Daron M Standley

Daron M Standley

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Daron M Standley

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Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications.

Appl Microbiol Biotechnol 2020 Apr 15;104(7):2897-2909. Epub 2020 Feb 15.

Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho Midori-ku, Yokohama, 226-8501, Japan.

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http://dx.doi.org/10.1007/s00253-020-10440-2DOI Listing
April 2020

Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis.

Immunity 2020 Mar;52(3):542-556.e13

Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan; Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2020.02.007DOI Listing
March 2020

Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production.

Sci Signal 2020 Mar 24;13(624). Epub 2020 Mar 24.

Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, 565-0871 Osaka, Japan.

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http://dx.doi.org/10.1126/scisignal.aay0574DOI Listing
March 2020

Structural Determinants of the APOBEC3G N-Terminal Domain for HIV-1 RNA Association.

Front Cell Infect Microbiol 2019 21;9:129. Epub 2019 May 21.

Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.3389/fcimb.2019.00129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6536580PMC
January 2020

Initial phospholipid-dependent Irgb6 targeting to vacuoles mediates host defense.

Life Sci Alliance 2020 Jan 18;3(1). Epub 2019 Dec 18.

Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan

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http://dx.doi.org/10.26508/lsa.201900549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6925386PMC
January 2020

Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain.

Appl Microbiol Biotechnol 2019 Dec 15;103(23-24):9543-9553. Epub 2019 Nov 15.

Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho Midori-ku, Yokohama, 226-8501, Japan.

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http://dx.doi.org/10.1007/s00253-019-10093-wDOI Listing
December 2019

Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction.

Appl Microbiol Biotechnol 2019 Dec 13;103(23-24):9529-9541. Epub 2019 Nov 13.

Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho Midori-ku, Yokohama, 226-8501, Japan.

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http://dx.doi.org/10.1007/s00253-019-10206-5DOI Listing
December 2019

Correction to: Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain.

Appl Microbiol Biotechnol 2019 12;103(23-24):9555

Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho Midori-ku, Yokohama, 226-8501, Japan.

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http://dx.doi.org/10.1007/s00253-019-10138-0DOI Listing
December 2019

MAFFT-DASH: integrated protein sequence and structural alignment.

Nucleic Acids Res 2019 Jul;47(W1):W5-W10

Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan.

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http://dx.doi.org/10.1093/nar/gkz342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602451PMC
July 2019

Structural Modeling of Lymphocyte Receptors and Their Antigens.

Methods Mol Biol 2019 ;2048:207-229

Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1007/978-1-4939-9728-2_17DOI Listing
January 2019

Arid5a stabilizes OX40 mRNA in murine CD4 T cells by recognizing a stem-loop structure in its 3'UTR.

Eur J Immunol 2018 04 5;48(4):593-604. Epub 2018 Feb 5.

Laboratory of Immune Regulation, World Premier International-Immunology Frontier Research Center, Osaka University, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.1002/eji.201747109DOI Listing
April 2018

Structural basis for the assembly of the Ragulator-Rag GTPase complex.

Nat Commun 2017 11 20;8(1):1625. Epub 2017 Nov 20.

Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.1038/s41467-017-01762-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696360PMC
November 2017

Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense.

Nat Immunol 2017 Aug 12;18(8):899-910. Epub 2017 Jun 12.

Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1038/ni.3767DOI Listing
August 2017

TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a.

Nucleic Acids Res 2017 03;45(5):2687-2703

Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/nar/gkx064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389518PMC
March 2017

Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines.

EBioMedicine 2017 Feb 1;15:127-136. Epub 2016 Dec 1.

Laboratory of Adjuvant Innovation, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan; Laboratory of Vaccine Science, WPI Immunology Frontier Research Centre, Osaka University, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2016.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5233800PMC
February 2017

Mapping circulating serum miRNAs to their immune-related target mRNAs.

Adv Appl Bioinform Chem 2017 2;10:1-9. Epub 2017 Feb 2.

Systems Immunology Lab; Lab of Integrated Biological Information, Institute for Virus Research Kyoto University, Kyoto, Japan.

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http://dx.doi.org/10.2147/AABC.S121598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5295801PMC
February 2017

A simple method to control over-alignment in the MAFFT multiple sequence alignment program.

Bioinformatics 2016 07 26;32(13):1933-42. Epub 2016 Feb 26.

Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan.

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http://bioinformatics.oxfordjournals.org/content/early/2016/
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http://dx.doi.org/10.1093/bioinformatics/btw108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920119PMC
July 2016

Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins.

Chem Sci 2016 Jan 30;7(1):308-314. Epub 2015 Sep 30.

Graduate School of Engineering , Osaka University , Osaka 565-0871 , Japan . Email:

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http://dx.doi.org/10.1039/c5sc02351cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5952543PMC
January 2016

RabGDIα is a negative regulator of interferon-γ-inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii.

Proc Natl Acad Sci U S A 2015 Aug 3;112(33):E4581-90. Epub 2015 Aug 3.

Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan 5650871; Laboratory of Immunoparasitology, World Premier International Research Center Immunology Frontier Research Center, Osaka University, Osaka, Japan 5650871;

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http://www.pnas.org/content/112/33/E4581.full.pdf
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http://www.pnas.org/lookup/doi/10.1073/pnas.1510031112
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http://dx.doi.org/10.1073/pnas.1510031112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547277PMC
August 2015

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms.

Cell 2015 May;161(5):1058-1073

Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan; CREST, JST, Kyoto 606-8507, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.04.029DOI Listing
May 2015

RNA-LIM: a novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure.

Anal Biochem 2015 Mar 3;472:52-61. Epub 2014 Dec 3.

Immunology Frontier Research Center (IFReC), Section on Systems Immunology, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1016/j.ab.2014.11.004DOI Listing
March 2015

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.

Bioinformatics 2014 Nov 26;30(22):3279-80. Epub 2014 Jul 26.

WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btu510DOI Listing
November 2014

Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex.

EMBO J 2014 Oct 8;33(20):2332-48. Epub 2014 Aug 8.

Laboratory of Infection and Prevention Institute for Virus Research Kyoto University, Sakyo-ku Kyoto, Japan CREST JST, Sakyo-ku Kyoto, Japan Laboratory of Host Defense WPI Immunology Frontier Research Center (IFReC), Osaka University Suita, Osaka, Japan

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http://dx.doi.org/10.15252/embj.201488447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253523PMC
October 2014

Quantifying sequence and structural features of protein-RNA interactions.

Nucleic Acids Res 2014 Sep 25;42(15):10086-98. Epub 2014 Jul 25.

Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan

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http://dx.doi.org/10.1093/nar/gku681DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150784PMC
September 2014

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations.

Proteins 2014 Aug 13;82(8):1624-35. Epub 2014 May 13.

Molecular Medicine Research laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki, 305-8585, Japan.

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http://dx.doi.org/10.1002/prot.24591DOI Listing
August 2014

A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein.

Biophys Chem 2014 Jun 13;190-191:50-5. Epub 2014 Feb 13.

Immunology Frontier Research Center (IFReC), Section on Systems Immunology. Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bpc.2014.01.005DOI Listing
June 2014

MAFFT: iterative refinement and additional methods.

Methods Mol Biol 2014 ;1079:131-46

Immunology Frontier Research Center, Osaka University, Suita, Japan.

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http://link.springer.com/10.1007/978-1-62703-646-7_8
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http://dx.doi.org/10.1007/978-1-62703-646-7_8DOI Listing
May 2014

Intrinsic disorder mediates cooperative signal transduction in STIM1.

J Mol Biol 2014 May 17;426(10):2082-97. Epub 2014 Mar 17.

Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2014.03.006DOI Listing
May 2014

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Proc Natl Acad Sci U S A 2014 Apr 27;111(14):5289-94. Epub 2014 Mar 27.

Departments of Experimental Immunology and Systems Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.

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http://dx.doi.org/10.1073/pnas.1312717110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986152PMC
April 2014

Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome.

Nat Commun 2014 Mar 18;5:3492. Epub 2014 Mar 18.

Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://www.nature.com/articles/ncomms4492
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http://dx.doi.org/10.1038/ncomms4492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959210PMC
March 2014

Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator.

Pac Symp Biocomput 2012 :164-75

Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.

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December 2013

Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling.

Proc Natl Acad Sci U S A 2013 Dec 19;110(49):19908-13. Epub 2013 Nov 19.

Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo 001-0021, Japan.

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http://dx.doi.org/10.1073/pnas.1222811110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3856793PMC
December 2013

Deconstructing RNA: optical measurement of composition and structure.

Phys Chem Chem Phys 2013 Aug;15(31):13199-208

Biophotonics Laboratory, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.

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http://dx.doi.org/10.1039/c3cp52406jDOI Listing
August 2013

The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling.

Cell Host Microbe 2013 Aug;14(2):148-58

Laboratory of Molecular Immunobiology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1016/j.chom.2013.07.011DOI Listing
August 2013

A novel function prediction approach using protein overlap networks.

BMC Syst Biol 2013 Jul 17;7:61. Epub 2013 Jul 17.

Systems Immunology Lab, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1186/1752-0509-7-61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720179PMC
July 2013

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.

BMC Genomics 2012 13;13 Suppl 7:S11. Epub 2012 Dec 13.

Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1186/1471-2164-13-S7-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521209PMC
June 2013

MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

Mol Biol Evol 2013 Apr 16;30(4):772-80. Epub 2013 Jan 16.

Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.

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http://dx.doi.org/10.1093/molbev/mst010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603318PMC
April 2013

Systems biology approaches to toll-like receptor signaling.

Wiley Interdiscip Rev Syst Biol Med 2012 Sep-Oct;4(5):497-507. Epub 2012 Jun 19.

Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.

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http://doi.wiley.com/10.1002/wsbm.1178
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http://dx.doi.org/10.1002/wsbm.1178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465798PMC
January 2013

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.

BMC Bioinformatics 2013 Jan 21;14:26. Epub 2013 Jan 21.

Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1186/1471-2105-14-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602658PMC
January 2013

Prediction of dinucleotide-specific RNA-binding sites in proteins.

BMC Bioinformatics 2011 30;12 Suppl 13:S5. Epub 2011 Nov 30.

Kyushu Institute of Technology, Fukuoka, Japan.

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http://dx.doi.org/10.1186/1471-2105-12-S13-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278845PMC
August 2012

Protein Loop Modeling with Optimized Backbone Potential Functions.

J Chem Theory Comput 2012 May 18;8(5):1820-7. Epub 2012 Apr 18.

Systems Immunology Lab, Immunology Frontier Research Center, Osaka University , Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.1021/ct300131pDOI Listing
May 2012

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

Nucleic Acids Res 2012 Jan 5;40(Database issue):D453-60. Epub 2011 Oct 5.

Institute for Protein Research and Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1093/nar/gkr811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245181PMC
January 2012

Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations.

Phys Rev E Stat Nonlin Soft Matter Phys 2011 Dec 15;84(6 Pt 1):062903. Epub 2011 Dec 15.

Laboratory of Host Defense, WPI Immunology Frontier Research Center, IFReC, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.

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http://sysimg.ifrec.osaka-u.ac.jp/sysbio/Slides/Teraguchi111
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http://link.aps.org/doi/10.1103/PhysRevE.84.062903
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http://dx.doi.org/10.1103/PhysRevE.84.062903DOI Listing
December 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
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http://dx.doi.org/10.1016/j.jmb.2011.09.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839241PMC
November 2011

Functional characterization of protein domains common to animal viruses and mouse.

BMC Genomics 2011 Nov 30;12 Suppl 3:S21. Epub 2011 Nov 30.

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

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http://dx.doi.org/10.1186/1471-2164-12-S3-S21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333181PMC
November 2011

Fast and accurate prediction of protein side-chain conformations.

Bioinformatics 2011 Oct 27;27(20):2913-4. Epub 2011 Aug 27.

Systems Immunology Lab, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187653PMC
October 2011

A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans.

J Clin Invest 2011 Oct 1;121(10):4150-60. Epub 2011 Sep 1.

Department of Immunology and Parasitology, Institute of Health Biosciences,University of Tokushima Graduate School, Tokushima, Japan.

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http://dx.doi.org/10.1172/JCI58414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195477PMC
October 2011

The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1.

Nat Immunol 2011 Oct 30;12(12):1167-75. Epub 2011 Oct 30.

Laboratory of Host Defense, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.

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http://www.nature.com/articles/ni.2137
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http://dx.doi.org/10.1038/ni.2137DOI Listing
October 2011

Binding energetics of ferredoxin-NADP+ reductase with ferredoxin and its relation to function.

Chembiochem 2011 Sep 7;12(13):2062-70. Epub 2011 Jul 7.

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

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http://dx.doi.org/10.1002/cbic.201100189DOI Listing
September 2011

Protein loop selection using orientation-dependent force fields derived by parameter optimization.

Proteins 2011 Jul 13;79(7):2260-7. Epub 2011 May 13.

Systems Immunology Lab, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.

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http://doi.wiley.com/10.1002/prot.23051
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http://dx.doi.org/10.1002/prot.23051DOI Listing
July 2011

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions.

J Comput Chem 2011 Jun 4;32(8):1680-6. Epub 2011 Mar 4.

Systems Immunology Lab, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1002/jcc.21747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072444PMC
June 2011

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster.

Protein Sci 2011 Jan;20(1):187-96

Graduate School of Frontier Biosciences, Osaka University, Open Laboratories for Advanced Bioscience and Biotechnology, Suita, Osaka 565-0874, Japan.

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http://doi.wiley.com/10.1002/pro.553
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http://dx.doi.org/10.1002/pro.553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047075PMC
January 2011

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis.

Immunome Res 2010 Nov 19;6:11. Epub 2010 Nov 19.

Laboratory of Systems Immunology, WPI Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1186/1745-7580-6-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995782PMC
November 2010

Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins.

BMC Bioinformatics 2010 Oct 15;11 Suppl 7:S7. Epub 2010 Oct 15.

Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1186/1471-2105-11-S7-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957690PMC
October 2010

SeSAW: balancing sequence and structural information in protein functional mapping.

Bioinformatics 2010 May 17;26(9):1258-9. Epub 2010 Mar 17.

WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859130PMC
May 2010

A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3.

J Exp Med 2009 Nov 9;206(12):2747-60. Epub 2009 Nov 9.

Department of Microbiology and Immunology, Graduate School of Medicine, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1084/jem.20091703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806617PMC
November 2009

Membrane attachment facilitates ligand access to the active site in monoamine oxidase A.

Biochemistry 2009 Jun;48(25):5864-73

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

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http://dx.doi.org/10.1021/bi900493nDOI Listing
June 2009

Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay.

Nature 2009 Apr 25;458(7242):1185-90. Epub 2009 Mar 25.

Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1038/nature07924DOI Listing
April 2009

Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

Proteins 2008 Sep;72(4):1333-51

Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1002/prot.22015DOI Listing
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

Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase.

Mol Microbiol 2008 Jun 29;68(6):1395-405. Epub 2008 Apr 29.

School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK.

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http://dx.doi.org/10.1111/j.1365-2958.2008.06228.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2440562PMC
June 2008

[From structures to functions: annotation by structural bioinformatics].

Tanpakushitsu Kakusan Koso 2008 Apr;53(5):638-44

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April 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

ASH structure alignment package: sensitivity and selectivity in domain classification.

BMC Bioinformatics 2007 Apr 4;8:116. Epub 2007 Apr 4.

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

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http://dx.doi.org/10.1186/1471-2105-8-116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955748PMC
April 2007

Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf ferredoxins.

Biochemistry 2006 Dec;45(48):14389-96

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

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http://dx.doi.org/10.1021/bi061779dDOI Listing
December 2006

Flexible docking of an amyloid-forming peptide from beta(2)-microglobulin.

FEBS Lett 2006 Nov 18;580(26):6199-205. Epub 2006 Oct 18.

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

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http://doi.wiley.com/10.1016/j.febslet.2006.10.022
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http://dx.doi.org/10.1016/j.febslet.2006.10.022DOI Listing
November 2006

GASH: an improved algorithm for maximizing the number of equivalent residues between two protein structures.

BMC Bioinformatics 2005 Sep 8;6:221. Epub 2005 Sep 8.

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

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-6-221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239909PMC
September 2005

Detecting local structural similarity in proteins by maximizing number of equivalent residues.

Proteins 2004 Nov;57(2):381-91

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

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http://dx.doi.org/10.1002/prot.20211DOI Listing
November 2004