biotechnol, 19, 205-210

02. Tomita M (2001) Towards computer aided design (CAD) of useful microorganisms, Bioinformatics, 17, 1091-1092

03. Sakai H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M (2001) Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes, Gene, 276, 101-105

04. Sakai H, Imamura C, Osada Y, Saito R, Washio T, Tomita M (2001) Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes, J Mol Evol, 52, 164-170

05. Ohno H, Sakai H, Washio T, Tomita M (2001) Preferential usage of some minor codons in bacteria, Gene, 276, 107-115

06. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schonbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y, Team RGERGPI, the FC (2001) Functional annotation of a full-length mouse cDNA collection, Nature, 409, 685-690

2000

01. Uno R, Nakayama Y, Arakawa K, Tomita M (2000) The orientation bias of Chi sequences is a general tendency of G-rich oligomers, Gene, 259, 207-215

02. Tomita M, Hashimoto K, Takahashi K, Matsuzaki Y, Matsushima R, Saito K, Yugi K, Miyoshi F, Nakano H, Tanida S, Saito Y, Kawase A, Watanabe N, Simizu T, Nakayama Y (2000) The E-CELL project: Towards integrative simulation of cellular processes, New Generation Computing, 18, 1-12

03. Toda Y, Saito R, Tomita M (2000) Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements, J Mol Evol, 50, 232-237

04. Saito R, Ozawa Y, Kuzuno N, Tomita M (2000) Computer analysis of potential stem structures of rRNA operons in various procaryote genomes, Gene, 259, 217-222

05. Goto M, Washio T, Tomita M (2000) Causal analysis of CpG suppression in the Mycoplasma genome, Microb Comp Genomics, 5, 51-58

06. Fukuda R, Hara J, Shankle WR, Tomita M (2000) Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex, Neurocomputing, 32-33, 749-755

1999

01. Tomita M, Wada M, Kawashima Y (1999) ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes, J Mol Evol, 49, 182-192

02. Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA, 3rd (1999) E-CELL: software environment for whole-cell simulation, Bioinformatics, 15, 72-84

03. Toda Y, Saito R, Tomita M (1999) Sequence patterns observed in 5' flanking regions of primate Alu elements, Ann N Y Acad Sci, 870, 369-374

04. Saito R, Tomita M (1999) On negative selection against ATG triplets near start codons in eukaryotic and prokaryotic genomes, J Mol Evol, 48, 213-217

05. Saito R, Tomita M (1999) Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation, Gene, 238, 79-83

06. Osada Y, Saito R, Tomita M (1999) Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes, Bioinformatics, 15, 578-581

07. Fukuda Y, Washio T, Tomita M (1999) Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae, Nucleic Acids Res, 27, 1847-1853

1998

01. Washio T, Sasayama J, Tomita M (1998) Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination, Nucleic Acids Res, 26, 5456-5463

02. Toda Y, Saito R, Tomita M (1998) Comprehensive Sequence Analyses of 5' Flanking Regions of Primate Alu Elements, Genome Inform Ser Workshop Genome Inform, 9, 41-48

1997

01. Tomita M, Hashimoto K, Takahashi K, Shimizu T, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA (1997) E-CELL: Software Environment for Whole Cell Simulation, Genome Inform Ser Workshop Genome Inform, 8, 147-155

02. Toda Y, Tomita M (1997) Alu elements as an aid in deciphering genome rearrangements, Gene, 205, 173-176

03. Shimizu TS, Takahashi K, Tomita M (1997) CpG distribution patterns in methylated and non-methylated species, Gene, 205, 103-107

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