Takuji Yamada

17 papers Journal 17
YearRankTypeTitle / Venue / Authors
2025 J jnl
DeepES: deep learning-based enzyme screening to identify orphan enzyme genes.
Bioinform.
Keisuke Hirota, Felix Salim, Takuji Yamada
2024 J jnl
Enteropathway: the metabolic pathway database for the human gut microbiota.
Briefings Bioinform.
Hirotsugu Shiroma, Youssef Darzi, Etsuko Terajima, Zenichi Nakagawa, Hirotaka Tsuchikura, Naoki Tsukuda, Yuki Moriya, Shujiro Okuda, Susumu Goto, Takuji Yamada
2024 J jnl
QNetDiff: a quantitative measurement of network rewiring.
BMC Bioinform.
Shota Nose, Hirotsugu Shiroma, Takuji Yamada, Yushi Uno
2019 J jnl
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization.
Bioinform.
Youssef Darzi, Yuta Yamate, Takuji Yamada
2018 J jnl
VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.
BMC Syst. Biol.
Hiroshi Mori, Takayuki Maruyama, Masahiro Yano, Takuji Yamada, Ken Kurokawa
2018 J jnl
iPath3.0: interactive pathways explorer v3.
Nucleic Acids Res.
Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada
2016 J jnl
Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.
J. Chem. Inf. Model.
Yuki Moriya, Takuji Yamada, Shujiro Okuda, Zenichi Nakagawa, Masaaki Kotera, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto
2015 J jnl
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.
BMC Bioinform.
Tianmin Wang, Hiroshi Mori, Chong Zhang, Ken Kurokawa, Xin-Hui Xing, Takuji Yamada
2014 J jnl
Addendum: Enterotypes of the human gut microbiome.
Nat.
Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Brüls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernández, Laurent Gautier, Torben Hansen, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, Henrik Bjørn Nielsen, Trine Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Pontén, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang, Francisco Guarner, Oluf Pedersen, Willem M. De Vos, Søren Brunak, Joël Dore, MetaHIT Consortium, Jean Weissenbach, S. Dusko Ehrlich, Peer Bork
2014 J jnl
CLAST: CUDA implemented large-scale alignment search tool.
BMC Bioinform.
Masahiro Yano, Hiroshi Mori, Yutaka Akiyama, Takuji Yamada, Ken Kurokawa
2011 J jnl
iPath2.0: interactive pathway explorer.
Nucleic Acids Res.
Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, Peer Bork
2008 J jnl
KEGG Atlas mapping for global analysis of metabolic pathways.
Nucleic Acids Res.
Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, Minoru Kanehisa
2007 J jnl
Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways.
J. Chem. Inf. Model.
Mina Oh, Takuji Yamada, Masahiro Hattori, Susumu Goto, Minoru Kanehisa
2007 J jnl
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.
Nucleic Acids Res.
Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi
2006 J jnl
Extraction of phylogenetic network modules from the metabolic network.
BMC Bioinform.
Takuji Yamada, Minoru Kanehisa, Susumu Goto
2005 J jnl
VisANT: data-integrating visual framework for biological networks and modules.
Nucleic Acids Res.
Zhenjun Hu, Joe Mellor, Jie Wu, Takuji Yamada, Dustin T. Holloway, Charles DeLisi
2004 J jnl
Clustering under the line graph transformation: application to reaction network.
BMC Bioinform.
Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu