Kengo Kinoshita

Kengo Kinoshita

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Kengo Kinoshita

Publications by authors named "Kengo Kinoshita"

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Identification of genetic alterations in extramammary Paget disease using whole exome analysis.

J Dermatol Sci 2019 Apr 11;94(1):229-235. Epub 2019 Apr 11.

Department of Dermatology, Shinshu University School of Medicine, Asahi 3-1-1, Matsumoto, 390-8621 Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S09231811193007
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http://dx.doi.org/10.1016/j.jdermsci.2019.03.006DOI Listing
April 2019

Outlier detection for questionnaire data in biobanks.

Int J Epidemiol 2019 Mar 8. Epub 2019 Mar 8.

Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.

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http://dx.doi.org/10.1093/ije/dyz012DOI Listing
March 2019

COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference.

Nucleic Acids Res 2019 Jan;47(D1):D55-D62

Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.

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http://dx.doi.org/10.1093/nar/gky1155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324053PMC
January 2019

Molecular Mechanism of Depolarization-Dependent Inactivation in W366F Mutant of Kv1.2.

J Phys Chem B 2018 12 26;122(48):10825-10833. Epub 2018 Nov 26.

Department of Applied Information Sciences, Graduate School of Information Sciences , Tohoku University , 6-3-09 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8579 , Japan.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.8b09446
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http://dx.doi.org/10.1021/acs.jpcb.8b09446DOI Listing
December 2018

Zn-Binding to the Voltage-Gated Proton Channel Hv1/VSOP.

J Phys Chem B 2018 10 25;122(39):9076-9080. Epub 2018 Sep 25.

Department of Biomedical Information Sciences, Graduate School of Information Sciences , Hiroshima City University , 3-4-1 Ozuka-Higashi , Asa-Minami-Ku, Hiroshima 731-3194 , Japan.

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http://dx.doi.org/10.1021/acs.jpcb.8b04890DOI Listing
October 2018

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data.

BMC Bioinformatics 2018 07 16;19(1):266. Epub 2018 Jul 16.

Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.

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http://dx.doi.org/10.1186/s12859-018-2279-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048772PMC
July 2018

De novo profile generation based on sequence context specificity with the long short-term memory network.

BMC Bioinformatics 2018 07 18;19(1):272. Epub 2018 Jul 18.

Graduate School of Information Sciences, Tohoku University, Sendai, Japan.

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http://dx.doi.org/10.1186/s12859-018-2284-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052547PMC
July 2018

jMorp: Japanese Multi Omics Reference Panel.

Nucleic Acids Res 2018 01;46(D1):D551-D557

Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.

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http://dx.doi.org/10.1093/nar/gkx978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753289PMC
January 2018

ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.

Plant Cell Physiol 2018 Jan;59(1):e3

Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.

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http://dx.doi.org/10.1093/pcp/pcx191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5914358PMC
January 2018

Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population.

Database (Oxford) 2016 1;2016. Epub 2016 Sep 1.

Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 9808575, Japan Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 9808579, Japan Institute for Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 9808575, Japan

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http://dx.doi.org/10.1093/database/baw124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009343PMC
November 2017

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

PLoS One 2016 1;11(12):e0167524. Epub 2016 Dec 1.

Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167524PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5132248PMC
June 2017

SR-B1 Is a Silica Receptor that Mediates Canonical Inflammasome Activation.

Cell Rep 2017 01;18(5):1298-1311

Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.01.004DOI Listing
January 2017

NLDB: a database for 3D protein-ligand interactions in enzymatic reactions.

J Struct Funct Genomics 2016 Dec 16;17(4):101-110. Epub 2016 Aug 16.

Graduate School of Information Sciences, Tohoku University, Aramaki-Aza-Aoba 6-3-09, Aoba-ku, Sendai, 980-8575, Japan.

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http://dx.doi.org/10.1007/s10969-016-9206-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274645PMC
December 2016

NCMine: Core-peripheral based functional module detection using near-clique mining.

Bioinformatics 2016 11 27;32(22):3454-3460. Epub 2016 Jul 27.

Graduate School of Information Sciences, Tohoku University, Sendai, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btw488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181566PMC
November 2016

Landscape of protein-small ligand binding modes.

Protein Sci 2016 09 4;25(9):1659-71. Epub 2016 Jul 4.

Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, 980-8597, Japan.

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http://dx.doi.org/10.1002/pro.2971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338237PMC
September 2016

Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction.

PLoS One 2016 7;11(3):e0150716. Epub 2016 Mar 7.

Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-aza Aoba, Aoba-ku, Sendai, Miyagi 980-8597, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150716PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780791PMC
August 2016

Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins.

Biophys Physicobiol 2016 14;13:157-163. Epub 2016 Jul 14.

Graduate School of Information Sciences, Tohoku University, Miyagi 980-8597, Japan; Tohoku Medical Megabank Organization, Tohoku University, Miyagi 980-8573, Japan; Institute of Development, Aging, and Cancer, Tohoku University, Miyagi 980-8575, Japan.

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http://dx.doi.org/10.2142/biophysico.13.0_157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042176PMC
July 2016

Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules.

PLoS One 2015 6;10(7):e0132039. Epub 2015 Jul 6.

Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan; Tohoku Medical Megabank Organization, Sendai, Miyagi, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132039PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493118PMC
April 2016

Structural basis for the membrane association of ankyrinG via palmitoylation.

Sci Rep 2016 Apr 5;6:23981. Epub 2016 Apr 5.

Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, JAPAN.

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http://dx.doi.org/10.1038/srep23981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820748PMC
April 2016

Distribution of single-nucleotide variants on protein-protein interaction sites and its relationship with minor allele frequency.

Protein Sci 2016 Feb 9;25(2):316-21. Epub 2015 Dec 9.

Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Miyagi, 980-8597, Japan.

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http://doi.wiley.com/10.1002/pro.2845
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http://dx.doi.org/10.1002/pro.2845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815344PMC
February 2016

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.

Plant Cell Physiol 2016 Jan 6;57(1):e5. Epub 2015 Nov 6.

Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan

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http://dx.doi.org/10.1093/pcp/pcv165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722172PMC
January 2016

ALCOdb: Gene Coexpression Database for Microalgae.

Plant Cell Physiol 2016 Jan 7;57(1):e3. Epub 2015 Dec 7.

Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan

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http://dx.doi.org/10.1093/pcp/pcv190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722175PMC
January 2016

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.

Nucleic Acids Res 2015 Jan 11;43(Database issue):D82-6. Epub 2014 Nov 11.

Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan Institute of Development, Aging, and Cancer, Tohoku University, Sendai 980-8575, Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan

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http://dx.doi.org/10.1093/nar/gku1163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383961PMC
January 2015

ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.

Plant Cell Physiol 2014 Jan 10;55(1):e6. Epub 2013 Dec 10.

Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.

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http://dx.doi.org/10.1093/pcp/pct178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894708PMC
January 2014

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

BMC Bioinformatics 2014 Jan 14;15:12. Epub 2014 Jan 14.

Graduate School of Information Sciences, Tohoku University, 6-3-09 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8597, Japan.

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http://dx.doi.org/10.1186/1471-2105-15-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897944PMC
January 2014

Exhaustive comparison and classification of ligand-binding surfaces in proteins.

Protein Sci 2013 Oct 4;22(10):1379-91. Epub 2013 Sep 4.

Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-aza-aoba, Aoba-ku, Sendai, Miyagi, 982-0036, Japan.

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http://dx.doi.org/10.1002/pro.2329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795496PMC
October 2013

Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel.

PLoS One 2013 13;8(2):e56342. Epub 2013 Feb 13.

Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Miyagi, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0056342PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3572011PMC
August 2013

Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening.

Molecules 2013 Aug 9;18(8):9567-81. Epub 2013 Aug 9.

Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Japan.

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http://dx.doi.org/10.3390/molecules18089567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6270271PMC
August 2013

Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins.

Protein Sci 2013 Jun 29;22(6):725-33. Epub 2013 Apr 29.

Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan.

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http://dx.doi.org/10.1002/pro.2255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690712PMC
June 2013

Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions.

J Chem Inf Model 2013 Jan 18;53(1):241-8. Epub 2012 Dec 18.

Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Miyagi 980-8597, Japan.

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http://dx.doi.org/10.1021/ci300377fDOI Listing
January 2013

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D1014-20. Epub 2012 Nov 29.

Graduate School of Information Sciences, Tohoku University, Sendai 980-8679, Japan.

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http://dx.doi.org/10.1093/nar/gks1014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531062PMC
January 2013

Dynamic features of homodimer interfaces calculated by normal-mode analysis.

Protein Sci 2012 Oct 17;21(10):1503-13. Epub 2012 Sep 17.

Division of Life Sciences, Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo-Ku, Tokyo 112-8610, Japan.

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http://dx.doi.org/10.1002/pro.2140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526992PMC
October 2012

A novel biclustering approach with iterative optimization to analyze gene expression data.

Adv Appl Bioinform Chem 2012 7;5:23-59. Epub 2012 Sep 7.

Department of Biological Sciences, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan ; Graduate School of Information Sciences, Tohoku University, Miyagi, Japan.

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http://dx.doi.org/10.2147/AABC.S32622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459542PMC
October 2012

Discrimination between biological interfaces and crystal-packing contacts.

Adv Appl Bioinform Chem 2008 2;1:99-113. Epub 2008 Nov 2.

Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169932PMC
November 2011

Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction.

Adv Appl Bioinform Chem 2009 22;2:79-100. Epub 2009 Sep 22.

Institute of Medical Science, University of Tokyo, Tokyo, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169947PMC
November 2011

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

J Mol Biol 2011 Nov 29;414(2):289-302. Epub 2011 Sep 29.

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

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http://kiharalab.org/web/paper/communitywidecapri_JMB2011.pd
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http://linkinghub.elsevier.com/retrieve/pii/S002228361101055
Publisher Site
http://dx.doi.org/10.1016/j.jmb.2011.09.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839241PMC
November 2011

Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks.

BMC Genomics 2011 Nov 30;12 Suppl 3:S19. Epub 2011 Nov 30.

Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1186/1471-2164-12-S3-S19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333178PMC
November 2011

Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states.

Proteins 2011 May 1;79(5):1550-63. Epub 2011 Mar 1.

Department of Applied Information Sciences, Graduate School of Information Science, Tohoku University, 6-3-09, Aoba, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8579, Japan.

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http://dx.doi.org/10.1002/prot.22982DOI Listing
May 2011

ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.

Plant Cell Physiol 2011 Feb 7;52(2):213-9. Epub 2011 Jan 7.

Graduate School of Information Science, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.

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http://dx.doi.org/10.1093/pcp/pcq203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037081PMC
February 2011

SAHG, a comprehensive database of predicted structures of all human proteins.

Nucleic Acids Res 2011 Jan 3;39(Database issue):D487-93. Epub 2010 Nov 3.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gkq1057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013665PMC
January 2011

COXPRESdb: a database to compare gene coexpression in seven model animals.

Nucleic Acids Res 2011 Jan 16;39(Database issue):D1016-22. Epub 2010 Nov 16.

Graduate School of Information Science, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.

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http://dx.doi.org/10.1093/nar/gkq1147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013720PMC
January 2011

Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network.

Protein Sci 2010 Aug;19(8):1461-8

Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1002/pro.425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923499PMC
August 2010

Ligand-binding site prediction of proteins based on known fragment-fragment interactions.

Bioinformatics 2010 Jun 13;26(12):1493-9. Epub 2010 May 13.

Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881410PMC
June 2010

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

J Plant Res 2010 May 10;123(3):311-9. Epub 2010 Apr 10.

Graduate School of Information Science, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.

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http://dx.doi.org/10.1007/s10265-010-0333-6DOI Listing
May 2010

Hub promiscuity in protein-protein interaction networks.

Int J Mol Sci 2010 Apr 26;11(4):1930-43. Epub 2010 Apr 26.

Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Japan.

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http://dx.doi.org/10.3390/ijms11041930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871146PMC
April 2010

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.

Bioinformatics 2009 Oct 20;25(20):2677-84. Epub 2009 Jul 20.

Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btp442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759550PMC
October 2009

Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.

DNA Res 2009 Oct 18;16(5):249-60. Epub 2009 Sep 18.

Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/dnares/dsp016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762411PMC
October 2009

Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression.

Genome Inform 2009 Oct;23(1):149-58

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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October 2009

Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials.

Protein Sci 2009 Sep;18(9):1906-15

Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1002/pro.201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777365PMC
September 2009

A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human.

Genome Inform 2008 ;20:212-21

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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July 2009

Development of new indices to evaluate protein-protein interfaces: assembling space volume, assembling space distance, and global shape descriptor.

J Mol Graph Model 2009 Feb 8;27(6):706-11. Epub 2008 Nov 8.

Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.

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http://dx.doi.org/10.1016/j.jmgm.2008.11.002DOI Listing
February 2009

[Correlation between structure and function of peptidyl-prolyl isomerase].

Tanpakushitsu Kakusan Koso 2009 Feb;54(2):167-72

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February 2009

PiSite: a database of protein interaction sites using multiple binding states in the PDB.

Nucleic Acids Res 2009 Jan 4;37(Database issue):D360-4. Epub 2008 Oct 4.

Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkn659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686547PMC
January 2009

ATTED-II provides coexpressed gene networks for Arabidopsis.

Nucleic Acids Res 2009 Jan 25;37(Database issue):D987-91. Epub 2008 Oct 25.

Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkn807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686564PMC
January 2009

Mutational analysis of block and facilitation of HERG current by a class III anti-arrhythmic agent, nifekalant.

Channels (Austin) 2007 May-Jun;1(3):198-208. Epub 2007 Jul 6.

Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.4161/chan.4691DOI Listing
October 2008

Effects of surface-to-volume ratio of proteins on hydrophilic residues: decrease in occurrence and increase in buried fraction.

Protein Sci 2008 Sep 12;17(9):1596-602. Epub 2008 Jun 12.

Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1110/ps.035592.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2525519PMC
September 2008

Protein structure databases with new web services for structural biology and biomedical research.

Brief Bioinform 2008 Jul 22;9(4):276-85. Epub 2008 Apr 22.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/bib/bbn015DOI Listing
July 2008

Prediction of disordered regions in proteins based on the meta approach.

Bioinformatics 2008 Jun 20;24(11):1344-8. Epub 2008 Apr 20.

Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btn195DOI Listing
June 2008

Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs.

BMC Genomics 2008 Apr 2;9:152. Epub 2008 Apr 2.

Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1186/1471-2164-9-152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335122PMC
April 2008

A cavity with an appropriate size is the basis of the PPIase activity.

Protein Eng Des Sel 2008 Feb 5;21(2):83-9. Epub 2008 Jan 5.

Laboratory of Structural Biology, School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Tokyo 113-8510, Japan.

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http://dx.doi.org/10.1093/protein/gzm087DOI Listing
February 2008

COXPRESdb: a database of coexpressed gene networks in mammals.

Nucleic Acids Res 2008 Jan 11;36(Database issue):D77-82. Epub 2007 Oct 11.

Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/nar/gkm840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238883PMC
January 2008

Identification of transient hub proteins and the possible structural basis for their multiple interactions.

Protein Sci 2008 Jan;17(1):72-8

Institute of Medical Science, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1110/ps.073196308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144588PMC
January 2008

Docking of protein molecular surfaces with evolutionary trace analysis.

Proteins 2007 Dec;69(4):832-8

Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1002/prot.21737DOI Listing
December 2007

PrDOS: prediction of disordered protein regions from amino acid sequence.

Nucleic Acids Res 2007 Jul 12;35(Web Server issue):W460-4. Epub 2007 Jun 12.

Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkm363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933209PMC
July 2007

eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.

Nucleic Acids Res 2007 Jul 12;35(Web Server issue):W398-402. Epub 2007 Jun 12.

Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkm351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933152PMC
July 2007

Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information.

Proteins 2007 Feb;66(3):655-63

Global Scientific Information and Computing Center, Tokyo Institute of Technology, Ookayama, Tokyo 152-8550, Japan.

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http://dx.doi.org/10.1002/prot.21240DOI Listing
February 2007

ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.

Nucleic Acids Res 2007 Jan 27;35(Database issue):D863-9. Epub 2006 Nov 27.

Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-14 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.

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http://dx.doi.org/10.1093/nar/gkl783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716726PMC
January 2007

Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity.

Protein Eng Des Sel 2006 Sep 12;19(9):421-9. Epub 2006 Jul 12.

Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/protein/gzl026DOI Listing
September 2006

PreBI: prediction of biological interfaces of proteins in crystals.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W320-4

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.1093/nar/gkl267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538861PMC
July 2006

DBTGR: a database of tunicate promoters and their regulatory elements.

Nucleic Acids Res 2006 Jan;34(Database issue):D552-5

Human Genome Center, The Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gkj064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347427PMC
January 2006