R. Saito

发表

Large-scale identification of protein-protein interaction of Escherichia coli K-12.

S. Kanaya, H. Mori, M. Tomita, 2006, Genome research.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

E. Birney, E. Lander, C. Bult, 2002, Nature.

Functional annotation of a full-length mouse cDNA collection

C. Bult, S. Batalov, Y. Matsuo, 2001, Nature.

Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.

M. Tomita, Y. Hayashizaki, D. Hume, 2003, Genome research.

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.

M. Fagiolini, T. Hensch, W. Pavan, 2003, Genome research.

Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model.

M. Tomita, R. Saito, A. Kanai, 2006, Gene.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Martin S. Taylor, Denis C. Bauer, Andrew M. Waterhouse, 2009, Nature Genetics.

Computational analysis of associations between alternative splicing and histone modifications

M. Tomita, R. Saito, T. Nozaki, 2013, FEBS letters.

Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice

J. Kawai, Piero Carninci, Y. Hayashizaki, 2003, Science.

Protein-protein interaction panel using mouse full-length cDNAs.

Y. Hayashizaki, H. Bono, Y. Okazaki, 2001, Genome research.

A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks

Masaru Tomita, Rintaro Saito, Shigeo Fujimori, 2010, PloS one.

Inferring higher functional information for RIKEN mouse full-length cDNA clones with FACTS.

Diego G. Silva, A. Konagaya, Harukazu Suzuki, 2003, Genome research.

Genome-wide analysis of expression modes and DNA methylation status at sense-antisense transcript loci in mouse.

Hajime Nakaoka, Rintaro Saito, Kuniya Abe, 2010, Genomics.

Comparative analysis of base correlations in 5' untranslated regions of various species.

Masaru Tomita, Rintaro Saito, M. Tomita, 2006, Gene.

In Silico Analysis of Phosphoproteome Data Suggests a Rich-get-richer Process of Phosphosite Accumulation over Evolution*S

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2009, Molecular & Cellular Proteomics.

Distribution Analysis of the Oligonucleotide around 5' Splice Sites in H. sapiens, M. musculus, D. melanogaster and A. thaliana pre-mRNAs

M. Tomita, Hitomi Itoh, T. Washio, 2002 .

Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes.

M. Tomita, J. Kawai, Piero Carninci, 2001, Gene.

On Negative Selection Against ATG Triplets Near Start Codons in Eukaryotic and Prokaryotic Genomes

Masaru Tomita, Rintaro Saito, M. Tomita, 1999, Journal of Molecular Evolution.

Tomita On Negative Selection Against ATG Triplets Near Start Codons in Archaebacterial Genomes

M. Tomita, R. Saito, 2000 .

Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation.

M. Tomita, R. Saito, 1999, Gene.

Protein Interaction Panel Using Mouse Full-Length cDNAs − Protein Material Supplemental

Y. Hayashizaki, H. Bono, Y. Okazaki, 2017 .

Global insights into protein complexes through integrated analysis of the reliable interactome and knockout lethality.

Y. Hayashizaki, Harukazu Suzuki, R. Saito, 2003, Biochemical and biophysical research communications.

T2BP, a novel TRAF2 binding protein, can activate NF-kappaB and AP-1 without TNF stimulation.

Y. Hayashizaki, Harukazu Suzuki, R. Saito, 2002, Biochemical and biophysical research communications.

Noise‐reduction filtering for accurate detection of replication termini in bacterial genomes

M. Tomita, R. Saito, K. Arakawa, 2007, FEBS letters.

Comparative analysis of cis-encoded antisense RNAs in eukaryotes.

M. Tomita, R. Saito, H. Kiyosawa, 2007, Gene.

Increasing confidence of protein-protein interactomes.

Mong-Li Lee, Limsoon Wong, See-Kiong Ng, 2006, Genome informatics. International Conference on Genome Informatics.

Construction of reliable protein-protein interaction networks with a new interaction generality measure

Yoshihide Hayashizaki, Rintaro Saito, Harukazu Suzuki, 2003, Bioinform..

Interaction generality, a measurement to assess the reliability of a protein-protein interaction.

Yoshihide Hayashizaki, Rintaro Saito, Y. Hayashizaki, 2002, Nucleic acids research.

A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene

Masaru Tomita, Atsushi Yoshiki, Rintaro Saito, 2004, Journal of Molecular Medicine.

Urinary Metabolome Analyses of Patients with Acute Kidney Injury Using Capillary Electrophoresis-Mass Spectrometry

M. Tomita, L. Natarajan, R. Saito, 2021, Metabolites.

Computational Analysis of Stop Codon Readthrough in D.melanogaster

Masaru Tomita, Rintaro Saito, Akio Kanai, 2003, Bioinform..

Instructions for use Title Protein-Protein Interaction Panel Using Mouse

Y. Hayashizaki, H. Bono, Y. Okazaki, 2017 .

Mouse Full-Length cDNA Encyclopedia Targeting a Complex Transcriptome: The Construction of the

M. Fagiolini, T. Hensch, W. Pavan, 2006 .

Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.

Masaru Tomita, Piero Carninci, Yoshihide Hayashizaki, 2002, Genome research.

Characteristic Sequence Pattern in the 5- to 20-bp Upstream Region of Primate Alu Elements

M. Tomita, R. Saito, Y. Toda, 2000, Journal of Molecular Evolution.

CDS annotation in full-length cDNA sequence.

Yoshihide Hayashizaki, Takeya Kasukawa, Rintaro Saito, 2003, Genome research.

Correlation Between Shine–Dalgarno Sequence Conservation and Codon Usage of Bacterial Genes

M. Tomita, Y. Osada, M. Tomita, 2001, Journal of Molecular Evolution.

Computational analysis of microRNA targets in Caenorhabditis elegans.

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2006, Gene.

Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map

Masaru Tomita, Naoyuki Sugiyama, Yasushi Ishihama, 2011, PLoS Comput. Biol..

Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data

Masaru Tomita, Yasushi Ishihama, Nozomu Yachie, 2010, BMC Bioinformatics.

Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes

N. Hiraiwa, R. Saito, H. Kiyosawa, 2009, BMC Genomics.

Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

Masaru Tomita, Rintaro Saito, Haruo Suzuki, 2007, EURASIP J. Bioinform. Syst. Biol..

Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2011, BMC Genomics.

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

Masaru Tomita, Jun Kawai, Piero Carninci, 2010, BMC Genomics.

A problem in multivariate analysis of codon usage data and a possible solution

Masaru Tomita, Rintaro Saito, M. Tomita, 2005, FEBS letters.

Measure of synonymous codon usage diversity among genes in bacteria

Masaru Tomita, Rintaro Saito, Haruo Suzuki, 2009, BMC Bioinformatics.

The 'weighted sum of relative entropy': a new index for synonymous codon usage bias.

Masaru Tomita, Rintaro Saito, M. Tomita, 2004, Gene.

Comparative expression analysis uncovers novel features of endogenous antisense transcription.

Masaru Tomita, Hajime Nakaoka, Rintaro Saito, 2008, Human molecular genetics.

Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes

M. Tomita, N. Ohkohchi, R. Saito, 2011, BMC Medical Genomics.

The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer.

Yoshihide Hayashizaki, Rintaro Saito, Christian Schönbach, 2003, Genome research.

On biased distribution of introns in various eukaryotes.

M. Tomita, Piero Carninci, Y. Hayashizaki, 2002, Gene.

Bioinformatic analysis of post‐transcriptional regulation by uORF in human and mouse

M. Tomita, R. Saito, Nozomu Yachie, 2007, FEBS letters.

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions

Hisashi Kashima, Masaru Tomita, Rintaro Saito, 2010, BMC Bioinformatics.

Analysis of Translation Initiation Sites in the Complete Genome of Mycoplasma genitalium Suggests That This Bacterium Uses Alternative Signal for Translation Initiation

M. Tomita, R. Saito, 1998 .

Comprehensive sequence analysis of translation termination sites in various eukaryotes.

M. Tomita, J. Kawai, Piero Carninci, 2002, Gene.

Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes

Masaru Tomita, Rintaro Saito, Y. Osada, 1999, Bioinform..

On Base-Pairing Potential Between 16 S rRNA and 5 ’ UTR in Archaebacterial Genomes

M. Tomita, R. Saito, Y. Osada, 2000 .

iDMET: network-based approach for integrating differential analysis of cancer metabolomics

M. Tomita, R. Saito, Hiroyuki Yamamoto, 2022, BMC Bioinformatics.

Quality Assessment of Untargeted Analytical Data in a Large-Scale Metabolomic Study

M. Tomita, R. Saito, M. Sugimoto, 2021, Journal of clinical medicine.

Interaction Generality, a Measurement to Assess the Reliability of a Protein-Protein Interaction

Yoshihide Hayashizaki, Rintaro Saito, Masaru Tomita, 2002 .

Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA.

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2011, Gene.

Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences

Masaru Tomita, Rintaro Saito, Noriyuki Kitagawa, 2010, FEBS letters.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Martin S. Taylor, Denis C. Bauer, Ariel S. Schwartz, 2009, Nature Genetics.

Heterogeneity in Synonymous Codon Usage among Genes of Diverse Bacterial Genomes

M. Tomita, R. Saito, Haruo Suzuki, 2003 .

Correlation Analysis between tRNA Composition and Codon Usage Using Diversity and Equitability Index

M. Tomita, R. Saito, K. Arakawa, 2002 .