BABA Tomoya

J-GLOBAL         Last updated: Nov 20, 2019 at 12:15
BABA Tomoya
Research Organization of Information and Systems
Job title

Research Areas


Awards & Honors

Nov 2006
Best Paper Award, The 3rd International E. coli Alliance Conference on Systems Biology
The 3rd International E. coli Alliance Conference on Systems Biology, Best Paper Award

Published Papers

Essential cellular modules for the proliferation of the primitive cell
Koichi Higashi, Yoshikazu Kawai, Tomoya Baba, Ken Kurokawa, Taku Oshima
Geoscience Frontiers   9(4) 1155-1161   Jul 2018   [Refereed]
Nakai R, Fujisawa T, Nakamura Y, Baba T, Nishijima M, Karray F, Sayadi S, Isoda H, Naganuma T, Niki H
Stand Genomic Sci.   11 90   Dec 2016   [Refereed]
Complete genome sequence of Aurantimicrobium minutum type strain KNCT, a planktonic ultramicrobacterium isolated from river water
Nakai R, Fujisawa T, Nakamura Y, Nishide H, Uchiyama I, Baba T, Toyoda A, Fujiyama A, Naganuma T, Niki H
Genome Announc.   4(3) e00616-16   Jul 2016   [Refereed]
Mori H, Baba T, Yokoyama K, Takeuchi R, Nomura W, Makishi K, Otsuka Y, Dose H, Wanner BL
Methods Mol Biol.   1279 45-65   Jan 2015
Ryosuke Nakai, Tomoya Baba, Hironori Niki, Miyuki Nishijima, Takeshi Naganuma
International Journal of Systematic and Evolutionary Microbiolog   65 4072-4079   Nov 2015   [Refereed]


Predicting Gene Knockout Effects by Minimal Pathway Enumeration
Takehide Soh, Katsumi Inoue, Tomoya Baba, Toyoyuki Takada and Toshihiko Shiroishi
International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies   4 11-19   2012   [Refereed]
*Aono E, *Baba T, *Ara T, Nishi T, Nakamichi1 T, Inamoto E, Toyonaga H, Hasegawa M, Takai Y, Okumura Y, Baba M, Tomita M, Kato C, Oshima T, Nakasone K, Mori H.(*equal contributions)
Mol. Biosyst.   6 1216-1226   2010
Hara KY, Shimodate N, Ito M, Baba T, Mori H, Mori H.
Metab. Eng.   11(1) 1-7   2009
Hara KY, Shimodate N, Hirokawa Y, Ito M, Baba T, Mori H, Mori H.
FEMS Microbiol. Lett.   297(2) 217-224   2009
Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C, Nakayama S, Nakazaki N, Shimizu Y, Shinpo S, Takahashi C, Wada T, Yamada M, Ohmido N, Hayashi M, Fukui K, Baba T, Nakamichi T, Mori H, Tabata S.
DNA Res.   15(4) 227-239   2008

Conference Activities & Talks

An AI strategy for detecting HGT relies on nucleotide compositional features [Invited]
Takashi Abe, Yu Akazawa, Tomoya Baba, Toshimichi Ikemura
The 42nd Annual Meeting of the Molecular Biology Society of Japan   4 Dec 2019   
Structural properties of bacterial genomes in an Antarctic lake
Consortium of Biological Sciences 2017   8 Dec 2017   
What is “Horizontal Gene Transfer (HGT)”?
BABA Tomoya, ABE Takashi
Consortium of Biological Sciences 2017 Fourum   6 Dec 2017   
Genomic Evolutions of Polar Bacteria
Tomoya Baba, Takashi Abe, Atsushi Toyoda, Ryosuke Nakai, Takeshi Naganuma, Asao Fujiyama, Satoshi Imura, Hiroshi Kanda, Hideaki Motoyama, Hironori Niki
Interdisciplinary Session "Systematic Analysis for Global Environmental Change and Life on Earth", The Sixth Symposium on Polar Science   19 Nov 2015   
Biosphere of an Antarctic Lake as a Natural Laboratory of Biological Evolutions
Tomoya BABA, Takashi ABE, Atsushi TOYOD
The Fifth Symposium on Polar Science   3 Dec 2014   

Research Grants & Projects

Study of Bacterial Adaptability to Antarctic Environment
Grant-in-Aid for Scientific Research
Project Year: 2009 - 2011
Antarctic Bacteria have been adapted to the environment of low temperature, pure nutrient and UV irradiation. We attempted the research of their mechanisms for environmental adaptability and evolutions on genome level.
Genome Analysis of Antarctic Bacteria
Project Year: 2007 - 2010
The interaction between life and the surrounding environment should have great impact on the evolution and diversity of life. We are developing genome analysis technologies for single cell of microorganisms, which is involved in the ice core on th...
Metabolic Modeling in Escherichia coli
New Energy Technology Research and Development
Project Year: 2001 - 2007
Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental ...
Systematic Study of Controlling mechanisms for Cell Growth in Escherichia coli
Project Year: 2005 - 2006
Our single-gene deletion mutants of all nonessential genes in Escherichia coli K-12 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 effec...
Construction of Systematic Single-Gene Knockout Mutant Collection and Functional Analysis in Escherichia coli
JST Basic Research Programs (Core Research for Evolutional Science and Technology :CREST)
Project Year: 2001 - 2003
We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by ...