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Author Details

Rintaro Saito
Institute for Advanced Biosciences, Keio University
1988
76
29
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36443658iDMET: network-based approach for integrating differential analysis of cancer metabolomics.BMC Bioinformatics2022
34677386Urinary Metabolome Analyses of Patients with Acute Kidney Injury Using Capillary Electrophoresis-Mass Spectrometry.Metabolites2021
33922230Quality Assessment of Untargeted Analytical Data in a Large-Scale Metabolomic Study.J Clin Med2021
32589682Identification of pathognomonic purine synthesis biomarkers by metabolomic profiling of adolescents with obesity and type 2 diabetes.PLoS One2020
30975860The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight.Science2019
29341863Distinct gene signatures predict insulin resistance in young mice with high fat diet-induced obesity.Physiol Genomics2018
30830355Urine metabolites are associated with glomerular lesions in type 2 diabetes.Metabolomics2018
28514688The E-Id Protein Axis Specifies Adaptive Lymphoid Cell Identity and Suppresses Thymic Innate Lymphoid Cell Development.Immunity2017
28501300A metabolite-GWAS (mGWAS) approach to unveil chronic kidney disease progression.Kidney Int2017
29128444Metabolomics and Gene Expression Analysis Reveal Down-regulation of the Citric Acid (TCA) Cycle in Non-diabetic CKD Patients.EBioMedicine2017
26203118Metabolomics Reveals a Key Role for Fumarate in Mediating the Effects of NADPH Oxidase 4 in Diabetic Kidney Disease.J Am Soc Nephrol2016
27777973Systems biology analysis reveals role of MDM2 in diabetic nephropathy.JCI Insight2016
25691468The E-Id protein axis modulates the activities of the PI3K-AKT-mTORC1-Hif1a and c-myc/p19Arf pathways to suppress innate variant TFH cell development, thymocyte expansion, and lymphomagenesis.Genes Dev2015
26103419Evolutionary trends and functional anatomy of the human expanded autophagy network.Autophagy2015
23353998Computational analysis of associations between alternative splicing and histone modifications.FEBS Lett2013
23949796Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease.J Am Soc Nephrol2013
24030101Quantitative proteomic and functional analysis of liver mitochondria from high fat diet (HFD) diabetic mice.Mol Cell Proteomics2013
23132118A travel guide to Cytoscape plugins.Nat Methods2012
21338662Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA.Gene2011
21846408Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification.BMC Genomics2011
21575255Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes.BMC Med Genomics2011
21298081Integrative features of the yeast phosphoproteome and protein-protein interaction map.PLoS Comput Biol2011
20409305Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns.BMC Genomics2010
20736060Genome-wide analysis of expression modes and DNA methylation status at sense-antisense transcript loci in mouse.Genomics2010
20459641Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data.BMC Bioinformatics2010
20584269Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions.BMC Bioinformatics2010
20206172Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences.FEBS Lett2010
20195357A comprehensive resource of interacting protein regions for refining human transcription factor networks.PLoS One2010
19136663In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution.Mol Cell Proteomics2009
19698135Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes.BMC Genomics2009
19377474The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.Nat Genet2009
19480720Measure of synonymous codon usage diversity among genes in bacteria.BMC Bioinformatics2009
18283053Comparative expression analysis uncovers novel features of endogenous antisense transcription.Hum Mol Genet2008
17250976Comparative analysis of cis-encoded antisense RNAs in eukaryotes.Gene2007
18350114Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria.EURASIP J Bioinform Syst Biol2007
17692847Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse.FEBS Lett2007
17688438eXpanda: an integrated platform for network analysis and visualization.In Silico Biol2007
17188685Noise-reduction filtering for accurate detection of replication termini in bacterial genomes.FEBS Lett2007
17150301Inferring rules of Escherichia coli translational efficiency using an artificial neural network.Biosystems2007
16356665Computational analysis of microRNA targets in Caenorhabditis elegans.Gene2006
17514831Increasing confidence of protein-protein interactomes.Genome Inform2006
16606699Large-scale identification of protein-protein interaction of Escherichia coli K-12.Genome Res2006
16618531Comparative analysis of base correlations in 5' untranslated regions of various species.Gene2006
16564143Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model.Gene2006
16289058A problem in multivariate analysis of codon usage data and a possible solution.FEBS Lett2005
15148580A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene.J Mol Med (Berl)2004
15669271[Refinement of genome-wide data].Tanpakushitsu Kakusan Koso2004
15194186The 'weighted sum of relative entropy': a new index for synonymous codon usage bias.Gene2004
12819125Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.Genome Res2003
12874049Computational analysis of stop codon readthrough in D.melanogaster.Bioinformatics2003
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Collaborators

Yoshihide Hayashizaki
Center for Integrative Medical Sciences
Co-authored papers 18
Harukazu Suzuki
RIKEN Center for Integrative Medical Sciences
Co-authored papers 13
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 10
Nozomu Yachie
The University of British Columbia
Co-authored papers 9
Jun Kawai
RIKEN Center for Integrative Medical Sciences
Co-authored papers 8
Yasushi Okazaki
Intractable Disease Research Center, Graduate School of Medicine, Juntendo University
Co-authored papers 7
Shinji Kondo
Co-authored papers 7
Kumar Sharma
Lady Hardinge Medical College and Associated SSK and KSC Hospitals
Co-authored papers 7
Kazuhiro Shibata
Co-authored papers 6
Hideaki Konno
Co-authored papers 6
Takahiro Arakawa
Tokyo University of Technology
Co-authored papers 6
Masayoshi Itoh
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Loki Natarajan
Herbert Wertheim School of Public Health, University of California
Co-authored papers 5
Shiro Fukuda
Graduate School of Medicine, Osaka University
Co-authored papers 5
Christian Schönbach
Co-authored papers 5
David A Hume
Mater Research Institute-UQ, Translational Research Institute
Co-authored papers 5
Hidemasa Bono
Hiroshima University
Co-authored papers 5
Manjula Darshi
Center for Renal Precision Medicine, University of Texas Health San Antonio
Co-authored papers 5
Masaaki Furuno
RIKEN Center for Integrative Medical Sciences
Co-authored papers 4
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 4
Takeya Kasukawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 4
Young-Hyun You
Kongju National University
Co-authored papers 3
Kazunori Waki
Co-authored papers 3
Toshiyuki Shiraki
Co-authored papers 3
John Quackenbush
Harvard T. H. Chan School of Public Health
Co-authored papers 3
Yasushi Ishihama
Graduate School of Pharmaceutical Sciences, Kyoto University
Co-authored papers 3
Takashi Gojobori
Co-authored papers 3
Daisuke Sasaki
Co-authored papers 3
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 3
Stefano Gustincich
Istituto Italiano di Tecnologia
Co-authored papers 3
Release 1.2