Takuji Yamada - Publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://www.embl.de/research/units/scb/bork/members/index.php?s_personId=4641

72 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Narii N, Zha L, Sobue T, Kitamura T, Komatsu M, Shimomura Y, Shiba S, Mizutani S, Yamada T, Yachida S. Intestinal Bacteria Fluctuating in Early-Stage Colorectal Cancer Carcinogenesis are Associated with Diet in Healthy Adults. Nutrition and Cancer. 1-8. PMID 38642022 DOI: 10.1080/01635581.2024.2344257  0.71
2023 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. High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection. Nature Communications. 14: 3863. PMID 37391427 DOI: 10.1038/s41467-023-39569-0  0.519
2023 Rynazal R, Fujisawa K, Shiroma H, Salim F, Mizutani S, Shiba S, Yachida S, Yamada T. Leveraging explainable AI for gut microbiome-based colorectal cancer classification. Genome Biology. 24: 21. PMID 36759888 DOI: 10.1186/s13059-023-02858-4  0.718
2023 Narii N, Zha L, Sobue T, Kitamura T, Shiba S, Mizutani S, Yamada T, Yachida S. Association Between Diet and Fusobacterium nucleatum in the Feces of Healthy Adults: A Hospital-based Cross-sectional Study. Cancer Prevention Research (Philadelphia, Pa.). OF1-OF8. PMID 36719965 DOI: 10.1158/1940-6207.CAPR-22-0399  0.697
2023 Salim F, Mizutani S, Zolfo M, Yamada T. Recent advances of machine learning applications in human gut microbiota study: from observational analysis toward causal inference and clinical intervention. Current Opinion in Biotechnology. 79: 102884. PMID 36623442 DOI: 10.1016/j.copbio.2022.102884  0.694
2022 Shimomura Y, Zha L, Komukai S, Narii N, Sobue T, Kitamura T, Shiba S, Mizutani S, Yamada T, Sawada N, Yachida S. Mediation effect of intestinal microbiota on the relationship between fiber intake and colorectal cancer. International Journal of Cancer. PMID 36522829 DOI: 10.1002/ijc.34398  0.703
2022 Narii N, Zha L, Sobue T, Kitamura T, Shiba S, Mizutani S, Yamada T, Yachida S. Association between Diet and Fusobacterium nucleatum in the Feces of Healthy Adults: A hospital-based cross-sectional study. Cancer Prevention Research (Philadelphia, Pa.). PMID 36474311 DOI: 10.1158/1940-6207.CAPR-22-0399  0.773
2022 Nakamura Y, Suzuki S, Murakami S, Nishimoto Y, Higashi K, Watarai N, Umetsu J, Ishii C, Ito Y, Mori Y, Kohno M, Yamada T, Fukuda S. Integrated gut microbiome and metabolome analyses identified fecal biomarkers for bowel movement regulation by BB536 supplementation: A RCT. Computational and Structural Biotechnology Journal. 20: 5847-5858. PMID 36382178 DOI: 10.1016/j.csbj.2022.10.026  0.761
2022 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. Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits. Msystems. 7: e0001822. PMID 35311577 DOI: 10.1128/msystems.00018-22  0.78
2021 Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. Variation and transmission of the human gut microbiota across multiple familial generations. Nature Microbiology. PMID 34969979 DOI: 10.1038/s41564-021-01021-8  0.608
2021 Hayashi T, Yamashita T, Takahashi T, Tabata T, Watanabe H, Gotoh Y, Shinohara M, Kami K, Tanaka H, Matsumoto K, Hayashi T, Yamada T, Hirata KI. Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis. Frontiers in Cardiovascular Medicine. 8: 789325. PMID 34912870 DOI: 10.3389/fcvm.2021.789325  0.592
2021 Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, ... ... Yamada T, et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine. PMID 34789871 DOI: 10.1038/s41591-021-01552-x  0.74
2021 Yamamoto N, Watarai N, Koyano H, Sawada K, Toyoda A, Kurokawa K, Yamada T. Analysis of genomic characteristics and their influence on metabolism in Aspergillus luchuensis albino mutants using genome sequencing. Fungal Genetics and Biology : Fg & B. 103601. PMID 34224861 DOI: 10.1016/j.fgb.2021.103601  0.753
2021 Nishimoto Y, Nomaguchi T, Mori Y, Ito M, Nakamura Y, Fujishima M, Murakami S, Yamada T, Fukuda S. The Nutritional Efficacy of Supplementation Depends on the Individual Gut Environment: A Randomised Control Study. Frontiers in Nutrition. 8: 648073. PMID 34136514 DOI: 10.3389/fnut.2021.648073  0.62
2021 Emoto T, Hayashi T, Tabata T, Yamashita T, Watanabe H, Takahashi T, Gotoh Y, Kami K, Yoshida N, Saito Y, Tanaka H, Matsumoto K, Hayashi T, Yamada T, Hirata KI. Metagenomic analysis of gut microbiota reveals its role in trimethylamine metabolism in heart failure. International Journal of Cardiology. PMID 34102245 DOI: 10.1016/j.ijcard.2021.06.003  0.557
2020 Watanabe H, Ng CH, Limviphuvadh V, Suzuki S, Yamada T. dominates the gut microbiome of the Asian palm civet that produces kopi luwak. Peerj. 8: e9579. PMID 32821539 DOI: 10.7717/Peerj.9579  0.713
2020 Yoshida N, Yamashita T, Kishino S, Watanabe H, Sasaki K, Sasaki D, Tabata T, Sugiyama Y, Kitamura N, Saito Y, Emoto T, Hayashi T, Takahashi T, Shinohara M, Osawa R, ... ... Yamada T, et al. A possible beneficial effect of Bacteroides on faecal lipopolysaccharide activity and cardiovascular diseases. Scientific Reports. 10: 13009. PMID 32747669 DOI: 10.1038/S41598-020-69983-Z  0.568
2020 Suzuki S, Yamada T. Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication. Peerj. 8: e8722. PMID 32257635 DOI: 10.7717/Peerj.8722  0.516
2020 Erawijantari PP, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Saito Y, Fukuda S, Yachida S, Yamada T. Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles. Gut. PMID 31953253 DOI: 10.1136/Gutjnl-2019-319188  0.753
2020 Mizutani S, Yamada T, Yachida S. Significance of the gut microbiome in multistep colorectal carcinogenesis. Cancer Science. PMID 31910311 DOI: 10.1111/Cas.14298  0.745
2019 Watarai N, Yamamoto N, Sawada K, Yamada T. Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 31755931 DOI: 10.1093/Dnares/Dsz024  0.771
2019 Nakamura Y, Hirose S, Taniguchi Y, Moriya Y, Yamada T. Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites. Metabolic Engineering Communications. 9: e00102. PMID 31720217 DOI: 10.1016/J.Mec.2019.E00102  0.606
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, ... ... Yamada T, et al. Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. PMID 31664237 DOI: 10.1038/S41591-019-0663-4  0.783
2019 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, ... ... Yamada T, et al. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nature Medicine. 25: 968-976. PMID 31171880 DOI: 10.1038/S41591-019-0458-7  0.788
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, ... ... Yamada T, et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine. PMID 30936548 DOI: 10.1038/S41591-019-0405-7  0.802
2019 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, ... ... Yamada T, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine. PMID 30936547 DOI: 10.1038/S41591-019-0406-6  0.8
2018 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, et al. Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis. Circulation. 138: 2486-2498. PMID 30571343 DOI: 10.1161/Circulationaha.118.033714  0.578
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, et al. Gut Microbiome and Plasma Microbiome-Related Metabolites in Patients With Decompensated and Compensated Heart Failure. Circulation Journal : Official Journal of the Japanese Circulation Society. 83: 182-192. PMID 30487369 DOI: 10.1253/Circj.Cj-18-0468  0.583
2018 Watanabe H, Nakamura I, Mizutani S, Kurokawa Y, Mori H, Kurokawa K, Yamada T. Minor taxa in human skin microbiome contribute to the personal identification. Plos One. 13: e0199947. PMID 30044822 DOI: 10.1371/Journal.Pone.0199947  0.762
2018 Darzi Y, Letunic I, Bork P, Yamada T. iPath3.0: interactive pathways explorer v3. Nucleic Acids Research. PMID 29718427 DOI: 10.1093/Nar/Gky299  0.722
2018 Mori H, Maruyama T, Yano M, Yamada T, Kurokawa K. VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. Bmc Systems Biology. 12: 30. PMID 29560821 DOI: 10.1186/S12918-018-0545-2  0.596
2016 Watanabe H, Goto S, Mori H, Higashi K, Hosomichi K, Aizawa N, Takahashi N, Tsuchida M, Suzuki Y, Yamada T, Horii A, Inoue I, Kurokawa K, Narita I. Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy. Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association. PMID 27683270 DOI: 10.1093/Ndt/Gfw343  0.569
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, et al. High-affinity monoclonal IgA regulates gut microbiota and prevents colitis in mice. Nature Microbiology. 1: 16103. PMID 27562257 DOI: 10.1038/Nmicrobiol.2016.103  0.587
2016 Nishimoto Y, Mizutani S, Nakajima T, Hosoda F, Watanabe H, Saito Y, Shibata T, Yachida S, Yamada T. High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy. Gut. PMID 27340192 DOI: 10.1136/Gutjnl-2016-311937  0.766
2016 Matsuki T, Yahagi K, Mori H, Matsumoto H, Hara T, Tajima S, Ogawa E, Kodama H, Yamamoto K, Yamada T, Matsumoto S, Kurokawa K. A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nature Communications. 7: 11939. PMID 27340092 DOI: 10.1038/Ncomms11939  0.569
2016 Moriya Y, Yamada T, Okuda S, Nakagawa Z, Kotera M, Tokimatsu T, Kanehisa M, Goto S. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. Journal of Chemical Information and Modeling. PMID 26822930 DOI: 10.1021/Acs.Jcim.5B00216  0.519
2016 Yamada T. Metabolic pathway database for human gut microbiome Japanese Journal of Lactic Acid Bacteria. 27: 87-92. DOI: 10.4109/Jslab.27.87  0.336
2015 Uchiyama T, Irie M, Mori H, Kurokawa K, Yamada T. FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data. Plos One. 10: e0126967. PMID 25974630 DOI: 10.1371/Journal.Pone.0126967  0.582
2015 Wang T, Mori H, Zhang C, Kurokawa K, Xing XH, Yamada T. DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. Bmc Bioinformatics. 16: 96. PMID 25888481 DOI: 10.1186/S12859-015-0499-Y  0.584
2014 Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K. CLAST: CUDA implemented large-scale alignment search tool. Bmc Bioinformatics. 15: 406. PMID 25495907 DOI: 10.1186/S12859-014-0406-Y  0.577
2014 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, ... ... Yamada T, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Molecular Systems Biology. 10: 766. PMID 25432777 DOI: 10.15252/Msb.20145645  0.795
2014 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, ... ... Yamada T, et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nature Biotechnology. 32: 822-8. PMID 24997787 DOI: 10.1038/Nbt.2939  0.798
2014 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, et al. Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nature Communications. 5: 3978. PMID 24865297 DOI: 10.1038/Ncomms4978  0.552
2014 Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P. Classification and quantification of bacteriophage taxa in human gut metagenomes. The Isme Journal. 8: 1391-402. PMID 24621522 DOI: 10.1038/Ismej.2014.30  0.716
2014 Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Addendum: Enterotypes of the human gut microbiome Nature. 506: 516-516. DOI: 10.1038/Nature13075  0.763
2013 Masuda S, Hori K, Maruyama F, Ren S, Sugimoto S, Yamamoto N, Mori H, Yamada T, Sato S, Tabata S, Ohta H, Kurokawa K. Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4. Genome Announcements. 1. PMID 23929476 DOI: 10.1128/Genomea.00577-13  0.597
2013 Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV. Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. Journal of Bacteriology. 195: 941-50. PMID 23222723 DOI: 10.1128/Jb.01801-12  0.707
2012 Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P. Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Molecular Systems Biology. 8: 581. PMID 22569339 DOI: 10.1038/Msb.2012.13  0.753
2012 MORI H, YAMADA T, KUROKAWA K. Current and future trends in metagenomics : Development of knowledge bases Journal of Information Processing and Management. 55: 167-175. DOI: 10.1241/Johokanri.55.167  0.524
2011 Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Research. 39: W412-5. PMID 21546551 DOI: 10.1093/Nar/Gkr313  0.752
2011 Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Enterotypes of the human gut microbiome. Nature. 473: 174-80. PMID 21508958 DOI: 10.1038/Nature09944  0.781
2011 Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology. 7: 473. PMID 21407210 DOI: 10.1038/Msb.2011.6  0.782
2011 Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, ... ... Yamada T, et al. The ecoresponsive genome of Daphnia pulex. Science (New York, N.Y.). 331: 555-61. PMID 21292972 DOI: 10.1126/Science.1197761  0.748
2011 Arumugam M, Raes J, Pelletier E, Paslier DL, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, et al. Erratum: Enterotypes of the human gut microbiome (Nature (2011) 473 (174-180)) Nature. 474: 666-666. DOI: 10.1038/Nature10187  0.768
2010 Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464: 59-65. PMID 20203603 DOI: 10.1038/Nature08821  0.797
2010 Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, ... ... Yamada T, et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (New York, N.Y.). 327: 343-8. PMID 20075255 DOI: 10.1126/Science.1178028  0.755
2009 Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, et al. Transcriptome complexity in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1268-71. PMID 19965477 DOI: 10.1126/Science.1176951  0.766
2009 Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, et al. Impact of genome reduction on bacterial metabolism and its regulation. Science (New York, N.Y.). 326: 1263-8. PMID 19965476 DOI: 10.1126/Science.1177263  0.787
2009 Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, et al. Proteome organization in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1235-40. PMID 19965468 DOI: 10.1126/Science.1176343  0.764
2009 Yamada T, Bork P. Evolution of biomolecular networks: lessons from metabolic and protein interactions. Nature Reviews. Molecular Cell Biology. 10: 791-803. PMID 19851337 DOI: 10.1038/Nrm2787  0.547
2009 Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/Pnas.0808022106  0.783
2008 Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M. KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Research. 36: W423-6. PMID 18477636 DOI: 10.1093/Nar/Gkn282  0.664
2008 Letunic I, Yamada T, Kanehisa M, Bork P. iPath: interactive exploration of biochemical pathways and networks. Trends in Biochemical Sciences. 33: 101-3. PMID 18276143 DOI: 10.1016/J.Tibs.2008.01.001  0.772
2007 Hu Z, Ng DM, Yamada T, Chen C, Kawashima S, Mellor J, Linghu B, Kanehisa M, Stuart JM, DeLisi C. VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Research. 35: W625-32. PMID 17586824 DOI: 10.1093/Nar/Gkm295  0.45
2007 Oh M, Yamada T, Hattori M, Goto S, Kanehisa M. Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. Journal of Chemical Information and Modeling. 47: 1702-12. PMID 17516640 DOI: 10.1021/Ci700006F  0.432
2006 Tanaka M, Yamada T, Itoh M, Okuda S, Goto S, Kanehisa M. Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes. Genome Informatics. International Conference On Genome Informatics. 17: 230-9. PMID 17503372 DOI: 10.11234/Gi1990.17.230  0.467
2006 Hashimoto K, Yoshizawa AC, Saito K, Yamada T, Kanehisa M. The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes. Genome Informatics. International Conference On Genome Informatics. 17: 173-83. PMID 17503367 DOI: 10.11234/Gi1990.17.173  0.411
2006 Yamada T, Kanehisa M, Goto S. Extraction of phylogenetic network modules from the metabolic network. Bmc Bioinformatics. 7: 130. PMID 16533389 DOI: 10.1186/1471-2105-7-130  0.415
2006 Nacher JC, Ochiai T, Yamada T, Kanehisa M, Akutsu T. The role of log-normal dynamics in the evolution of biochemical pathways. Bio Systems. 83: 26-37. PMID 16236424 DOI: 10.1016/J.Biosystems.2005.09.003  0.416
2005 Yamada T, Kawashima S, Mamitsuka H, Goto S, Kanehisa M. Comprehensive analysis and prediction of synthetic lethality using subcellular locations. Genome Informatics. International Conference On Genome Informatics. 16: 150-8. PMID 16362917 DOI: 10.11234/Gi1990.16.150  0.448
2004 Yamada T, Goto S, Kanehisa M. Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Informatics. International Conference On Genome Informatics. 15: 249-58. PMID 15712127 DOI: 10.11234/Gi1990.15.249  0.465
2004 Nacher JC, Ueda N, Yamada T, Kanehisa M, Akutsu T. Clustering under the line graph transformation: application to reaction network. Bmc Bioinformatics. 5: 207. PMID 15617578 DOI: 10.1186/1471-2105-5-207  0.372
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