Takuji Yamada
Takuji Yamada
Associate Professor, Tokyo Institute of Technology
Verified email at
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A human gut microbial gene catalogue established by metagenomic sequencing
J Qin, R Li, J Raes, M Arumugam, KS Burgdorf, C Manichanh, T Nielsen, ...
nature 464 (7285), 59-65, 2010
Enterotypes of the human gut microbiome
M Arumugam, J Raes, E Pelletier, D Le Paslier, T Yamada, DR Mende, ...
nature 473 (7346), 174-180, 2011
Richness of human gut microbiome correlates with metabolic markers
E Le Chatelier, T Nielsen, J Qin, E Prifti, F Hildebrand, G Falony, ...
Nature 500 (7464), 541-546, 2013
An integrated catalog of reference genes in the human gut microbiome
J Li, H Jia, X Cai, H Zhong, Q Feng, S Sunagawa, M Arumugam, ...
Nature biotechnology 32 (8), 834-841, 2014
The ecoresponsive genome of Daphnia pulex
JK Colbourne, ME Pfrender, D Gilbert, WK Thomas, A Tucker, TH Oakley, ...
Science 331 (6017), 555-561, 2011
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
HB Nielsen, M Almeida, AS Juncker, S Rasmussen, J Li, S Sunagawa, ...
Nature biotechnology 32 (8), 822-828, 2014
Potential of fecal microbiota for early‐stage detection of colorectal cancer
G Zeller, J Tap, AY Voigt, S Sunagawa, JR Kultima, PI Costea, A Amiot, ...
Molecular systems biology 10 (11), 766, 2014
Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer
S Yachida, S Mizutani, H Shiroma, S Shiba, T Nakajima, T Sakamoto, ...
Nature medicine 25 (6), 968-976, 2019
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
JH Werren, S Richards, CA Desjardins, O Niehuis, J Gadau, ...
Science 327 (5963), 343, 2010
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
J Wirbel, PT Pyl, E Kartal, K Zych, A Kashani, A Milanese, JS Fleck, ...
Nature medicine 25 (4), 679-689, 2019
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
AM Thomas, P Manghi, F Asnicar, E Pasolli, F Armanini, M Zolfo, ...
Nature medicine 25 (4), 667-678, 2019
Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation
K Hori, F Maruyama, T Fujisawa, T Togashi, N Yamamoto, M Seo, S Sato, ...
Nature communications 5 (1), 3978, 2014
Proteome organization in a genome-reduced bacterium
S KŁhner, V van Noort, MJ Betts, A Leo-Macias, C Batisse, M Rode, ...
Science 326 (5957), 1235-1240, 2009
KEGG Atlas mapping for global analysis of metabolic pathways
S Okuda, T Yamada, M Hamajima, M Itoh, T Katayama, P Bork, S Goto, ...
Nucleic acids research 36 (suppl_2), W423-W426, 2008
Transcriptome complexity in a genome-reduced bacterium
M GŁell, V Van Noort, E Yus, WH Chen, J Leigh-Bell, K Michalodimitrakis, ...
Science 326 (5957), 1268-1271, 2009
Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis
N Yoshida, T Emoto, T Yamashita, H Watanabe, T Hayashi, T Tabata, ...
Circulation 138 (22), 2486-2498, 2018
Impact of genome reduction on bacterial metabolism and its regulation
E Yus, T Maier, K Michalodimitrakis, V van Noort, T Yamada, WH Chen, ...
science 326 (5957), 1263-1268, 2009
iPath2. 0: interactive pathway explorer
T Yamada, I Letunic, S Okuda, M Kanehisa, P Bork
Nucleic acids research 39 (suppl_2), W412-W415, 2011
A key genetic factor for fucosyllactose utilization affects infant gut microbiota development
T Matsuki, K Yahagi, H Mori, H Matsumoto, T Hara, S Tajima, E Ogawa, ...
Nature communications 7 (1), 11939, 2016
Evolution of biomolecular networks—lessons from metabolic and protein interactions
T Yamada, P Bork
Nature Reviews Molecular Cell Biology 10 (11), 791-803, 2009
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