Publications of T. Yamada

Publications of T. Yamada

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2019 3 publication(s).
24.
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
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 Apr 1; 25(4): 667-678. PubMed: 30936548.
Abstract + PDF
23.
Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
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 Dec 29; 25(12): 1948. PubMed: 31664237.
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22.
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.
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 Apr 1; 25(4): 679-689. PubMed: 30936547.
Abstract + PDF
2018 1 publication(s).
21.
iPath3.0: interactive pathways explorer v3.
Darzi Y, Letunic I, Bork P, Yamada T
2018 Jul 2; 46: W510-W513. PubMed: 29718427.
Abstract + PDF
2014 4 publication(s).
20.
Addendum: Enterotypes of the human gut microbiome.
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, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, MetaHIT C, Weissenbach J, Ehrlich SD, Bork P
2014 Feb 27; 506(7489): 516. PubMed: 24572424.
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19.
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
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 C, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD
2014 Aug 6; 32(8): 822-8. Epub 2014 Jul 6; PubMed: 24997787.
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18.
Classification and quantification of bacteriophage taxa in human gut metagenomes.
Waller AS, Yamada T, Kristensen DM, Kultima JR, Sunagawa S, Koonin EV, Bork P
2014 Jul 13; 8(7): 1391-402. Epub 2014 Mar 13; PubMed: 24621522.
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17.
Potential of fecal microbiota for early-stage detection of colorectal cancer.
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 Nov 28; 10(11): 766. PubMed: 25432777.
Abstract + PDF
2013 1 publication(s).
16.
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.
Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV
2013 Mar 7; 195(5): 941-50. Epub 2012 Dec 7; PubMed: 23222723.
Abstract + PDF
2012 1 publication(s).
15.
Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.
Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P
2012 May 8; 8: 581. PubMed: 22569339.
Abstract + PDF
2011 4 publication(s).
14.
Enterotypes of the human gut microbiome.
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, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Consortium M, Weissenbach J, Ehrlich SD, Bork P
2011 May 12; 473(7346): 174-80. Epub 2011 Apr 20; PubMed: 21508958.
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13.
The ecoresponsive genome of Daphnia pulex.
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, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL
2011 Feb 4; 331(6017): 555-61. PubMed: 21292972.
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12.
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
2011 Mar 15; 7: 473. PubMed: 21407210.
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11.
iPath2.0: interactive pathway explorer.
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P
2011 Jul 5; 39 Suppl 2: W412-5. Epub 2011 May 5; PubMed: 21546551.
Abstract + PDF
2010 3 publication(s).
10.
[Metagenomics of the intestinal microbiota: potential applications].
Dusko Ehrlich S, MetaHIT Consortium , Antolin M, Artiguenave F, Arumugam M, Batto JM, Bertalan M, Blottiere H, Bork P, Borruel N, Brechot C, Brunak S, Bruls T, Burgdorf KS, Cao J, Casellas F, Chervaux C, Colombel JF, Cultrone A, Doré J, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, Guarner F, Guchte Mv, Guedon E, Haimet F, Hansen T, Jamet A, Jian M, Juste C, Kaci G, Kleerebezem M, Knol J, Kristiansen K, Layec S, Le Roux K, Leclerc M, Le Paslier D, Levenez F, Li D, Li J, Li S, Li S, Li S, Li Y, Liang H, Mende D, Maguin E, Manichanh C, Minardi RM, Mrini C, Nielsen HB, Nielsen T, Oozeer R, Parkhill J, Pons N, Pedersen O, Pelletier E, Qin J, Raes J, Renault P, Rescigno M, Ruiqiang L, Sanchez N, Sicheritz-Ponten T, Tims S, Torrejon T, Turner K, Varela E, Vos Wd, Wang B, Wang J, Wang J, Weissenbach J, Winogradsky Y, Xie Y, Xu J, Yamada T, Yang H, Yu C, Zhang X, Zheng H, Zhu H, Zhou Y, Zoetendal E.
2010 Sep; 34 Suppl 1: S23-8. PubMed: 20889001.
Abstract
9.
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.
Nasonia Genome Working Group , Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA
2010 Jan 15; 327(5963): 343-8. PubMed: 20075255.
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8.
A human gut microbial gene catalogue established by metagenomic sequencing.
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, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J, MetaHIT Consortium
2010 Mar 4; 464(7285): 59-65. PubMed: 20203603.
Abstract + PDF
2009 5 publication(s).
7.
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB
2009 Feb 3; 106(5): 1374-9. Epub 2009 Jan 22; PubMed: 19164758.
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6.
Transcriptome complexity in a genome-reduced bacterium.
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, Serrano L
2009 Nov 27; 326(5957): 1268-71. PubMed: 19965477.
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5.
Proteome organization in a genome-reduced bacterium.
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 DP, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC
2009 Nov 27; 326(5957): 1235-40. PubMed: 19965468.
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4.
Evolution of biomolecular networks - lessons from metabolic and protein interactions.
Yamada T, Bork P
2009 Nov; 10(11): 791-803. PubMed: 19851337.
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3.
Impact of genome reduction on bacterial metabolism and its regulation.
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, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L
2009 Nov 27; 326(5957): 1263-8. PubMed: 19965476.
Abstract + PDF
2008 2 publication(s).
2.
iPath: interactive exploration of biochemical pathways and networks.
Letunic I, Yamada T, Kanehisa M, Bork P
2008 Mar 12; 33(3): 101-3. Epub 2008 Feb 13; PubMed: 18276143.
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1.
KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M
2008 Jul 1; 36: W423-6. Epub 2008 May 13; PubMed: 18477636.
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