"Takuji Yamada","Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer",,"Nature Medicine",,,,,2019,June
"Yuki Moriya,Takuji Yamada,Shujiro Okuda,Masaaki Kotera,Zenichi Nakagawa,Toshiaki Tokimatsu,Susumu Goto,Minoru Kanehisa","Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs",,"Journal of Chemical Information and Modeling",,"Vol. 56","No. 3","pp. 510-516",2016,Feb.
"Masahiro Yano,Hiroshi Mori,Yutaka Akiyama,Takuji Yamada,Ken Kurokawa","CLAST: CUDA implemented large-scale alignment search tool",,"BMC Bioinformatics 2014",,"  15","  406",,2014,Dec.
"T. Yamada,A. S. Waller,J. Raes,A. Zelezniak,N. Perchat,A. Perret,M. Salanoubat,K. R. Patil,J. Weissenbach,P. Bork","Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours",,"Mol Syst Biol",,"Vol. 8",,"pp. 581",2012,
"D. M. Kristensen,A. S. Waller,T. Yamada,P. Bork,A. R. Mushegian,E. V. Koonin","Orthologous gene clusters and taxon signature genes for viruses of prokaryotes",,"J Bacteriol",,,,,2012,
"J. Raes,I. Letunic,T. Yamada,L. J. Jensen,P. Bork","Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data",,"Mol Syst Biol",,"Vol. 7",,"pp. 473",2011,
"J. K. Colbourne,M. E. Pfrender,D. Gilbert,W. K. Thomas,A. Tucker,T. H. Oakley,S. Tokishita,A. Aerts,G. J. Arnold,M. K. Basu,D. J. Bauer,C. E. C.ceres,L. Carmel,C. Casola,J. H. Choi,J. C. Detter,Q. Dong,S. Dusheyko,B. D. Eads,T. Fr?lich,K. A. Geiler-Samerotte,D. Gerlach,P. Hatcher,S. Jogdeo,J. Krijgsveld,E. V. Kriventseva,D. K. ltz,C. Laforsch,E. Lindquist,J. Lopez,J. R. Manak,J. Muller,J. Pangilinan,R. P. Patwardhan,S. Pitluck,E. J. Pritham,A. Rechtsteiner,M. Rho,I. B. Rogozin,O. Sakarya,A. Salamov,S. Schaack,H. Shapiro,Y. Shiga,C. Skalitzky,Z. Smith,A. Souvorov,W. Sung,Z. Tang,D. Tsuchiya,H. Tu,H. Vos,M. Wang,Y. I. Wolf,H. Yamagata,T. Yamada,Y. Ye,J. R. Shaw,J. Andrews,T. J. Crease,H. Tang,S. M. Lucas,H. M. Robertson,P. Bork,E. V. Koonin,E. M. Zdobnov,I. V. Grigoriev,M. Lynch,J. L. Boore","The ecoresponsive genome of Daphnia pulex",,"Science",,"Vol. 331",,"pp. 555-61",2011,
"M. Arumugam,J. Raes,E. Pelletier,D. Le Paslier,T. Yamada,D. R. Mende,G. R. Fernandes,J. Tap,T. Bruls,J. M. Batto,M. Bertalan,N. Borruel,F. Casellas,L. Fernandez,L. Gautier,T. Hansen,M. Hattori,T. Hayashi,M. Kleerebezem,K. Kurokawa,M. Leclerc,F. Levenez,C. Manichanh,H. B. Nielsen,T. Nielsen,N. Pons,J. Poulain,J. Qin,T. Sicheritz-Ponten,S. Tims,D. Torrents,E. Ugarte,E. G. Zoetendal,J. Wang,F. Guarner,O. Pedersen,W. M. de Vos,S. Brunak,J. Dore,M. Antoln,F. Artiguenave,H. M. Blottiere,M. Almeida,C. Brechot,C. Cara,C. Chervaux,A. Cultrone,C. Delorme,G. Denariaz,R. Dervyn,K. U. Foerstner,C. Friss,M. van de Guchte,E. Guedon,F. Haimet,W. Huber,J. van Hylckama-Vlieg,A. Jamet,C. Juste,G. Kaci,J. Knol,O. Lakhdari,S. Layec,K. Le Roux,E. Maguin,A. Mérieux,R. Melo Minardi,C. M'rini,J. Muller,R. Oozeer,J. Parkhill,P. Renault,M. Rescigno,N. Sanchez,S. Sunagawa,A. Torrejon,K. Turner,G. Vandemeulebrouck,E. Varela,Y. Winogradsky,G. Zeller,J. Weissenbach,S. D. Ehrlich,P. Bork,MetaHIT Consortium","Enterotypes of the human gut microbiome",,"Nature",,"Vol. 473",,"pp. 174-80",2011,
"J. Raes,I. Letunic,T. Yamada,L. J. Jensen,P. Bork","Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data",,"Mol Syst Biol",,"Vol. 7",,"pp. 473",2011,
"T. Yamada,I. Letunic,S. Okuda,M. Kanehisa,P. Bork","iPath2.0: interactive pathway explorer",,"Nucleic Acids Res",,"Vol. 39",,"pp. W412-5",2011,
"J. Qin,R. Li,J. Raes,M. Arumugam,K. S. Burgdorf,C. Manichanh,T. Nielsen,N. Pons,F. Levenez,T. Yamada,D. R. Mende,J. Li,J. Xu,S. Li,D. Li,J. Cao,B. Wang,H. Liang,H. Zheng,Y. Xie,J. Tap,P. Lepage,M. Bertalan,J. M. Batto,T. Hansen,D. Le Paslier,A. Linneberg,H. B. Nielsen,E. Pelletier,P. Renault,T. Sicheritz-Ponten,K. Turner,H. Zhu,C. Yu,M. Jian,Y. Zhou,Y. Li,X. Zhang,N. Qin,H. Yang,J. Wang,S. Brunak,J. Dore,F. Guarner,K. Kristiansen,O. Pedersen,J. Parkhill,J. Weissenbach,P. Bork,S. D. Ehrlich,MetaHIT Consortium","A human gut microbial gene catalogue established by metagenomic sequencing",,"Nature",,"Vol. 464",,"pp. 59-65",2010,
"J. H. Werren,S. Richards,C. A. Desjardins,O. Niehuis,J. Gadau,J. K. Colbourne,L. W. Beukeboom,C. Desplan,C. G. Elsik,C. J. Grimmelikhuijzen,P. Kitts,J. A. Lynch,T. Murphy,D. C. Oliveira,C. D. Smith,L. van de Zande,K. C. Worley,E. M. Zdobnov,M. Aerts,S. Albert,V. H. Anaya,J. M. Anzola,A. R. Barchuk,S. K. Behura,A. N. Bera,M. R. Berenbaum,R. C. Bertossa,M. M. Bitondi,S. R. Bordenstein,P. Bork,E. Bornberg-Bauer,M. Brunain,G. Cazzamali,L. Chaboub,J. Chacko,D. Chavez,C. P. Childers,J. H. Choi,M. E. Clark,C. Claudianos,R. A. Clinton,A. G. Cree,A. S. Cristino,P. M. Dang,A. C. Darby,D. C. de Graaf,B. Devreese,H. H. Dinh,R. Edwards,N. Elango,E. Elhaik,O. Ermolaeva,J. D. Evans,S. Foret,G. R. Fowler,D. Gerlach,J. D. Gibson,D. G. Gilbert,D. Graur,S. Grnder,D. E. Hagen,Y. Han,F. Hauser,D. Hultmark,H. C. Hunter,G. D. Hurst,S. N. Jhangian,H. Jiang,R. M. Johnson,A. K. Jones,T. Junier,T. Kadowaki,A. Kamping,Y. Kapustin,B. Kechavarzi,J. Kim,B. Kiryutin,T. Koevoets,C. L. Kovar,E. V. Kriventseva,R. Kucharski,H. Lee,S. L. Lee,K. Lees,L. R. Lewis,D. W. Loehlin,J. M. Logsdon,J. A. Lopez,R. J. Lozado,D. Maglott,R. Maleszka,A. Mayampurath,D. J. Mazur,M. A. McClure,A. D. Moore,M. B. Morgan,J. Muller,M. C. Munoz-Torres,D. M. Muzny,L. V. Nazareth,S. Neupert,N. B. Nguyen,F. M. Nunes,J. G. Oakeshott,G. O. Okwuonu,B. A. Pannebakker,V. R. Pejaver,Z. Peng,S. C. Pratt,R. Predel,L. L. Pu,H. Ranson,R. Raychoudhury,A. Rechtsteiner,J. T. Reese,J. G. Reid,M. Riddle,H. M. Robertson,J. Romero-Severson,M. Rosenberg,T. B. Sackton,D. B. Sattelle,H. Schlns,T. Schmitt,M. Schneider,A. Schler,A. M. Schurko,D. M. Shuker,Z. L. Simies,S. Sinha,Z. Smith,V. Solovyev,A. Souvorov,A. Springauf,E. Stafflinger,D. E. Stage,M. Stanke,Y. Tanaka,A. Telschow,C. Trent,S. Vattathil,E. C. Verhulst,L. Viljakainen,K. W. Wanner,R. M. Waterhouse,J. B. Whitfield,T. E. Wilkes,M. Williamson,J. H. Willis,F. Wolschin,S. Wyder,T. Yamada,S. V. Yi,C. N. Zecher,L. Zhang,R. A. Gibbs,Nasonia Genome Working Group","Functional and evolutionary insights from the genomes of three parasitoid Nasonia species",,"Science",,"Vol. 327",,"pp. 343-8",2010,
"T. A. Gianoulis,J. Raes,P. V. Patel,R. Bjornson,J. O. Korbel,I. Letunic,T. Yamada,A. Paccanaro,L. J. Jensen,M. Snyder,P. Bork,M. B. Gerstein","Quantifying environmental adaptation of metabolic pathways in metagenomics",,"Proc Natl Acad Sci U S A",,"Vol. 106",,"pp. 1374-9",2009,
"E. Yus,T. Maier,K. Michalodimitrakis,V. van Noort,T. Yamada,W. H. Chen,J. A. Wodke,M. Guell,S. Martnez,R. Bourgeois,S. Kuhner,E. Raineri,I. Letunic,O. V. Kalinina,M. Rode,R. Herrmann,R. GutiErrez-Gallego,R. B. Russell,A. C. Gavin,P. Bork,L. Serrano","Impact of genome reduction on bacterial metabolism and its regulation",,"Science",,"Vol. 326",,"pp. 1263-8",2009,
"M. Guell,V. van Noort,E. Yus,W. H. Chen,J. Leigh-Bell,K. Michalodimitrakis,T. Yamada,M. Arumugam,T. Doerks,S. Kuhner,M. Rode,M. Suyama,S. Schmidt,A. C. Gavin,P. Bork,L. Serrano","Transcriptome complexity in a genome-reduced bacterium",,"Science",,"Vol. 326",,"pp. 1268-71",2009,
"T. Yamada,P. Bork","Evolution of biomolecular networks: lessons from metabolic and protein interactions",,"Nat Rev Mol Cell Biol",,"Vol. 10",,"pp. 791-803",2009,
"S. Kuhner,V. van Noort,M. J. Betts,A. Leo-Macias,C. Batisse,M. Rode,T. Yamada,T. Maier,S. Bader,P. Beltran-Alvarez,D. Castao-Diez,W. H. Chen,D. Devos,M. Guell,T. Norambuena,I. Racke,V. Rybin,A. Schmidt,E. Yus,R. Aebersold,R. Herrmann,B. Bttcher,A. S. Frangakis,R. B. Russell,L. Serrano,P. Bork,A. C. Gavin","Proteome organization in a genome-reduced bacterium",,"Science",,"Vol. 326",,"pp. 1235-40",2009,
"I. Letunic,T. Yamada,M. Kanehisa,P. Bork","iPath: interactive exploration of biochemical pathways and networks",,"Trends Biochem Sci",,"Vol. 33",,"pp. 101-3",2008,
"S. Okuda,T. Yamada,M. Hamajima,M. Itoh,T. Katayama,P. Bork,S. Goto,M. Kanehisa","KEGG Atlas mapping for global analysis of metabolic pathways",,"Nucleic Acids Res",,"Vol. 36",,"pp. W423-6",2008,