List of all our publications sorted by year
Year 2014
Hall D, Li S, Yamashita K, Azuma R, Carver JA, Standley DM: RNA-LIM: A Novel Procedure for Analyzing Protein/Single-Stranded RNA Propensity Data with Concomitant Estimation of Interface Structure, Analytical biochemistry, 2014, in press
Morimoto Y, Ishii S, Ishibashi J, Katoh K, Tsujiuchi T, Kagawa T, Fukushima N: Functional lysophosphatidic acid receptors expressed in Oryzias latipes, Gene, 2014, 551 (2), 189-200
Yamashita K, Ikeda K, Amada KM, Liang S, Tsuchiya Y, Nakamura H, Shirai H, Standley DM: Kotai Antibody Builder: automated high-resolution structural modeling of antibodies, Bioinformatics, 2014, 30 (22), 3279-3280
Tartey S, Matsushita K, Vandenbon A, Ori D, Imamura T, Mino T, Standley DM, Hoffmann JA, Reichhart JM, Akira S, Takeuchi O: Akirin2 is critical for inducing inflammatory genes by bridging IκB‐ζ and the SWI/SNF complex, The EMBO journal, 2014, 33 (20), 2332-2348
Li S, Yamashita K, Amada KM, Standley DM: Quantifying sequence and structural features of protein–RNA interactions, Nucleic acids research, 2014, 42 (15), 10086-10098
Shan Y, Gnanasambandan K, Ungureanu D, Kim ET, Hammarén H, Yamashita K, Silvennoinen O, Shaw DE, Hubbard SR: Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase, Nature structural & molecular biology, 2014, 21 (7), 579-584
Hall D, Li S, Yamashita K, Azuma R, Carver JA, Standley DM: A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein, Biophysical chemistry, 2014, 190, 50-55
Furukawa Y, Teraguchi S, Ikegami T, Dagliyan O, Jin L, Hall D, Dokholyan NV, Namba K, Akira S, Kurosaki T, Baba Y, Standley DM:Intrinsic Disorder Mediates Cooperative Signal Transduction in STIM1, Journal of molecular biology, 2014, 426 (10), 2082-2097
Shirai H, Ikeda H, Yamashita K, Tsuchiya Y, Sarmiento J, Liang S, Morokata T, Mizuguchi K, Higo J, Standley DM, Nakamura H: High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations, Proteins: Structure, Function, and Bioinformatics, 2014, 82 (8), 1624-1635
Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Standley DM, Date H, Sakaguchi S: Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation, FANTOM Consortium Proceedings of the National Academy of Sciences, 2014, 111 (14), 5289-5294
Lensink MF, ..., Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, ...: Blind prediction of interfacial water positions in CAPRI, Proteins: Structure, Function, and Bioinformatics, 2014, 82 (4), 620-632
Takemura N, Kawasaki T, Kunisawa J, Sato S, Lamichhane A, Kobiyama K, Aoshi T, Ito J, Mizuguchi K, Karuppuchamy T, Matsunaga K, Miyatake S, Mori N, Tsujimura T, Satoh T, Kumagai Y, Kawai T, Standley DM, Ishii KJ, Kiyono H, Akira S, Uematsu S: Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome, Nature communications, 2014, 5:3492
Katoh K, Standley DM: MAFFT: iterative refinement and additional methods, Multiple Sequence Alignment Methods, Methods in Molecular Biology, 2014, 1079, 131-146
Year 2013
Liang S, Zhang C, Zhou Y: LEAP: Highly Accurate Prediction of Protein Loop Conformations by Integrating Coarse-Grained Sampling and Optimized Energy Scores with All-Atom Refinement of Backbone and Side Chains, Journal of Computational Chemistry, 2014, 35 (4), 335-341
Enokizono Y, Kumeta H, Funami K, Horiuchi M, Sarmiento J, Yamashita K, Standley DM, Matsumoto M, Seya T, Inagaki F: Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling, Proceedings of the National Academy of Sciences, 2013, 110 (49), 19908-19913
Moretti R, ..., Sarmiento J, Liang S, Teraguchi S, Standley DM, ...: Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions, Proteins: Structure, Function, and Bioinformatics, 2013, 81 (11), 1980-1987
Kawasaki T, Takemura N, Standley DM, Akira S, Kawai T: The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling, Cell host & microbe, 2013, 14 (2), 148-158
Liang S, Zheng D, Standley DM, Guo H, Zhang C: A novel function prediction approach using protein overlap networks, BMC systems biology, 2013, 7 (1), 61
Hobro AJ, Standley DM, Ahmad S, Smith NI: Deconstructing RNA: optical measurement of composition and structure, Physical Chemistry Chemical Physics, 2013, 15 (31), 13199-13208
Kuraku S, Zmasek CM, Nishimura O, Katoh K: aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity, Nucleic acids research, 2013, 41, W22-W28
Yao B, Zheng D, Liang S, Zhang C: Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods, PLoS One, 2013, 8 (4), e62249
Uehata T, Iwasaki H, Vandenbon A, Matsushita K, Hernandez-Cuellar E, Kuniyoshi K, Satoh T, Mino T, Suzuki Y, Standley DM, Tsujimura T, Rakugi H, Isaka Y, Takeuchi O, Akira S: Malt1-induced cleavage of Regnase-1 in CD4+ helper T cells regulates immune activation, Cell, 2013, Volume 153, Issue 5, 1036-1049.
Kuraku S, Zmasek C, Nishimura 0, Katoh K: aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity, Nucleic Acids Research 2013; doi: 10.1093/nar/gkt389
Katoh K, Standley DM: MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, 2013, Volume 30, Issue 4; Mol Biol Evol (2013) 30 (4): 772-780.
Vandenbon A, Kumagai Y, Teraguchi S, Amada KM, Akira S, Standley DM: A Parzen window-based approach for the detection of locally enriched transcription factor binding sites, BMC Bioinformatics, 2013, Volume 14, 26.
Year 2012
Katoh K, Frith MC: Adding unaligned sequences into an existing alignment using MAFFT and LAST, Bioinformatics. 2012 28:3144-6
Maruyama K, Fukasaka M, Vandenbon A, Saitoh T, Kawasaki T, Kondo T, Yokoyama KK, Kidoya H, Takakura N, Standley DM, Takeuchi O, Akira S: The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation, Immunity 2012, Volume 37 (6): 1024-36.
Vandenbon A *, Kumagai Y *, Akira S, Standley DM: A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription, BMC Genomics, 2012, Volume 13 Supplement 7, S11. * : equal contribution
Vandenbon A *, Teraguchi S *, Akira S, Takeda K, Standley DM: Systems biology approaches to toll-like receptor signaling, WIREs Syst Biol Med, 2012. * : equal contribution
Liang S, Zhang C, Sarmiento J, Standley DM: Protein loop modeling with optimized backbone potential functions. J Chem Theory Comput 2012, 8: 1820-1827.
Standley DM, van der Giezen M: Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly Research and Reports in Biochemistry 2012, 2:1-8.
Year 2011
Teraguchi S, Kumagai Y, Vandenbon A, Akira S, Standley DM: Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations. Phys Rev E 2011, 84:062903.
Patil A, Teraguchi S, Dinh H, Nakai K, Standley DM: Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using Idd Navigator. Pac Symp Biocomput 2011, 17:164-175.
Lis M, Kim T, Sarmiento J, Kuroda D, Dinh H, Kinjo AR, Devadas S, Nakamura H, Standley DM: Bridging the gap between single-template and fragment based protein structure modeling using Spanner. Immunome Research 2011, 7.
Liang S, Zhou Y, Grishin N, Standley DM: Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J COMPUT CHEM 2011, 32:1680-1686.
Liang S, Zheng D, Zhang C, Standley DM: Fast and accurate prediction of protein side-chain conformations. Bioinformatics 2011, 27:2913-2914.
Liang S, Zhang C, Standley DM: Protein loop selection using orientation-dependent force fields derived by parameter optimization. Proteins 2011, 79:2260-2267.
Lee YH, Ikegami T, Standley DM, Sakurai K, Hase T, Goto Y: Binding Energetics of Ferredoxin-NADP(+) Reductase with Ferredoxin and Its Relation to Function. ChemBioChem 2011.
Kitamura A, Maekawa Y, Uehara H, Izumi K, Kawachi I, Nishizawa M, Toyoshima Y, Takahashi H, Standley DM, Tanaka K, et al: A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans. J Clin Invest 2011, 121:4150-4160.
Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H: Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res 2011, 40:D453-460.
Kinjo AR, Kumagai Y, Dinh H, Takeuchi O, Standley DM: Functional characterization of protein domains common to animal viruses and mouse. BMC Genomics 2011, 12 Suppl 3:S21.
Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Matsushita M, Standley DM, Akira S: The IκB kinase complex regulates TLR/IL-1R-induced cytokine mRNA stability by controlling Regnase-1 degradation. Nature Immunology 2011, 12:1165-75.
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, (+50 authors), Standley DM, (+35 authors): Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol 2011, 414:289-302.
Fernandez M, Kumagai Y, Standley DM, Sarai A, Mizuguchi K, Ahmad S: Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinformatics 2011, 12 Suppl 13:S5.
Year 2010
Teraguchi S, Patil A, Standley DM: Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins. BMC Bioinformatics 2010, 11:S7.
Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H: SeSAW: balancing sequence and structural information in protein functional mapping. Bioinformatics 2010, 26:1258-1259.
Satoh T, Takeuchi O, Vandenbon A, Yasuda K, Tanaka Y, Kumagai Y, Miyake T, Matsushita K, Okazaki T, Saitoh T, Honma K, Matsuyama T, Yui K, Tsujimura T, Standley DM, Nakanishi K, Nakai K, Akira S: The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol 2010 10:936-44.
Milewski RJ, Kumagai Y, Fujita K, Standley DM, Smith NI: Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis. Immunome Res 2010, 6:11.
Liang SD, Zheng DD, Standley DM, Yao B, Zacharias M, Zhang C: EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results. BMC Bioinformatics 2010, 11:381.
Katayama T, Arakawa K, Nakao M, Ono K, K.F A-K, Yamamoto Y, Aerts J, Aranda B, Barboza LH, Bonnal R, (+36 authors), Standley DM, (+10 authors): The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics 2010, 1.
Ikebe J, Standley DM, Nakamura H, Higo J: Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster. Protein Science 2010, 20:187-196.
Year 2009
Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, et al: A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3. J Exp Med 2009, 206:2747-2760.
Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, (+ 16 authors), Standley DM, (+5 authors): Outcome of a workshop on applications of protein models in biomedical research. Structure 2009, 17:151-159.
Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S: Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 2009, 458:1185-1190.
Apostolov R, Yonezawa Y, Standley DM, Kikugawa G, Takano Y, Nakamura H: Membrane attachment facilitates ligand access to the active site in monoamine oxidase A. Biochemistry 2009, 48:5864-5873.
Year 2008
Yonezawa Y, Standley DM, Nakamura H: Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis-trans isomerization of N-Methylacetamide. Chemical Physics Letters 2008, 503:139-144.
Standley DM, Toh H, Nakamura H: Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan. Proteins 2008, 72:1333-1351.
Standley DM, Nakamura H: [From structures to functions: annotation by structural bioinformatics]. Tanpakushitsu Kakusan Koso 2008, 53:638-644.
Standley DM, Kinjo AR, Lis M, van der Giezen M, Nakamura H: Structure-based functional annotation of protein sequences guided by comparative models. Optimization and Systems Biology 2008:395-403.
Standley DM, Kinjo AR, Kinoshita K, Nakamura H: Protein structure databases with new web services for structural biology and biomedical research. Brief Bioinform 2008, 9:276-285.
Hamblin K, Standley DM, Rogers MB, Stechmann A, Roger AJ, Maytum R, van der Giezen M: Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase. Mol Microbiol 2008, 68:1395-1405.
Year 2007
Standley DM, Toh H, Nakamura H: ASH structure alignment package: sensitivity and selectivity in domain classification. BMC Bioinformatics 2007, 8:116.
Kanamori E, Murakami Y, Tsuchiya Y, Standley DM, Nakamura H, Kinoshita K: Docking of protein molecular surfaces with evolutionary trace analysis. Proteins 2007, 69:832-838.