Rintaro Saito

Rintaro Saito

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Rintaro Saito

Rintaro Saito

Publications by authors named "Rintaro Saito"

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The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight.

Science 2019 04;364(6436)

Northwestern University, Evanston, IL, USA.

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http://dx.doi.org/10.1126/science.aau8650DOI Listing
April 2019

Radiographic fibrosis score predicts survival in systemic sclerosis-associated interstitial lung disease.

Respirology 2018 04 19;23(4):385-391. Epub 2017 Sep 19.

Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki, Japan.

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http://dx.doi.org/10.1111/resp.13175DOI Listing
April 2018

Distinct gene signatures predict insulin resistance in young mice with high fat diet-induced obesity.

Physiol Genomics 2018 03 8;50(3):144-157. Epub 2018 Jan 8.

Department of Pediatrics, University of California at San Diego , La Jolla, California.

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http://dx.doi.org/10.1152/physiolgenomics.00045.2017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5899230PMC
March 2018

Metabolomics and Gene Expression Analysis Reveal Down-regulation of the Citric Acid (TCA) Cycle in Non-diabetic CKD Patients.

EBioMedicine 2017 Dec 31;26:68-77. Epub 2017 Oct 31.

Kidney Research Institute, University of Washington, Seattle, WA, United States; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, United States.

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http://dx.doi.org/10.1016/j.ebiom.2017.10.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832558PMC
December 2017

A metabolite-GWAS (mGWAS) approach to unveil chronic kidney disease progression.

Kidney Int 2017 06;91(6):1274-1276

Center for Renal Translational Medicine, Division of Nephrology-Hypertension, Institute of Metabolomic Medicine, University of California-San Diego, La Jolla, California, USA; Division of Nephrology-Hypertension, VA San Diego Healthcare System, La Jolla, California, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00852538173022
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http://dx.doi.org/10.1016/j.kint.2017.03.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5989707PMC
June 2017

Metabolomics Reveals a Key Role for Fumarate in Mediating the Effects of NADPH Oxidase 4 in Diabetic Kidney Disease.

J Am Soc Nephrol 2016 Feb 22;27(2):466-81. Epub 2015 Jul 22.

Division of Nephrology-Hypertension, Institute of Metabolomic Medicine, Center for Renal Translational Medicine, University of California-San Diego, La Jolla, California; Division of Medical Genetics, Department of Medicine, University of California-San Diego, La Jolla, California; and Division of Nephrology-Hypertension, Veterans Affairs San Diego Healthcare System, La Jolla, California

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http://dx.doi.org/10.1681/ASN.2015030302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731129PMC
February 2016

Computational analysis of associations between alternative splicing and histone modifications.

FEBS Lett 2013 Mar 24;587(5):516-21. Epub 2013 Jan 24.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.

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http://dx.doi.org/10.1016/j.febslet.2013.01.032DOI Listing
March 2013

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

BMC Genomics 2011 Aug 17;12:416. Epub 2011 Aug 17.

Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.

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http://dx.doi.org/10.1186/1471-2164-12-416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170308PMC
August 2011

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

Gene 2011 May 19;476(1-2):10-4. Epub 2011 Feb 19.

Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.

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http://dx.doi.org/10.1016/j.gene.2011.02.004DOI Listing
May 2011

Integrative features of the yeast phosphoproteome and protein-protein interaction map.

PLoS Comput Biol 2011 Jan 27;7(1):e1001064. Epub 2011 Jan 27.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.

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http://dx.doi.org/10.1371/journal.pcbi.1001064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029238PMC
January 2011

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

Genomics 2010 Dec 22;96(6):333-41. Epub 2010 Aug 22.

Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan.

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http://linkinghub.elsevier.com/retrieve/pii/S088875431000182
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http://dx.doi.org/10.1016/j.ygeno.2010.08.007DOI Listing
December 2010

Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria.

EURASIP J Bioinform Syst Biol 2007 :61374

Institute for Advanced Biosciences, Keio University, Yamagata, Japan.

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http://dx.doi.org/10.1155/2007/61374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3171346PMC
June 2010

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

BMC Bioinformatics 2010 Jun 28;11:350. Epub 2010 Jun 28.

Institute for Advanced Biosciences, Keio University, 403-1, Daihoji, Tsuruoka, Yamagata 997-0017, Japan.

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http://dx.doi.org/10.1186/1471-2105-11-350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905371PMC
June 2010

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

BMC Bioinformatics 2010 May 7;11:232. Epub 2010 May 7.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.

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http://dx.doi.org/10.1186/1471-2105-11-232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875242PMC
May 2010

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

FEBS Lett 2010 Apr 3;584(8):1498-502. Epub 2010 Mar 3.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.

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http://dx.doi.org/10.1016/j.febslet.2010.02.067DOI Listing
April 2010

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

BMC Genomics 2009 Aug 22;10:392. Epub 2009 Aug 22.

Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center (BRC), RIKEN Tsukuba Institute, Ibaraki 305-0074, Japan.

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http://dx.doi.org/10.1186/1471-2164-10-392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741491PMC
August 2009

Measure of synonymous codon usage diversity among genes in bacteria.

BMC Bioinformatics 2009 Jun 1;10:167. Epub 2009 Jun 1.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.

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http://dx.doi.org/10.1186/1471-2105-10-167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697163PMC
June 2009

In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution.

Mol Cell Proteomics 2009 May 9;8(5):1061-71. Epub 2009 Jan 9.

Institute for Advanced Biosciences, Keio University, 403-1, Daihoji, Tsuruoka, Yamagata 997-0017, Japan.

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http://dx.doi.org/10.1074/mcp.M800466-MCP200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689765PMC
May 2009

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

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

Comparative expression analysis uncovers novel features of endogenous antisense transcription.

Hum Mol Genet 2008 Jun 18;17(11):1631-40. Epub 2008 Feb 18.

Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.

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http://dx.doi.org/10.1093/hmg/ddn051DOI Listing
June 2008

eXpanda: an integrated platform for network analysis and visualization.

In Silico Biol 2007 ;7(2):141-4

Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan.

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January 2008

Inferring rules of Escherichia coli translational efficiency using an artificial neural network.

Biosystems 2007 Sep-Oct;90(2):414-20. Epub 2006 Oct 26.

Institute for Advanced Biosciences, Keio University, Baba 14-1, Tsuruoka, Yamagata 997-0035, Japan.

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http://dx.doi.org/10.1016/j.biosystems.2006.10.005DOI Listing
November 2007

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

FEBS Lett 2007 Sep 3;581(22):4184-8. Epub 2007 Aug 3.

Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan.

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http://dx.doi.org/10.1016/j.febslet.2007.07.057DOI Listing
September 2007

Increasing confidence of protein-protein interactomes.

Genome Inform 2006 ;17(2):284-97

National University of Singapore, Graduate School of Computing, Singapore.

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June 2007

Comparative analysis of cis-encoded antisense RNAs in eukaryotes.

Gene 2007 May 13;392(1-2):134-41. Epub 2006 Dec 13.

Graduate School of Media and Governance, Bioinformatics Program, Keio University, Fujisawa, 252-8520, Japan.

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http://dx.doi.org/10.1016/j.gene.2006.12.005DOI Listing
May 2007

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

FEBS Lett 2007 Jan 18;581(2):253-8. Epub 2006 Dec 18.

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://doi.wiley.com/10.1016/j.febslet.2006.12.021
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http://dx.doi.org/10.1016/j.febslet.2006.12.021DOI Listing
January 2007

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

Gene 2006 Jun 17;375:80-6. Epub 2006 Apr 17.

Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa, 252-8520, Japan.

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http://dx.doi.org/10.1016/j.gene.2006.02.018DOI Listing
June 2006

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

Gene 2006 May 24;372:171-81. Epub 2006 Mar 24.

Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0035, Japan.

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http://dx.doi.org/10.1016/j.gene.2005.12.034DOI Listing
May 2006

Computational analysis of microRNA targets in Caenorhabditis elegans.

Gene 2006 Jan 13;365:2-10. Epub 2005 Dec 13.

Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.

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http://dx.doi.org/10.1016/j.gene.2005.09.035DOI Listing
January 2006

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

FEBS Lett 2005 Nov 2;579(28):6499-504. Epub 2005 Nov 2.

Institute for Advanced Biosciences, Keio University, Japan.

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http://dx.doi.org/10.1016/j.febslet.2005.10.032DOI Listing
November 2005

[Refinement of genome-wide data].

Tanpakushitsu Kakusan Koso 2004 Dec;49(17 Suppl):2882-8

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December 2004

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

J Mol Med (Berl) 2004 Jul 18;82(7):414-22. Epub 2004 May 18.

Department of Genetic Disease Research, Osaka City University Graduate School of Medicine, Asahi-machi 1-4-3 Abeno, 545-8585 Osaka, Japan.

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http://link.springer.com/content/pdf/10.1007/s00109-004-0550
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http://link.springer.com/10.1007/s00109-004-0550-3
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http://dx.doi.org/10.1007/s00109-004-0550-3DOI Listing
July 2004

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

Gene 2004 Jun;335:19-23

Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.

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http://dx.doi.org/10.1016/j.gene.2004.03.001DOI Listing
June 2004

Computational analysis of stop codon readthrough in D.melanogaster.

Bioinformatics 2003 Jul;19(11):1371-80

Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btg183DOI Listing
July 2003

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

Genome Res 2003 Jun;13(6B):1301-6

Graduate School of Media and Governance, Bioinformatics Program, Keio University, Fujisawa, Kanagawa 252-8520, Japan.

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http://dx.doi.org/10.1101/gr.1011603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403720PMC
June 2003

CDS annotation in full-length cDNA sequence.

Genome Res 2003 Jun;13(6B):1478-87

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.1060303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403693PMC
June 2003

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

Genome Res 2003 Jun;13(6B):1520-33

Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.1019903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403704PMC
June 2003

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

Genome Res 2003 Jun;13(6B):1534-41

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://www.genome.org/cgi/doi/10.1101/gr.956303
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http://dx.doi.org/10.1101/gr.956303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403706PMC
June 2003

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

Bioinformatics 2003 Apr;19(6):756-63

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Tsurumi-ku, Yokohama 230-0045, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btg070DOI Listing
April 2003

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

Biochem Biophys Res Commun 2003 Feb;301(3):633-40

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama, Japan.

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http://dx.doi.org/10.1016/s0006-291x(03)00013-5DOI Listing
February 2003

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

Nucleic Acids Res 2002 Mar;30(5):1163-8

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC101243PMC
http://dx.doi.org/10.1093/nar/30.5.1163DOI Listing
March 2002

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

Biochem Biophys Res Commun 2002 Jan;290(3):1108-13

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), 1-7-22 Suehiro-cho, Yokohama, Tsurumi-ku, 230-0045, Japan.

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http://dx.doi.org/10.1006/bbrc.2001.6315DOI Listing
January 2002