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2024

  • Felix Salim, Sayaka Mizutani, Satoshi Shiba, Hiroyuki Takamaru, Masayoshi Yamada, Takeshi Nakajima, Tatsuo Yachida, Tomoyoshi Soga, Yutaka Saito, Shinji Fukuda , Shinichi Yachida, Takuji Yamada(2024) Fusobacterium species are distinctly associated with patients with Lynch syndrome colorectal cancer.  iScience

2023

  • Ryza Rynazal, Kota Fujisawa, Hirotsugu Shiroma, Felix Salim, Sayaka Mizutani, Satoshi Shiba, Shinichi Yachida & Takuji Yamada(2023) Leveraging explainable AI for gut microbiome-based colorectal cancer classification. Genome Biology
  • Felix Salim, Sayaka Mizutani, Moreno Zolfo, Takuji Yamada(2023)

    Recent advances of machine learning applications in human gut microbiota study: from observational analysis toward causal inference and clinical intervention.Current Opinion in Biotechnology

2022

  • Hirotsugu Shiroma, Satoshi Shiba, Pande Putu Erawijantari, Hiroyuki Takamaru, Masayoshi Yamada, Taku Sakamoto, Yukihide Kanemitsu, Sayaka Mizutani, Tomoyoshi Soga, Yutaka Saito, Tatsuhiro Shibata, Shinji Fukuda, Shinichi Yachida, Takuji Yamada(2022) Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits. ASM Journals

2021

  • Sawada K, Koyano H, Yamamoto N, Yamada T. (2021) The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites. PeerJ
  • Sawada K, Koyano H, Yamamoto N, Yamada T. (2021) The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds. Scientific Reports
  • Yamamoto N, Watarai N, Koyano H, Sawada K, Toyoda A, Kurokawa K, Yamada T. (2021) Analysis of genomic characteristics and their influence on metabolism in Aspergillus luchuensis albino mutants using genome sequencing. Fungal Genetics and Biology
  • Ueda A, Shinkai S, Shiroma H, Taniguchi Y, Tsuchida S, Kariya T, Kawahara T, Kobayashi Y, Kohda N, Ushida K, Kitamura A,Yamada T.(2021) Identification of Faecalibacterium prausnitzii strains for gut microbiome-based intervention in Alzheimer’s-type dementia. Cell Reports Medicine

2020

  • Watanabe H, Chong HN, Vachiranee L, Suzuki S, Yamada T. (2020) Gluconobacter dominates the gut microbiome of the Asian palm civet Paradoxurus hermaphroditusthat produces kopi luwak. PeerJ
  • Suzuki S, Yamada T. (2020) Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication. PeerJ 8:e8722
  • Mizutani S, Yamada T, Yachida S. (2020) Significance of the gut microbiome in multistep colorectal carcinogenesis. Cancer science. 2020;111:766-773. Cancer Science
  • 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;0:1-12. BMJ journals
  • Imamoto Akira, 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 Science Alliance3 (2). Life Science Alliance

2019

  • Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A,Segata N. (2019) Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature medicine, 25(12):1948-1948. nature
  • Nakamura Y, Hirose S, Taniguchi Y, Moriya Y, Yamada T. (2019) Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites. ScienceDirect
  • Watarai N, Yamamoto N, Sawada K, Yamada T. (2019) Evolution of Aspergillus oryzae before and after domesticationinferred by large-scale comparative genomic analysis. DNA Research. PubMed
  • Yoshida N, Yamashita T, Emoto T, Tabata T, Saito Y, Watanabe H, Yamada T, Hirata K. (2019) Bacteroides Protect Against Atherosclerosis by Regulating Gut Microbial Lipopolysaccharide Production. Circulation 140 Suppl_1, A10273-A10273. AHA/ASA Journal
  • 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. Scientific reports, 9(1):1-7. nature
  • Darzi Y, Yamate Y, Yamada T. (2019) FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization. Bioinformatics, 35(21):4519-4521. PubMed
  • 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 metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nature medicine, 25(6):968-976. PubMed
  • Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. (2019) Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature medicine, 25(4): 667-678. PubMed
  • Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G. (2019) Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature medicine, 25(4):679-689. PubMed
  • Kobayashi A, Tsuchida S, Ueda A, Yamada T, Murata K, Nakamura H, Ushida K. (2019) Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan. Journal of Veterinary Medical Science, 81(9):1389-1399. PubMed

2018

  • Hayashi T, Yamashita T, Watanabe H, Kami K, Yoshida N, Tabata T, Emoto T, Sasaki N, Mizoguchi T, Irino Y, Toh R, Shinohara M, Okada Y, Ogawa W, Yamada T, Hirata KI. (2018) Gut microbiome and plasma microbiome-related metabolites in patients with decompensated and compensated heart failure.Circulation Journal, 83(1):182-192. PubMed
  • Yoshida N, Emoto T, Yamashita T, Watanabe H, Hayashi T, Tabata T, Hoshi N, Hatano N, Ozawa G, Sasaki N, Mizoguchi T, Amin HZ, Hirota Y, Ogawa W, Yamada T, Hirata KI. (2018) Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis. Circulation, 138(22):2486-2498. PubMed
  • Ueda A, Kobayashi A, Tsuchida S, Yamada T, Murata K, Nakamura H,  Ushida K. (2018) Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans (Lagopus muta japonica) Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria.Microorganisms, 6(3). PubMed
  • Watanabe H, Nakamura I, Mizutani S, Kurokawa Y, Mori H, Kurokawa K, Yamada T. (2018) Minor taxa in human skin microbiome contribute to the personal identification. PloS one, 13 (7), e01999472018. PubMed
  • Y Darzi, Letunic I, P Bork, Yamada T. (2018) iPath3. 0: interactive pathways explorer v3. Nucleic acids research, 46(W1):W510-W513. PubMed
  • Mori H, Maruyama T, Yano M, Yamada T, Kurokawa K. (2018) VITCOMIC2: Visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.BMC systems biology, 12(Suppl 2):3. PubMed

2017

2016

  • Okai S, Usui F, Yokota S, Hori-i Y, Hasegawa M, Nakamura T, Kurosawa M, Okada S, Yamamoto K, Nishiyama E, Mori H, Yamada T, Kurokawa K, Matsumoto S, Nanno M, Naito T, Watanabe Y, Kato T, Miyauchi E, Ohno H, Shinkura R. (2016) High-affinity monoclonal IgA regulates gut microbiota and prevents colitis in mice. Nature Microbio. 1:16103. Japanese Press release
  • Matsuki T†, Yahagi K†, Mori H†, Matsumoto H†, Hara T, Tajima S, Ogawa E, Kodama H, Yamamoto K, Yamada T, Matsumoto S, Kurokawa K. (2016) A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nature Commun. 7:11939. PubMed Japanese Press release
  • Nishimoto Y, Mizutani S, Nakajima T, Hosoda F, Watanabe H, Saito Y, Shibata T, Yachida S, Yamada T. (2016) High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy. Gut. in press. PubMed Japanese Press release
  • Moriya, Y., Yamada, T., Okuda, S., Nakagawa, Z., Kotera, M., Tokimatsu, T., Kanehisa, M. & Goto, S. (2016). Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate–Product Pairs. Journal of Chemical Information and Modeling. PubMed

2015

  • Yoshida K, Maekawa T, Zhu Y, Renard-Guillet C, Chatton B, Inoue K, Uchiyama T, Ishibashi KI, Yamada T, Ohno N, Shirahige K, Okada-Hatakeyama M, Ishii S. (2015) The transcription factor ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory. Nat Immunol. 2015 Oct;16(10):1034-43. PubMed
  • Sato Y, Yamagishi J, Yamashita R, Shinozaki N, Ye B, Yamada T, Yamamoto M, Nagasaki M, Tsuboi A. (2015) Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals. PLoS One 10:e0131607 PubMed
  • Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T. (2015) FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data. PLoS One 10:e0126967 PubMed
  • Wang T, Mori H, Zhang C, Kurokawa K, Xing X, Yamada T. (2015) DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. BMC Bioinformatics 16:96 PubMed

2014

  • Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K. (2014) CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinformatics 15:406 PubMed
  • Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. (2014) Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol. Syst. Biol. 10:766 PubMed
  • Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW,Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD. (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnol. 2014 Jul 06. PubMed
  • Hori K, Maruyama F, Fujisawa T, Togashi T, Yamamoto N, Seo M, Sato S, Yamada T, Mori H, Tajima N, Moriyama T, Ikeuchi M, Watanabe M, Wada H, Kobayashi K, Saito M, Masuda T, Sasaki-Sekimoto Y, Mashiguchi K, Awai K, Shimojima M, Masuda S, Iwai M, Nobusawa T, Narise T, Kondo S, Saito H, Sato R, Murakawa M, Ihara Y, Oshima-Yamada Y, Ohtaka K, Satoh M, Sonobe K, Ishii M, Ohtani R, Kanamori-Sato M, Honoki R, Miyazaki D, Mochizuki H, Umetsu J, Higashi K, Shibata D, Kamiya Y, Sato N, Nakamura Y, Tabata S, Ida S, Kurokawa K, Ohta H. (2014) Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat. Commun. 5:3978 PubMed
  • Alison S Waller, Yamada T, David M Kristensen, Jens Roat Kultima, Shinichi Sunagawa, Eugene V Koonin and Peer Bork. (2014) Classification and quantification of bacteriophage taxa in human gut metagenomes. The ISME Journal , (13 March 2014) | doi:10.1038/ismej.2014.30 [ PubMed ]

2013

  • Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O, Guedon E, Delorme C, Layec S, Khaci G, van de Guchte M, Vandemeulebrouck G, Jamet A, Dervyn R, Sanchez N, Maguin E, Haimet F, Winogradski Y, Cultrone A, Leclerc M, Juste C, Blottière H, Pelletier E, LePaslier D, Artiguenave F, Bruls T, Weissenbach J, Turner K, Parkhill J, Antolin M, Manichanh C, Casellas F, Boruel N, Varela E, Torrejon A, Guarner F, Denariaz G, Derrien M, van Hylckama Vlieg JE, Veiga P, Oozeer R, Knol J, Rescigno M, Brechot C, M’Rini C, Mérieux A, Yamada T. (2013) Richness of human gut microbiome correlates with metabolic markers. Nature. 29;500(7464):541-6. PubMed
  • Masuda S, Hori K, Maruyama F, Ren S, Sugimoto S, Yamamoto N, Mori H, Yamada T, Sato S, Tabata S, Ohta H, Kurokawa K (2013) Whole-genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum strain W4. Genome Announc., 1:e00577-13. PubMed
  • Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV (2013) Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J. Bacteriol., 195:941-50. PubMed

和文総説・著書

  • 中村祐哉, 山田拓司 (2019) 腸内環境を”視る”方法, 実験医学別冊 もっとよくわかる！シリーズ, もっとよくわかる！腸内細菌叢 健康と疾患を司る”もう１つの臓器”, 羊土社, pp107-111
  • ロブ・ナイト, ブレンダン・ビューラー(著), 山田拓司, 東京工業大学 山田研究室(訳) (2018) 細菌が人をつくる, 朝日出版社
  • 山田拓司 (2016)腸内環境制御にむけた腸内代謝データベース構築, 実験医学4月号, 明かされる”もう一つの臓器” 腸内細菌叢を制御せよ！ 宿主との相互作用のメカニズムから便移植の実際、バイオベンチャーの動向まで, 羊土社, pp892-896
  • 森宙史, 東光一, 山田拓司, 黒川顕 (2015) 微生物統合データベースによる微生物と環境の研究への貢献, 難培養微生物研究の最新技術 III—微生物の生き様に迫り課題解決へ—, シーエムシー出版, pp10-19.
  • 山本希, 森宙史, 山田拓司, 黒川顕 (2014) メタゲノミクスの現状と未来, 生命のビッグデータ利用の最前線, シーエムシー出版, pp48-57.
  • 森宙史, 山田拓司, 黒川顕 (2013) ヒトメタゲノムの大規模コホート研究, 遺伝, pp279-282, 2013年5月号:67(3).
  • 森宙史, 山田拓司, 黒川顕（2012）メタゲノム解析の現状と将来, 情報管理, 55(3):167-175.

 

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