M
Masaru Tomita
Researcher at Keio University
Publications - 702
Citations - 45555
Masaru Tomita is an academic researcher from Keio University. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 76, co-authored 677 publications receiving 40415 citations. Previous affiliations of Masaru Tomita include Mitsui Chemicals & Carnegie Mellon University.
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Journal ArticleDOI
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Tomoya Baba,Takeshi Ara,Miki Hasegawa,Yuki Takai,Yoshiko Okumura,Miki Baba,Kirill A. Datsenko,Masaru Tomita,Barry L. Wanner,Hirotada Mori,Hirotada Mori +10 more
TL;DR: These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome‐wide testing of mutational effects in a common strain background, E. coli K‐12 BW25113.
Journal ArticleDOI
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells
Yukihiro Furusawa,Yuuki Obata,Shinji Fukuda,Takaho A. Endo,Gaku Nakato,Daisuke Takahashi,Yumiko Nakanishi,Chikako Uetake,Keiko Kato,Tamotsu Kato,Masumi Takahashi,Noriko N. Fukuda,Shinnosuke Murakami,Eiji Miyauchi,Shingo Hino,Koji Atarashi,Satoshi Onawa,Yumiko Fujimura,Trevor Lockett,Julie M. Clarke,David L. Topping,Masaru Tomita,Shohei Hori,Osamu Ohara,Tatsuya Morita,Haruhiko Koseki,Jun Kikuchi,Kenya Honda,Koji Hase,Hiroshi Ohno +29 more
TL;DR: It is shown that a large bowel microbial fermentation product, butyrate, induces the differentiation of colonic Treg cells in mice and ameliorated the development of colitis induced by adoptive transfer of CD4+ CD45RBhi T cells in Rag1−/− mice.
Journal ArticleDOI
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Journal ArticleDOI
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Yasushi Okazaki,Masaaki Furuno,Takeya Kasukawa,Jun Adachi,Hidemasa Bono,S. Kondo,Itoshi Nikaido,Naoki Osato,Rintaro Saito,Harukazu Suzuki,Itaru Yamanaka,H. Kiyosawa,Ken Yagi,Yasuhiro Tomaru,Yuki Hasegawa,A. Nogami,Christian Schönbach,Takashi Gojobori,Richard M. Baldarelli,David P. Hill,Carol J. Bult,David A. Hume,John Quackenbush,Lynn M. Schriml,Alexander Kanapin,Hideo Matsuda,Serge Batalov,Kirk W. Beisel,Judith A. Blake,Dirck W. Bradt,Vladimir Brusic,Cyrus Chothia,Lori E. Corbani,S. Cousins,Emiliano Dalla,Tommaso A. Dragani,Colin F. Fletcher,Colin F. Fletcher,Alistair R. R. Forrest,K. S. Frazer,Terry Gaasterland,Manuela Gariboldi,Carmela Gissi,Adam Godzik,Julian Gough,Sean M. Grimmond,Stefano Gustincich,Nobutaka Hirokawa,Ian J. Jackson,Erich D. Jarvis,Akio Kanai,Hideya Kawaji,Hideya Kawaji,Yuka Imamura Kawasawa,Rafal M. Kedzierski,Benjamin L. King,Akihiko Konagaya,Igor V. Kurochkin,Yong-Hwan Lee,Boris Lenhard,Paul A. Lyons,Donna Maglott,Lois J. Maltais,Luigi Marchionni,Louise M. McKenzie,Harukata Miki,Takeshi Nagashima,Koji Numata,Toshihisa Okido,William J. Pavan,Geo Pertea,Graziano Pesole,Nikolai Petrovsky,Ramesh S. Pillai,Joan Pontius,D. Qi,Sridhar Ramachandran,Timothy Ravasi,Jonathan C. Reed,Deborah J Reed,Jeffrey G. Reid,Brian Z. Ring,M. Ringwald,Albin Sandelin,Claudio Schneider,Colin A. Semple,Mitsutoshi Setou,K. Shimada,Razvan Sultana,Yoichi Takenaka,Martin S. Taylor,Rohan D. Teasdale,Masaru Tomita,Roberto Verardo,Lukas Wagner,Claes Wahlestedt,Y. Wang,Yoshiki Watanabe,Christine A. Wells,Laurens G. Wilming,Anthony Wynshaw-Boris,Masashi Yanagisawa,Ivana V. Yang,L. Yang,Zheng Yuan,Mihaela Zavolan,Yunhui Zhu,Anne M. Zimmer,Piero Carninci,N. Hayatsu,Tomoko Hirozane-Kishikawa,Hideaki Konno,M. Nakamura,Naoko Sakazume,K. Sato,Toshiyuki Shiraki,Kazunori Waki,Jun Kawai,Katsunori Aizawa,Takahiro Arakawa,S. Fukuda,A. Hara,W. Hashizume,K. Imotani,Y. Ishii,Masayoshi Itoh,Ikuko Kagawa,A. Miyazaki,K. Sakai,D. Sasaki,K. Shibata,Akira Shinagawa,Ayako Yasunishi,Masayasu Yoshino,Robert H. Waterston,Eric S. Lander,Jane Rogers,Ewan Birney,Yoshihide Hayashizaki +138 more
TL;DR: The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Journal ArticleDOI
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs
TL;DR: The successful prediction of CDK1-regulated nucleocytoplasmic shuttling proteins is reported using a prediction system for nuclear localization signals (NLSs) and the application of this strategy to other functional linear motifs should be useful in systematic studies of protein–protein networks.