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Takuji Yamada
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2020 – today
- 2024
- [j15]Shota Nose, Hirotsugu Shiroma, Takuji Yamada, Yushi Uno:
QNetDiff: a quantitative measurement of network rewiring. BMC Bioinform. 25(1): 118 (2024)
2010 – 2019
- 2019
- [j14]Youssef Darzi, Yuta Yamate, Takuji Yamada:
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization. Bioinform. 35(21): 4519-4521 (2019) - 2018
- [j13]Hiroshi Mori, Takayuki Maruyama, Masahiro Yano, Takuji Yamada, Ken Kurokawa:
VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. BMC Syst. Biol. 12(S-2): 47-58 (2018) - [j12]Youssef Darzi, Ivica Letunic, Peer Bork, Takuji Yamada:
iPath3.0: interactive pathways explorer v3. Nucleic Acids Res. 46(Webserver-Issue): W510-W513 (2018) - 2016
- [j11]Yuki Moriya, Takuji Yamada, Shujiro Okuda, Zenichi Nakagawa, Masaaki Kotera, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto:
Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs. J. Chem. Inf. Model. 56(3): 510-516 (2016) - 2015
- [j10]Tianmin Wang, Hiroshi Mori, Chong Zhang, Ken Kurokawa, Xin-Hui Xing, Takuji Yamada:
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. BMC Bioinform. 16: 96:1-96:15 (2015) - 2014
- [j9]Masahiro Yano, Hiroshi Mori, Yutaka Akiyama, Takuji Yamada, Ken Kurokawa:
CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinform. 15: 406 (2014) - [j8]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:
Addendum: Enterotypes of the human gut microbiome. Nat. 506(7489): 516 (2014) - 2011
- [j7]Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, Peer Bork:
iPath2.0: interactive pathway explorer. Nucleic Acids Res. 39(Web-Server-Issue): 412-415 (2011)
2000 – 2009
- 2008
- [j6]Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, Minoru Kanehisa:
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res. 36(Web-Server-Issue): 423-426 (2008) - 2007
- [j5]Mina Oh, Takuji Yamada, Masahiro Hattori, Susumu Goto, Minoru Kanehisa:
Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways. J. Chem. Inf. Model. 47(4): 1702-1712 (2007) - [j4]Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, Charles DeLisi:
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res. 35(Web-Server-Issue): 625-632 (2007) - 2006
- [j3]Takuji Yamada, Minoru Kanehisa, Susumu Goto:
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinform. 7: 130 (2006) - 2005
- [j2]Zhenjun Hu, Joe Mellor, Jie Wu, Takuji Yamada, Dustin T. Holloway, Charles DeLisi:
VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res. 33(Web-Server-Issue): 352-357 (2005) - 2004
- [j1]Jose C. Nacher, Nobuhisa Ueda, Takuji Yamada, Minoru Kanehisa, Tatsuya Akutsu:
Clustering under the line graph transformation: application to reaction network. BMC Bioinform. 5: 207 (2004)
Coauthor Index
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