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Masaru Tomita

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Publications

TOP 3
Kosugi Shunichi; Hasebe Masako; Tomita Masaru; Yanagawa Hiroshi
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs.
Hirayama Akiyoshi; Kami Kenjiro; Sugimoto Masahiro; Sugawara Maki; Toki Naoko; Onozuka Hiroko; Kinoshita Taira; Saito Norio; Ochiai Atsushi; Tomita Masaru; Esumi Hiroyasu; Soga Tomoyoshi
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry.
Iwasaki Mio; Masuda Takeshi; Tomita Masaru; Ishihama Yasushi
Chemical cleavage-assisted tryptic digestion for membrane proteome analysis.

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All Publications

2009: Kosugi Shunichi; Hasebe Masako; Tomita Masaru; Yanagawa Hiroshi
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(25):10171-6.
2009: Hirayama Akiyoshi; Kami Kenjiro; Sugimoto Masahiro; Sugawara Maki; Toki Naoko; Onozuka Hiroko; Kinoshita Taira; Saito Norio; Ochiai Atsushi; Tomita Masaru; Esumi Hiroyasu; Soga Tomoyoshi
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry.
Cancer research 2009;69(11):4918-25.
2009: Iwasaki Mio; Masuda Takeshi; Tomita Masaru; Ishihama Yasushi
Chemical cleavage-assisted tryptic digestion for membrane proteome analysis.
Journal of proteome research 2009;8(6):3169-75.
2009: Yachie Nozomu; Saito Rintaro; Sugahara Junichi; Tomita Masaru; Ishihama Yasushi
In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution.
Molecular & cellular proteomics : MCP 2009;8(5):1061-71.
2009: Kanai Akio; Sato Asako; Fukuda Yoko; Okada Kiyoshi; Matsuda Takashi; Sakamoto Taiichi; Muto Yutaka; Yokoyama Shigeyuki; Kawai Gota; Tomita Masaru
Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus.
RNA (New York, N.Y.) 2009;15(3):420-31.
2009: Selvarajoo Kumar; Tomita Masaru; Tsuchiya Masa
Can complex cellular processes be governed by simple linear rules?
Journal of bioinformatics and computational biology 2009;7(1):243-68.
2009: Fujishima Kosuke; Sugahara Junichi; Kikuta Kaoru; Hirano Reiko; Sato Asako; Tomita Masaru; Kanai Akio
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(8):2683-7.
2009: Tsuchiya Daisuke; Shimizu Nobutaka; Tomita Masaru
Cooperativity of two active sites in bacterial homodimeric aconitases.
Biochemical and biophysical research communications 2009;379(2):485-8.
2009: Kosugi Shunichi; Hasebe Masako; Matsumura Nobutaka; Takashima Hideaki; Miyamoto-Sato Etsuko; Tomita Masaru; Yanagawa Hiroshi
Six classes of nuclear localization signals specific to different binding grooves of importin alpha.
The Journal of biological chemistry 2009;284(1):478-85.
2009: Kono Nobuaki; Arakawa Kazuharu; Ogawa Ryu; Kido Nobuhiro; Oshita Kazuki; Ikegami Keita; Tamaki Satoshi; Tomita Masaru
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
PloS one 2009;4(11):e7710.
2009: Arakawa Kazuharu; Oshita Kazuki; Tomita Masaru
A web server for interactive and zoomable Chaos Game Representation images.
Source code for biology and medicine 2009;4():6.
2009: Nakahigashi Kenji; Toya Yoshihiro; Ishii Nobuyoshi; Soga Tomoyoshi; Hasegawa Miki; Watanabe Hisami; Takai Yuki; Honma Masayuki; Mori Hirotada; Tomita Masaru
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.
Molecular systems biology 2009;5():306.
2009: Suzuki Haruo; Saito Rintaro; Tomita Masaru
Measure of synonymous codon usage diversity among genes in bacteria.
BMC bioinformatics 2009;10():167.
2009: Tsuchiya Masa; Piras Vincent; Choi Sangdun; Akira Shizuo; Tomita Masaru; Giuliani Alessandro; Selvarajoo Kumar
Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages.
PloS one 2009;4(3):e4905.
2009: Helmy Mohamed; Gohda Jin; Inoue Jun-Ichiro; Tomita Masaru; Tsuchiya Masa; Selvarajoo Kumar
Predicting novel features of toll-like receptor 3 signaling in macrophages.
PloS one 2009;4(3):e4661.
2009: Arakawa Kazuharu; Tamaki Satoshi; Kono Nobuaki; Kido Nobuhiro; Ikegami Keita; Ogawa Ryu; Tomita Masaru
Genome Projector: zoomable genome map with multiple views.
BMC bioinformatics 2009;10():31.
2008: Sugahara Junichi; Kikuta Kaoru; Fujishima Kosuke; Yachie Nozomu; Tomita Masaru; Kanai Akio
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales.
Molecular biology and evolution 2008;25(12):2709-16.
2008: Kosugi Shunichi; Hasebe Masako; Tomita Masaru; Yanagawa Hiroshi
Nuclear export signal consensus sequences defined using a localization-based yeast selection system.
Traffic (Copenhagen, Denmark) 2008;9(12):2053-62.
2008: Ohtani Naoto; Tomita Masaru; Itaya Mitsuhiro
Junction ribonuclease activity specified in RNases HII/2.
The FEBS journal 2008;275(21):5444-55.
2008: Tsuchiya Daisuke; Shimizu Nobutaka; Tomita Masaru
Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase.
Biochimica et biophysica acta 2008;1784(11):1847-56.
2008: Kyono Yutaka; Sugiyama Naoyuki; Imami Koshi; Tomita Masaru; Ishihama Yasushi
Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.
Journal of proteome research 2008;7(10):4585-93.
2008: Kosugi Shunichi; Hasebe Masako; Entani Tetsuyuki; Takayama Seiji; Tomita Masaru; Yanagawa Hiroshi
Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling.
Chemistry & biology 2008;15(9):940-9.
2008: Ohtani Naoto; Sato Mitsuru; Tomita Masaru; Itaya Mitsuhiro
Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168.
Bioscience, biotechnology, and biochemistry 2008;72(9):2472-5.
2008: Shinoda Kosaku; Tomita Masaru; Ishihama Yasushi
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments.
Bioinformatics (Oxford, England) 2008;24(14):1590-5.
2008: Yachie Nozomu; Ohashi Yoshiaki; Tomita Masaru
Stabilizing synthetic data in the DNA of living organisms.
Systems and synthetic biology 2008;2(1-2):19-25.
2008: Ohtani Naoto; Tomita Masaru; Itaya Mitsuhiro
Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex.
The Biochemical journal 2008;412(3):517-26.
2008: Okada Yuki; Tashiro Chiaki; Numata Koji; Watanabe Kazufumi; Nakaoka Hajime; Yamamoto Naoyuki; Okubo Kazue; Ikeda Rieko; Saito Rintaro; Kanai Akio; Abe Kuniya; Tomita Masaru; Kiyosawa Hidenori
Comparative expression analysis uncovers novel features of endogenous antisense transcription.
Human molecular genetics 2008;17(11):1631-40.
2008: Krishnan Arun; Zbilut Joseph P; Tomita Masaru; Giuliani Alessandro
Proteins as networks: usefulness of graph theory in protein science.
Current protein & peptide science 2008;9(1):28-38.
2008: Shinoda Kosaku; Sugimoto Masahiro; Tomita Masaru; Ishihama Yasushi
Informatics for peptide retention properties in proteomic LC-MS.
Proteomics 2008;8(4):787-98.
2008: Masuda Takeshi; Tomita Masaru; Ishihama Yasushi
Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis.
Journal of proteome research 2008;7(2):731-40.
2008: Imami Koshi; Sugiyama Naoyuki; Kyono Yutaka; Tomita Masaru; Ishihama Yasushi
Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column.
Analytical sciences : the international journal of the Japan Society for Analytical Chemistry 2008;24(1):161-6.
2008: Ishii Kyota; Nakamura Seira; Morohashi Mineo; Sugimoto Masahiro; Ohashi Yoshiaki; Kikuchi Shinichi; Tomita Masaru
Comparison of metabolite production capability indices generated by network analysis methods.
Bio Systems 2008;91(1):166-70.
2008: Kuroki Azusa; Toda Tsutomu; Matsui Kuniko; Uotsu-Tomita Rie; Tomita Masaru; Itaya Mitsuhiro
Reshuffling of the Bacillus subtilis 168 genome by multifold inversion.
Journal of biochemistry 2008;143(1):97-105.
2008: Kratz Anton; Tomita Masaru; Krishnan Arun
GeNESiS: gene network evolution simulation software.
BMC bioinformatics 2008;9():541.
2008: Selvarajoo Kumar; Takada Yasunari; Gohda Jin; Helmy Mohamed; Akira Shizuo; Tomita Masaru; Tsuchiya Masa; Inoue Jun-Ichiro; Matsuo Koichi
Signaling flux redistribution at toll-like receptor pathway junctions.
PloS one 2008;3(10):e3430.
2008: Sato Shigeru; Arita Masanori; Soga Tomoyoshi; Nishioka Takaaki; Tomita Masaru
Time-resolved metabolomics reveals metabolic modulation in rice foliage.
BMC systems biology 2008;2():51.
2008: Krishnan Arun; Giuliani Alessandro; Zbilut Joseph P; Tomita Masaru
Implications from a network-based topological analysis of ubiquitin unfolding simulations.
PloS one 2008;3(5):e2149.
2008: Sugiyama Naoyuki; Nakagami Hirofumi; Mochida Keiichi; Daudi Arsalan; Tomita Masaru; Shirasu Ken; Ishihama Yasushi
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis.
Molecular systems biology 2008;4():193.
2008: Laborde Thomas; Tomita Masaru; Krishnan Arun
GANDivAWeb: a web server for detecting early folding units ("foldons") from protein 3D structures.
BMC structural biology 2008;8():15.
2008: Fujishima Kosuke; Sugahara Junichi; Tomita Masaru; Kanai Akio
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.
PloS one 2008;3(2):e1622.
2008: Matsubara Yoshiya; Kikuchi Shinichi; Sugimoto Masahiro; Oka Kotaro; Tomita Masaru
Algebraic method for the analysis of signaling crosstalk.
Artificial life 2008;14(1):81-94.
2008: Ogawa Yukino; Arakawa Kazuharu; Kaizu Kazunari; Miyoshi Fumihiko; Nakayama Yoichi; Tomita Masaru
Comparative study of circadian oscillatory network models of Drosophila.
Artificial life 2008;14(1):29-48.
2008: Ohno Hiroshi; Naito Yasuhiro; Nakajima Hiromu; Tomita Masaru
Construction of a biological tissue model based on a single-cell model: a computer simulation of metabolic heterogeneity in the liver lobule.
Artificial life 2008;14(1):3-28.
2007: Soma Akiko; Onodera Akinori; Sugahara Junichi; Kanai Akio; Yachie Nozomu; Tomita Masaru; Kawamura Fujio; Sekine Yasuhiko
Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae.
Science (New York, N.Y.) 2007;318(5849):450-3.
2007: Matsuzaki Yuri; Kikuchi Shinichi; Tomita Masaru
Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis.
Artificial intelligence in medicine 2007;41(2):145-50.
2007: Krishnan Arun; Giuliani Alessandro; Zbilut Joseph P; Tomita Masaru
Network scaling invariants help to elucidate basic topological principles of proteins.
Journal of proteome research 2007;6(10):3924-34.
2007: Watanabe Yuka; Kishi Atsuko; Yachie Nozomu; Kanai Akio; Tomita Masaru
Computational analysis of microRNA-mediated antiviral defense in humans.
FEBS letters 2007;581(24):4603-10.
2007: Monton Maria Rowena N; Tomita Masaru; Soga Tomoyoshi; Ishihama Yasushi
Polymer entrapment in polymerized silicate for preparing highly stable capillary coatings for CE and CE-MS.
Analytical chemistry 2007;79(20):7838-44.
2007: Matsui Motomu; Yachie Nozomu; Okada Yuki; Saito Rintaro; Tomita Masaru
Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse.
FEBS letters 2007;581(22):4184-8.
2007: Kuroki Azusa; Ohtani Naoto; Tsuge Kenji; Tomita Masaru; Itaya Mitsuhiro
Conjugational transfer system to shuttle giant DNA cloned by Bacillus subtilis genome (BGM) vector.
Gene 2007;399(1):72-80.
2007: Mori Koya; Saito Rintaro; Kikuchi Shinichi; Tomita Masaru
Inferring rules of Escherichia coli translational efficiency using an artificial neural network.
Bio Systems 2007;90(2):414-20.
2007: Soga Tomoyoshi; Ishikawa Takamasa; Igarashi Saori; Sugawara Kaori; Kakazu Yuji; Tomita Masaru
Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique.
Journal of chromatography. A 2007;1159(1-2):125-33.
2007: Toya Yoshihiro; Ishii Nobuyoshi; Hirasawa Takashi; Naba Miki; Hirai Kenta; Sugawara Kaori; Igarashi Saori; Shimizu Kazuyuki; Tomita Masaru; Soga Tomoyoshi
Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis.
Journal of chromatography. A 2007;1159(1-2):134-41.
2007: Fujishima Kosuke; Komasa Mizuki; Kitamura Sayaka; Suzuki Haruo; Tomita Masaru; Kanai Akio
Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus.
DNA research : an international journal for rapid publication of reports on genes and genomes 2007;14(3):91-102.
2007: Tsuchiya Masa; Wong Sum T; Yeo Zhen X; Colosimo Alfredo; Palumbo Maria C; Farina Lorenzo; Crescenzi Marco; Mazzola Alessia; Negri Rodolfo; Bianchi Michele M; Selvarajoo Kumar; Tomita Masaru; Giuliani Alessandro
Gene expression waves. Cell cycle independent collective dynamics in cultured cells.
The FEBS journal 2007;274(11):2878-86.
2007: Sugiyama Naoyuki; Masuda Takeshi; Shinoda Kosaku; Nakamura Akihiro; Tomita Masaru; Ishihama Yasushi
Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.
Molecular & cellular proteomics : MCP 2007;6(6):1103-9.
2007: Sugahara Junichi; Yachie Nozomu; Arakawa Kazuharu; Tomita Masaru
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.
RNA (New York, N.Y.) 2007;13(5):671-81.
2007: Arakawa Kazuharu; Uno Reina; Nakayama Yoichi; Tomita Masaru
Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli.
Gene 2007;392(1-2):239-46.
2007: Numata Koji; Okada Yuki; Saito Rintaro; Kiyosawa Hidenori; Kanai Akio; Tomita Masaru
Comparative analysis of cis-encoded antisense RNAs in eukaryotes.
Gene 2007;392(1-2):134-41.
2007: Ishii Nobuyoshi; Nakahigashi Kenji; Baba Tomoya; Robert Martin; Soga Tomoyoshi; Kanai Akio; Hirasawa Takashi; Naba Miki; Hirai Kenta; Hoque Aminul; Ho Pei Yee; Kakazu Yuji; Sugawara Kaori; Igarashi Saori; Harada Satoshi; Masuda Takeshi; Sugiyama Naoyuki; Togashi Takashi; Hasegawa Miki; Takai Yuki; Yugi Katsuyuki; Arakawa Kazuharu; Iwata Nayuta; Toya Yoshihiro; Nakayama Yoichi; Nishioka Takaaki; Shimizu Kazuyuki; Mori Hirotada; Tomita Masaru
Multiple high-throughput analyses monitor the response of E. coli to perturbations.
Science (New York, N.Y.) 2007;316(5824):593-7.
2007: Kinoshita Ayako; Tsukada Kosuke; Soga Tomoyoshi; Hishiki Takako; Ueno Yuki; Nakayama Yoichi; Tomita Masaru; Suematsu Makoto
Roles of hemoglobin Allostery in hypoxia-induced metabolic alterations in erythrocytes: simulation and its verification by metabolome analysis.
The Journal of biological chemistry 2007;282(14):10731-41.
2007: Hu Bin; Tomita Masaru
The Hsp70 chaperone system maintains high concentrations of active proteins and suppresses ATP consumption during heat shock.
Systems and synthetic biology 2007;1(1):47-58.
2007: Itoh Hitomi; Naito Yasuhiro; Tomita Masaru
Simulation of developmental changes in action potentials with ventricular cell models.
Systems and synthetic biology 2007;1(1):11-23.
2007: Kinoshita Ayako; Nakayama Yoichi; Kitayama Tomoya; Tomita Masaru
Simulation study of methemoglobin reduction in erythrocytes. Differential contributions of two pathways to tolerance to oxidative stress.
The FEBS journal 2007;274(6):1449-58.
2007: Yachie Nozomu; Sekiyama Kazuhide; Sugahara Junichi; Ohashi Yoshiaki; Tomita Masaru
Alignment-based approach for durable data storage into living organisms.
Biotechnology progress 2007;23(2):501-5.
2007: Tamaki Satoshi; Arakawa Kazuharu; Kono Nobuaki; Tomita Masaru
Restauro-G: a rapid genome re-annotation system for comparative genomics.
Genomics, proteomics & bioinformatics / Beijing Genomics Institute 2007;5(1):53-8.
2007: Ishii Nobuyoshi; Suga Yoshihiro; Hagiya Akiko; Watanabe Hisami; Mori Hirotada; Yoshino Masataka; Tomita Masaru
Dynamic simulation of an in vitro multi-enzyme system.
FEBS letters 2007;581(3):413-20.
2007: Miyoshi Fumihiko; Nakayama Yoichi; Kaizu Kazunari; Iwasaki Hideo; Tomita Masaru
A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria.
Journal of biological rhythms 2007;22(1):69-80.
2007: Arakawa Kazuharu; Saito Rintaro; Tomita Masaru
Noise-reduction filtering for accurate detection of replication termini in bacterial genomes.
FEBS letters 2007;581(2):253-8.
2007: Arakawa Kazuharu; Tomita Masaru
The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection.
Evolutionary bioinformatics online 2007;3():159-68.
2007: Arakawa Kazuharu; Tomita Masaru
Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes.
Evolutionary bioinformatics online 2007;3():279-86.
2007: Suzuki Haruo; Saito Rintaro; Tomita Masaru
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria.
EURASIP journal on bioinformatics & systems biology 2007;():61374.
2007: Hashimoto Masahiko; Ishihama Yasushi; Tomita Masaru; Soga Tomoyoshi
Microelectrospray interface with coaxial sheath flow for high-resolution capillary electrophoresis/mass spectrometry separation.
Rapid communications in mass spectrometry : RCM 2007;21(22):3579-84.
2007: Watanabe Yuka; Tomita Masaru; Kanai Akio
Computational methods for microRNA target prediction.
Methods in enzymology 2007;427():65-86.
2007: Yeo Zhen Xuan; Wong Sum Thai; Arjunan Satya Nanda Vel; Piras Vincent; Tomita Masaru; Selvarajoo Kumar; Giuliani Alessandro; Tsuchiya Masa
Sequential logic model deciphers dynamic transcriptional control of gene expressions.
PloS one 2007;2(1):e776.
2007: Negishi Yoshiteru; Nakamura Hiroyuki; Yachie Nozomu; Saito Rintaro; Tomita Masaru
eXpanda: an integrated platform for network analysis and visualization.
In silico biology 2007;7(2):141-4.
2007: Kochiwa Hiromi; Tomita Masaru; Kanai Akio
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes.
BMC evolutionary biology 2007;7():128.
2007: Krishnan Arun; Giuliani Alessandro; Tomita Masaru
Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity.
PloS one 2007;2(6):e562.
2007: Ishii Nobuyoshi; Nakayama Yoichi; Tomita Masaru
Distinguishing enzymes using metabolome data for the hybrid dynamic/static method.
Theoretical biology & medical modelling 2007;4():19.
2007: Baran Richard; Robert Martin; Suematsu Makoto; Soga Tomoyoshi; Tomita Masaru
Visualization of three-way comparisons of omics data.
BMC bioinformatics 2007;8():72.
2006: Yachie Nozomu; Arakawa Kazuharu; Tomita Masaru
On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli.
FEBS letters 2006;580(30):6909-14.
2006: Uno Reina; Nakayama Yoichi; Tomita Masaru
Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12.
Gene 2006;380(1):30-7.
2006: Saito Natsumi; Robert Martin; Kitamura Sayaka; Baran Richard; Soga Tomoyoshi; Mori Hirotada; Nishioka Takaaki; Tomita Masaru
Metabolomics approach for enzyme discovery.
Journal of proteome research 2006;5(8):1979-87.
2006: Hu Bin; Mayer Matthias P; Tomita Masaru
Modeling Hsp70-mediated protein folding.
Biophysical journal 2006;91(2):496-507.
2006: Osada Yuko; Saito Rintaro; Tomita Masaru
Comparative analysis of base correlations in 5' untranslated regions of various species.
Gene 2006;375():80-6.
2006: Soga Tomoyoshi; Baran Richard; Suematsu Makoto; Ueno Yuki; Ikeda Satsuki; Sakurakawa Tadayuki; Kakazu Yuji; Ishikawa Takamasa; Robert Martin; Nishioka Takaaki; Tomita Masaru
Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption.
The Journal of biological chemistry 2006;281(24):16768-76.
2006: Yachie Nozomu; Numata Koji; Saito Rintaro; Kanai Akio; Tomita Masaru
Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model.
Gene 2006;372():171-81.
2006: Kochiwa Hiromi; Itaya Mitsuhiro; Tomita Masaru; Kanai Akio
Stage-specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements.
The FEBS journal 2006;273(2):420-9.
2006: Watanabe Yuka; Yachie Nozomu; Numata Koji; Saito Rintaro; Kanai Akio; Tomita Masaru
Computational analysis of microRNA targets in Caenorhabditis elegans.
Gene 2006;365():2-10.
2006: Kanai Akio; Sato Asako; Imoto Jun; Tomita Masaru
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein.
The Biochemical journal 2006;393(Pt 1):373-9.
2006: Kono Nobuaki; Arakawa Kazuharu; Tomita Masaru
MEGU: pathway mapping web-service based on KEGG and SVG.
In silico biology 2006;6(6):621-5.
2006: Sugahara Junichi; Yachie Nozomu; Sekine Yasuhiko; Soma Akiko; Matsui Motomu; Tomita Masaru; Kanai Akio
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.
In silico biology 2006;6(5):411-8.
2006: Baran Richard; Kochi Hayataro; Saito Natsumi; Suematsu Makoto; Soga Tomoyoshi; Nishioka Takaaki; Robert Martin; Tomita Masaru
MathDAMP: a package for differential analysis of metabolite profiles.
BMC bioinformatics 2006;7():530.
2006: Kitayama Tomoya; Kinoshita Ayako; Sugimoto Masahiro; Nakayama Yoichi; Tomita Masaru
A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles.
Theoretical biology & medical modelling 2006;3():24.
2006: Arakawa Kazuharu; Nakayama Yoichi; Tomita Masaru
GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness.
In silico biology 2006;6(1-2):49-60.
2006: Baba Tomoya; Ara Takeshi; Hasegawa Miki; Takai Yuki; Okumura Yoshiko; Baba Miki; Datsenko Kirill A; Tomita Masaru; Wanner Barry L; Mori Hirotada
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Molecular systems biology 2006;2():2006.0008.
2006: Matsubara Yoshiya; Kikuchi Shinichi; Sugimoto Masahiro; Tomita Masaru
Parameter estimation for stiff equations of biosystems using radial basis function networks.
BMC bioinformatics 2006;7():230.
2006: Arakawa Kazuharu; Yamada Yohei; Shinoda Kosaku; Nakayama Yoichi; Tomita Masaru
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.
BMC bioinformatics 2006;7():168.
2006: Ishii Kyota; Washio Takanori; Uechi Tamayo; Yoshihama Maki; Kenmochi Naoya; Tomita Masaru
Characteristics and clustering of human ribosomal protein genes.
BMC genomics 2006;7():37.
2005: Suzuki Haruo; Saito Rintaro; Tomita Masaru
A problem in multivariate analysis of codon usage data and a possible solution.
FEBS letters 2005;579(28):6499-504.
2005: Arakawa Kazuharu; Suzuki Haruo; Fujishima Kosuke; Fujimoto Kenji; Ueda Sho; Matsui Motomu; Tomita Masaru
A comprehensive software suite for the analysis of cDNAs.
Genomics, proteomics & bioinformatics / Beijing Genomics Institute 2005;3(3):179-88.
2005: Arita Masanori; Robert Martin; Tomita Masaru
All systems go: launching cell simulation fueled by integrated experimental biology data.
Current opinion in biotechnology 2005;16(3):344-9.
2005: Ohtani Naoto; Saito Natsumi; Tomita Masaru; Itaya Mitsuhiro; Itoh Aya
The SCO2299 gene from Streptomyces coelicolor A3(2) encodes a bifunctional enzyme consisting of an RNase H domain and an acid phosphatase domain.
The FEBS journal 2005;272(11):2828-37.
2005: Sugimoto Masahiro; Kikuchi Shinichi; Tomita Masaru
Reverse engineering of biochemical equations from time-course data by means of genetic programming.
Bio Systems 2005;80(2):155-64.
2005: Kitagawa Noriyuki; Washio Takanori; Kosugi Shunichi; Yamashita Tomoya; Higashi Kenji; Yanagawa Hiroshi; Higo Kenichi; Satoh Koji; Ohtomo Yasuhiro; Sunako Tomomi; Murakami Kazuo; Matsubara Kenichi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Kikuchi Shoshi; Tomita Masaru
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
Bioinformatics (Oxford, England) 2005;21(9):1758-63.
2005: Takahashi Kouichi; Arjunan Satya Nanda Vel; Tomita Masaru
Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.
FEBS letters 2005;579(8):1783-8.
2005: Ohashi Yoshiaki; Yamashiro Akiko; Washio Takanori; Ishii Nobuyoshi; Ohshima Hideyuki; Michishita Tetsuko; Tomita Masaru; Itaya Mitsuhiro
In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations.
Gene 2005;347(1):11-9.
2005: Sugimoto Masahiro; Kikuchi Shinichi; Arita Masanori; Soga Tomoyoshi; Nishioka Takaaki; Tomita Masaru
Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks.
Analytical chemistry 2005;77(1):78-84.
2005: Yugi Katsuyuki; Nakayama Yoichi; Kojima Shigen; Kitayama Tomoya; Tomita Masaru
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks.
BMC bioinformatics 2005;6():299.
2005: Arakawa Kazuharu; Kono Nobuaki; Yamada Yohei; Mori Hirotada; Tomita Masaru
KEGG-based pathway visualization tool for complex omics data.
In silico biology 2005;5(4):419-23.
2005: Yugi Katsuyuki; Nakayama Yoichi; Kinoshita Ayako; Tomita Masaru
Hybrid dynamic/static method for large-scale simulation of metabolism.
Theoretical biology & medical modelling 2005;2():42.
2005: Nakayama Yoichi; Kinoshita Ayako; Tomita Masaru
Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition.
Theoretical biology & medical modelling 2005;2():18.
2005: Fujimori Shigeo; Washio Takanori; Tomita Masaru
GC-compositional strand bias around transcription start sites in plants and fungi.
BMC genomics 2005;6(1):26.
2004: Qiu Dongru; Mao Likai; Kikuchi Shinichi; Tomita Masaru
Sustained MAPK activation is dependent on continual NGF receptor regeneration.
Development, growth & differentiation 2004;46(5):393-403.
2004: Sato Shigeru; Soga Tomoyoshi; Nishioka Takaaki; Tomita Masaru
Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection.
The Plant journal : for cell and molecular biology 2004;40(1):151-63.
2004: Ishii Nobuyoshi; Robert Martin; Nakayama Yoichi; Kanai Akio; Tomita Masaru
Toward large-scale modeling of the microbial cell for computer simulation.
Journal of biotechnology 2004;113(1-3):281-94.
2004: Ohtani Naoto; Yanagawa Hiroshi; Tomita Masaru; Itaya Mitsuhiro
Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction.
The Biochemical journal 2004;381(Pt 3):795-802.
2004: Itoh Aya; Ohashi Yoshiaki; Soga Tomoyoshi; Mori Hirotada; Nishioka Takaaki; Tomita Masaru
Application of capillary electrophoresis-mass spectrometry to synthetic in vitro glycolysis studies.
Electrophoresis 2004;25(13):1996-2002.
2004: Soga Tomoyoshi; Kakazu Yuji; Robert Martin; Tomita Masaru; Nishioka Takaaki
Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry.
Electrophoresis 2004;25(13):1964-72.
2004: Itoh Hitomi; Washio Takanori; Tomita Masaru
Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes.
RNA (New York, N.Y.) 2004;10(7):1005-18.
2004: Yugi Katsuyuki; Tomita Masaru
A general computational model of mitochondrial metabolism in a whole organelle scale.
Bioinformatics (Oxford, England) 2004;20(11):1795-6.
2004: Kitamura-Abe Sumie; Itoh Hitomi; Washio Takanori; Tsutsumi Akihiro; Tomita Masaru
Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs.
Journal of bioinformatics and computational biology 2004;2(2):309-31.
2004: Suzuki Haruo; Saito Rintaro; Tomita Masaru
The 'weighted sum of relative entropy': a new index for synonymous codon usage bias.
Gene 2004;335():19-23.
2004: Takahashi Kouichi; Kaizu Kazunari; Hu Bin; Tomita Masaru
A multi-algorithm, multi-timescale method for cell simulation.
Bioinformatics (Oxford, England) 2004;20(4):538-46.
2004: Ohtani Naoto; Yanagawa Hiroshi; Tomita Masaru; Itaya Mitsuhiro
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7.
Nucleic acids research 2004;32(19):5809-19.
2003: Fukuda Yoko; Nakayama Yoichi; Tomita Masaru
On dynamics of overlapping genes in bacterial genomes.
Gene 2003;323():181-7.
2003: Kikuchi Shinichi; Fujimoto Kenji; Kitagawa Noriyuki; Fuchikawa Taro; Abe Michiko; Oka Kotaro; Takei Kohtaro; Tomita Masaru
Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A.
Neural networks : the official journal of the International Neural Network Society 2003;16(9):1389-98.
2003: Fujimori Shigeo; Washio Takanori; Higo Kenichi; Ohtomo Yasuhiro; Murakami Kazuo; Matsubara Kenichi; Kawai Jun; Carninci Piero; Hayashizaki Yoshihide; Kikuchi Shoshi; Tomita Masaru
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription.
FEBS letters 2003;554(1-2):17-22.
2003: Takahashi K; Ishikawa N; Sadamoto Y; Sasamoto H; Ohta S; Shiozawa A; Miyoshi F; Naito Y; Nakayama Y; Tomita M
E-Cell 2: multi-platform E-Cell simulation system.
Bioinformatics (Oxford, England) 2003;19(13):1727-9.
2003: Soga Tomoyoshi; Ohashi Yoshiaki; Ueno Yuki; Naraoka Hisako; Tomita Masaru; Nishioka Takaaki
Quantitative metabolome analysis using capillary electrophoresis mass spectrometry.
Journal of proteome research 2003;2(5):488-94.
2003: Sato Asako; Kanai Akio; Itaya Mitsuhiro; Tomita Masaru
Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus.
Biochemical and biophysical research communications 2003;309(1):247-52.
2003: Sato Misaki; Umeki Hitomi; Saito Rintaro; Kanai Akio; Tomita Masaru
Computational analysis of stop codon readthrough in D.melanogaster.
Bioinformatics (Oxford, England) 2003;19(11):1371-80.
2003: Numata Koji; Kanai Akio; Saito Rintaro; Kondo Shinji; Adachi Jun; Wilming Laurens G; Hume David A; Hayashizaki Yoshihide; Tomita Masaru;
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.
Genome research 2003;13(6B):1301-6.
2003: Miyoshi Fumihiko; Nakayama Yoichi; Tomita Masaru
[E-Cell simulation system and its application to the modeling of circadian rhythm]
Seikagaku. The Journal of Japanese Biochemical Society 2003;75(1):5-16.
2003: Arakawa K; Mori K; Ikeda K; Matsuzaki T; Kobayashi Y; Tomita M
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining.
Bioinformatics (Oxford, England) 2003;19(2):305-6.
2002: Soga Tomoyoshi; Ueno Yuki; Naraoka Hisako; Matsuda Keiko; Tomita Masaru; Nishioka Takaaki
Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions.
Analytical chemistry 2002;74(24):6224-9.
2002: Sakurai A; Fujimori S; Kochiwa H; Kitamura-Abe S; Washio T; Saito R; Carninci P; Hayashizaki Y; Tomita M
On biased distribution of introns in various eukaryotes.
Gene 2002;300(1-2):89-95.
2002: Ozawa Y; Hanaoka S; Saito R; Washio T; Nakano S; Shinagawa A; Itoh M; Shibata K; Carninci P; Konno H; Kawai J; Hayashizaki Y; Tomita M
Comprehensive sequence analysis of translation termination sites in various eukaryotes.
Gene 2002;300(1-2):79-87.
2002: Kochiwa Hiromi; Suzuki Ryosuke; Washio Takanori; Saito Rintaro; Bono Hidemasa; Carninci Piero; Okazaki Yasushi; Miki Rika; Hayashizaki Yoshihide; Tomita Masaru;
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.
Genome research 2002;12(8):1286-93.
2002: Soga Tomoyoshi; Ueno Yuki; Naraoka Hisako; Ohashi Yoshiaki; Tomita Masaru; Nishioka Takaaki
Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry.
Analytical chemistry 2002;74(10):2233-9.
2001: Ohno H; Sakai H; Washio T; Tomita M
Preferential usage of some minor codons in bacteria.
Gene 2001;276(1-2):107-15.
2001: Sakai H; Washio T; Saito R; Shinagawa A; Itoh M; Shibata K; Carninci P; Konno H; Kawai J; Hayashizaki Y; Tomita M
Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.
Gene 2001;276(1-2):101-5.
2001: Tomita M
Whole-cell simulation: a grand challenge of the 21st century.
Trends in biotechnology 2001;19(6):205-10.
2001: Sakai H; Imamura C; Osada Y; Saito R; Washio T; Tomita M
Correlation between Shine--Dalgarno sequence conservation and codon usage of bacterial genes.
Journal of molecular evolution 2001;52(2):164-70.
2000: Uno R; Nakayama Y; Arakawa K; Tomita M
The orientation bias of Chi sequences is a general tendency of G-rich oligomers.
Gene 2000;259(1-2):207-15.
2000: Toda Y; Saito R; Tomita M
Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements.
Journal of molecular evolution 2000;50(3):232-7.
2000: Goto M; Washio T; Tomita M
Causal analysis of CpG suppression in the Mycoplasma genome.
Microbial & comparative genomics 2000;5(1):51-8.
1999: Saito R; Tomita M
Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation.
Gene 1999;238(1):79-83.
1999: Tomita M; Wada M; Kawashima Y
ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes.
Journal of molecular evolution 1999;49(2):182-92.
1999: Osada Y; Saito R; Tomita M
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes.
Bioinformatics (Oxford, England) 1999;15(7-8):578-81.
1999: Toda Y; Saito R; Tomita M
Sequence patterns observed in 5' flanking regions of primate Alu elements.
Annals of the New York Academy of Sciences 1999;870():369-74.
1999: Fukuda Y; Washio T; Tomita M
Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae.
Nucleic acids research 1999;27(8):1847-53.
1999: Saito R; Tomita M
On negative selection against ATG triplets near start codons in eukaryotic and prokaryotic genomes.
Journal of molecular evolution 1999;48(2):213-7.
1999: Tomita M; Hashimoto K; Takahashi K; Shimizu T S; Matsuzaki Y; Miyoshi F; Saito K; Tanida S; Yugi K; Venter J C; Hutchison C A
E-CELL: software environment for whole-cell simulation.
Bioinformatics (Oxford, England) 1999;15(1):72-84.
1998: Washio T; Sasayama J; Tomita M
Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination.
Nucleic acids research 1998;26(23):5456-63.
1997: Shimizu T S; Takahashi K; Tomita M
CpG distribution patterns in methylated and non-methylated species.
Gene 1997;205(1-2):103-7.

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