発表論文

List of Publications since October 2006
2017
  • 1. 夏目やよい、水口賢司
    “計算システム生物学による創薬:分子、構造からネットワークへ “
    日本薬理学雑誌, 2017 Feb 2,149(2): 91-95, J-STAGE
  • 2. Murakami Y., Tripathi L. P., Prathipati P., Mizuguchi K.
    “Network analysis and in silico prediction of protein–protein interactions with applications in drug discovery. “
    Current Opinion in Structural Biology, 2017 June, PubMed:28364585
  • 3. Nyström-Persson J., Natsume-Kitatani Y., Igarashi Y., Satoh D., MizuguchiK.
    “Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates “
    Scientific Reports, 2017 May 3, PubMed:28469246
  • 4. Yoshimaru T., Ono M., Bando Y., Chen Y. A., Mizuguchi K., Komatsu M., Shima H., Imoto I., Izumi K., Honda J., Miyoshi H., Sasa M., Katagiri T.
    “A-kinase anchoring protein BIG3 coordinates oestrogen signaling in breast cancer cells “
    Nature Communications, 2017 May 30, PubMed:28555617
  • 5. Andrabi M., Hutchins A.P., Miranda-Saavedra D., Kono H., Nussinov R., Mizuguchi K., Ahmad S.
    “Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. “
    Sci. Rep., 2017 Jun 22, 7(1): 4071, PubMed:28642456
  • 6. Sowdhamini R., Mizuguchi K.
    “Editorial-Sequences and topology. “
    Curr. Opin. Struct. Biol., 2017 Jun 3, pii: S0959-440X(17)30066-0, PubMed:28587734
  • 7. 江崎剛史、渡邉怜子、川島和、夏目やよい、水口賢司
    “創薬支援インフォマティクスシステム構築プロジェクト:薬物動態,毒性の統合解析プラットフォーム “
    薬剤学, 2017 Jul 1, 77(4): 211-215, J-STAGE
2016
  • 1. Yotsukura S., duVerle D., Hancock T., Natsume-Kitatani Y., Mamitsuka H.
    “Computational recognition for long non-coding RNA (lncRNA): Software and databases. “
    Brief Bioinform, 2016 Feb2, PubMed:26839320
  • 2. Chen Y. A., Tripathi L. P., Mizuguchi K.
    “An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. “
    Database (Oxford), 2016 Mar17, PubMed:26989145
  • 3. Natsume-Kitatani Y., Mamitsuka H.
    “Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns. “
    PLoS One, 2016 Mar22, 11(3):e0115369, PubMed:27003446
  • 4. Tsuchiya Y., Mizuguchi K.
    “The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops. “
    The Protein Society, 2016 Jan8, PubMed:26749247
  • 5. Tsuchiya Y., Jounai N., Takeshita F., Ishii J K., Mizuguchi K.
    ” Ligand-induced Ordering of the C-terminal Tail Primes STING for Phosphorylation by TBK1. “
    EBioMedicine, 2016 June1, PII: S2352-3964(16):30241-9, doi:10.1016/j.ebiom.2016.05.039
  • 6. Tsuchiya Y., Mizuguchi K.
    “Sequence and structural determinants of antigen binding in antibody CDR
    loops. “
    Asia-Pacific Biotech News 20:29-31, 2016
  • 7. Murakami Y., Omori S., Kinoshita K.
    “NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. “
    J. Struct. Funct. Genomics, 2016, Aug 16, 1-10, PubMed:27530928
  • 8. Sakane A., Yoshizawa S., Nishimura M., Tsuchiya Y., Matsushita N., Miyake K., Horikawa K., Imoto I., Mizuguchi C., Saito H., Ueno T, Matsushita S., Haga H., Deguchi S., Mizuguchi K., Yokota H., Sasaki T.
    “Conformational plasticity of JRAB/MICAL-L2 provides ‘law and order’ in collective cell migration. “
    Mol. Bio. Cell, 2016, Aug 31, PubMed:27582384
  • 9. Prathipati P., Nagao C., Ahmad S., Mizuguchi K.
    “Improved pose and affinity predictions using different protocols tailored on the basis of data availability. “
    J. Comput. Aided Mol. Des., 30(9), 2016 Sep, PubMed:27714493
  • 10. Takashima S., Oka Y., Fujiki F., Morimoto S., Nakajima H., Nakae Y., Nakata J., Nishida S., Hosen N., Tatsumi N., Mizuguchi K., Hashimoto N., Oji Y., Tsuboi A., Kumanogoh A., Sugiyama H.
    “Syndecan-4 as a biomarker to predict clinical outcome for glioblastoma multiforme treated with WT1 peptide vaccine. “
    Future Sci. OA, 2(4) 2016 Dec, PubMed:28116121

  • 13.Hamano Y, Kida H, Ihara S, Murakami A, Yanagawa M, Ueda K, Honda O, Tripathi LP, Arai T, Hirose M, Hamasaki T, Yano Y, Kimura T, Kato Y, Takamatsu H, Otsuka T, Minami T, Hirata H, Inoue K, Nagatomo I, Takeda Y, Mori M, Nishikawa H, Mizuguchi K, Kijima T, Kitaichi M, Tomiyama N, Inoue Y, Kumanogoh A,
    “Classification of idiopathic interstitial pneumonias using anti-myxovirus resistance-protein 1 autoantibody “,Scientific Reports, 7:13201,2017 Feb, PubMed:28230086
  • 14.Yotsukura S., duVerle D., Hancock T., Natsume-Kitatani Y., Mamitsuka H.,
    “Computational recognition for long non-coding RNA (lncRNA): Software and databases ” Briefings in Bioinformatics, 15427, 2016 Feb2,doi:10.1038/ncomms15427
2015
  • 1. Koo CX., Kobiyama K., Shen YJ., LeBert N., Ahmad S., Khatoo M., Aoshi T., Gasser S., Ishii KJ.
    “RNA Polymerase III Regulates Cytosolic RNA:DNA Hybrids and Intracellular MicroRNA Expression. “
    J Biol Chem, 2015 Jan 26, PubMed:25623070
  • 2. Camargo LM., Zhang XD., Loerch P., Caceres RM., Marine SD., Uva P., Ferrer M., Rinaldis E., Stone DJ., Majercak J., Ray WJ., Chen Y. A., Shearman MS., Mizuguchi K.
    “Pathway-Based Analysis of Genome-Wide siRNA Screens Reveals the Regulatory Landscape of App Processing. “
    PLoS One, 2015, 10(2):e0115369, PubMed:25723573
  • 3. Ito M., Nakagawa S., Mizuguchi K., Okumura T.
    “Integration of Disease Entries Across OMIM, Orphanet, and a Proprietary Knowledge Base. “
    IEA/AIE, 2015 May 1,9101(120-130) URL:http://link.springer.com/chapter/10.1007/978-3-319-19066-2_12
  • 4. Kim N. H., Yoshimaru T., Chen Y. A., Matsuo T., Komatsu M., Miyoshi Y., Tanaka E., Sasa M., Mizuguchi K., Katagiri T.
    “BIG3 Inhibits the Estrogen-Dependent Nuclear Translocation of PHB2 via Multiple Karyopherin-Alpha Proteins in Breast Cancer Cells. “
    PLoS One,2015 June,10(6):e0127707, PubMed:26052702
  • 5. Nakae Y, Oka Y, Fujiki F, Morimoto S, Kamiya T, Takashima S, Nakata J, Nishida S, Nakajima H, Hosen N, Tsuboi A, Kyo T, Oji Y, Mizuguchi K, Kumanogoh A, Sugiyama H.
    “Two distinct effector memory cell populations of WT1 (Wilms’ tumor gene 1)-specific cytotoxic T lymphocytes in acute myeloid leukemia patients. “
    Cancer Immunol Immunother 64:791-804 (2015).PubMed:25835542
  • 6. Tsujii A., Miyamoto Y., Moriyama T., Tsuchiya Y., Obuse C., Mizuguchi K., Oka M., Yoneda Y.
    “Retinoblastoma Binding Protein 4-Regulated Classical Nuclear Transport Is Involved in Cellular Senescence. “
    J Biol Chem, 2015 Oct 21,.PubMed:26491019
  • 7. Prathipati P., Mizuguchi K.
    “Integration of Ligand and Structure Based Approaches for CSAR-2014 “
    J. Chem. Inf. Model,2015 Nov 5., PubMed:26492437
  • 8. Prathipati P.,Mizuguchi K.
    “Systems Biology Approaches to a Rational Drug Discovery Paradigm. “
    Current Topics in Medicinal Chemistry, 2015 Aug 26.,16(9): 1009-1025, PubMed:26306988
  • 9. Chiba S., Ikeda K., Ishida T., Gromiha M., Taguchi Y., Iwadate M., Umeyama H., Hsin K., Kitano H., Yamamoto K., Sugaya N., Kato K., Okuno T., Chikenji G., Mochizuki M., Yasuo N., Yoshino R., Yanagisawa K., Ban T T., Teramoto R., Ramakrishnan C., Thangakani A. M., Velmurugan D., Prathipati P., Ito J., Tsuchiya Y., Mizuguchi K., Honma T., Hirokawa T., Akiyama Y., Sekijima M.
    “Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. “
    Scientific Reports 5, 2015 Nov 26, PubMed:26607293
  • 10. Lee J., Park E.J.,Yuki Y., Ahmad S., Mizuguchi K., Ishii K. J, Shimaoka M., Kiyono H.
    “Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis. “
    Scientific Reports 5,2015 Dec 9, PubMed:26647826
2014
  • 1. Nagao C., Nagano N., Mizuguchi K.
    “Prediction of detailed enzyme functions and identification of specificity determining residues by random forests. “
    PLoS One, 2014 Jan 8, 9(1):e84623, PubMed:24416252
  • 2. Katayama T., Chen YA., Igarashi Y., Ito M., Morita M., Nystrom-Persson J., Yamasaki C., Takagi T., et. al.
    “BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. “
    J Biomed Semantics, 2014 Feb 5, 5(1):5, PubMed:24495517
  • 3. 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. “
    Nat Commun, 2014 Mar 18, 5:3492, PubMed:24637670
  • 4. Lensink MF., Moal IH., Bates PA., Kastritis PL., Melquiond AS., Karaca E., Schmitz C., van Dijk M., Bonvin AM., Eisenstein M., Jiménez-García B., Grosdidier S., Solernou A., Pérez-Cano L., Pallara C., Fernández-Recio J., Xu J., Muthu P., Praneeth Kilambi K., Gray JJ., Grudinin S., Derevyanko G., Mitchell JC., Wieting J., Kanamori E., Tsuchiya Y., Murakami Y., Sarmiento J., Standley DM., Shirota M., Kinoshita K., Nakamura H., Chavent M., Ritchie DW., Park H., Ko J., Lee H., Seok C., Shen Y., Kozakov D., Vajda S., Kundrotas PJ., Vakser IA., Pierce BG., Hwang H., Vreven T., Weng Z., Buch I., Farkash E., Wolfson HJ., Zacharias M., Qin S., Zhou HX., Huang SY., Zou X., Wojdyla JA., Kleanthous C., Wodak SJ.
    “Blind prediction of interfacial water positions in CAPRI. “
    Proteins, 2014 Apr, 82(4):620-32, PubMed:24155158
  • 5. Fujita J., Maeda Y., Nagao C., Tsuchiya Y., Miyazaki Y., Hirose M., Mizohata E., Matsumoto Y., Inoue T., Mizuguchi K., Matsumura H.
    “Crystal structure of FtsA from Staphylococcus aureus. “
    FEBS Lett, 2014 May, 588(10):1879-85, PubMed:24746687
  • 6. Chen YA., Tripathi LP., Dessailly BH.
    “Nyström-Persson J., Ahmad S., Mizuguchi K., Integrated pathway clusters with coherent biological themes for target prioritisation. “
    PLoS One, 2014, 9(6):e99030, PubMed:24918583
  • 7. Murakami Y., Mizuguchi K., Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators., BMC Bioinformatics, 2014 Jun 23, 15(1):213, PubMed:24953126
  • 8. Chen YA., Murakami Y., Ahmad S., Yoshimaru T., Katagri T., Mizuguchi K.
    ” Brefeldin a-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type alpha-helical structure. “
    BMC Res Notes, 2014 Jul 6, 7(1):435, PubMed:24997568
  • 9. Shirai H., Ikeda K., 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, 2014 Aug, 82(8):1624-35, PubMed:24756852
  • 10. Ito JI., Ikeda K., Yamada K., Mizuguchi K., Tomii K.
    “PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. “
    Nucleic Acids Res, 2014 Nov 17, PubMed:25404129
  • 11. Yamada H., Nagao C., Haredy AM., Mori Y., Mizuguchi K., Yamanishi K., Okamoto S.
    “Dextran sulfate-resistant A/Puerto Rico/8/34 influenza virus is associated with the emergence of specific mutations in the neuraminidase glycoprotein. “
    Antiviral Res, 2014 Nov, 111:69-77, PubMed:25234090
  • 12. Yamashita K., Ikeda K., Amada K., Liang S., Tsuchiya Y., Nakamura H., Shirai H., Standley DM.
    “Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. “
    Bioinformatics, 2014 Nov 15, 30(22):3279-80, PubMed:25064566
  • 13. Kumagai A., Fujita A., Yokoyama T., Nonobe Y., Hasaba Y., Sasaki T., Itoh Y., Koura M., Suzuki O., Adachi S., Ryo H., Kohara A., Tripathi LP., Sanosaka M., Fukushima T., Takahashi H., Kitagawa K., Nagaoka Y., Kawahara H., Mizuguchi K., Nomura T., Matsuda J., Tabata T., Takemori H.
    “Altered Actions of Memantine and NMDA-Induced Currents in a New Grid2-Deleted Mouse Line. “
    Genes (Basel), 2014 Dec 11, 5(4):1095-114, PubMed:25513882
2013
  • 1. Hutchins AP., Diez D., Takahashi Y., Ahmad S., Jauch R., Tremblay ML., Miranda-Saavedra D.
    “Distinct transcriptional regulatory modules underlie STAT3′s cell type-independent and cell type-specific functions. “
    Nucleic Acids Res, 2013 Feb 1, 41(4):2155-70, PubMed:23295670
  • 2. Tiwari P., Tripathi LP., Nishikawa-Matsumura T., Ahmad S., Song SN., Isobe T., Mizuguchi K., Yoshizaki K.
    “Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter. “
    Biochim Biophys Acta, 2013 Jun, 1830(6):3650-5, PubMed:23391827
  • 3. Tang CK., Aoshi T., Jounai N., Ito J., Ohata K., Kobiyama K., Dessailly BH., Kuroda E., Akira S., Mizuguchi K., Coban C., Ishii KJ.
    “The chemotherapeutic agent DMXAA as a unique IRF3-dependent type-2 vaccine adjuvant. “
    PLoS One, 2013, 8(3):e60038, PubMed:23555875
  • 4. Dessailly BH., Dawson NL., Mizuguchi K., Orengo CA.
    “Functional site plasticity in domain superfamilies. “
    Biochim Biophys Acta, 2013 May, 1834(5):874-89, PubMed:23499848
  • 5. Tripathi LP., Kambara H., Chen YA., Nishimura Y., Moriishi K., Okamoto T., Morita E., Abe T., Mori Y., Matsuura Y., Mizuguchi K.
    “Understanding the biological context of NS5A-host interactions in HCV infection: a network-based approach. “
    J Proteome Res, 2013 Jun 7, 12(6):2537-51, PubMed:23682656
  • 6. Fujita J., Miyazaki Y., Hirose M., Nagao C., Mizohata E., Matsumoto Y., Mizuguchi K., Inoue T., Matsumura H.
    “Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus. “
    Acta Crystallogr Sect F Struct Biol Cryst Commun, 2013 Aug, 69(Pt 8):895-8, PubMed:23908037
  • 7. Nyström-Persson J., Igarashi Y., Ito M., Morita M., Nakatsu N., Yamada H., Mizuguchi K.
    “Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform. “
    Bioinformatics, 2013 Dec 1, 29(23):3080-6, PubMed:24048354
  • 8. Yoshimaru T., Komatsu M., Matsuo T., Chen YA., Murakami Y., Mizuguchi K., Mizohata E., Inoue T., Akiyama M., Yamaguchi R., Imoto S., Miyano S., Miyoshi Y., Sasa M., Nakamura Y., Katagiri T.
    “Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells. “
    Nat Commun, 2013, 4:2443, PubMed:24051437
  • 9. Andrabi M., Mizuguchi K., Ahmad S.
    “Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability. “
    Proteins, 2013 Oct 31, PubMed:24265157
  • 10. Hobro AJ., Standley DM., Ahmad S., Smith NI.
    “Deconstructing RNA: optical measurement of composition and structure. “
    Phys Chem Chem Phys, 2013 Aug 21, 15(31):13199-208, PubMed:23824161
  • 11. Moretti R., Fleishman SJ., Agius R., Torchala M., Bates PA., Kastritis PL., Rodrigues JP., Trellet M., Bonvin AM., Cui M., Rooman M., Gillis D., Dehouck Y., Moal I., Romero-Durana M., Perez-Cano L., Pallara C., Jimenez B., Fernandez-Recio J., Flores S., Pacella M., Praneeth Kilambi K., Gray JJ., Popov P., Grudinin S., Esquivel-Rodríguez J., Kihara D., Zhao N., Korkin D., Zhu X., Demerdash ON., Mitchell JC., Kanamori E., Tsuchiya Y., Nakamura H., Lee H., Park H., Seok C., Sarmiento J., Liang S., Teraguchi S., Standley DM., Shimoyama H., Terashi G., Takeda-Shitaka M., Iwadate M., Umeyama H., Beglov D., Hall DR., Kozakov D., Vajda S., Pierce BG., Hwang H., Vreven T., Weng Z., Huang Y., Li H., Yang X., Ji X., Liu S., Xiao Y., Zacharias M., Qin S., Zhou HX., Huang SY., Zou X., Velankar S., Janin J., Wodak SJ., Baker D.
    “Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. “
    Proteins, 2013 Nov, 81(11):1980-7, PubMed:23843247
2012
  • 1. Nagao C., Izako N., Soga S., Khan S.H., Kawabata S., Shirai H., Mizuguchi K.
    “Computational design, construction and characterization of a set of specificity determining residues in protein-protein interactions. “
    Proteins, 2012 PubMed
  • 2. Tripathi L. P., Kambara, H., Moriishi, K., Morita, E., Abe, T., Mori, Y., Chen, Y. A., Matsuura, Y., Mizuguchi, K.
    “Proteomic Analysis of Hepatitis C Virus (HCV) Core Protein Transfection and Host Regulator PA28gamma Knockout in HCV Pathogenesis: A Network-Based Study. “
    J Proteome Res, 2012 PubMed
  • 3. Blower T. R., Short F. L., Rao F., Mori T., Mizuguchi K., Pei X. Y., Fineran P. C., Luisi B. F., Salmond G. P.
    “Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes. “
    Nucleic Acids Res, 2012 PubMed
  • 4. Ihara S., Kida H., Arase H., et al.
    “Inhibitory Roles of Signal Transducer and Activator of Transcription 3 in Antitumor Immunity during Carcinogen-Induced Lung Tumorigenesis. “
    Cancer Reserch, 72(12); 1–10, 2012 PubMed
  • 5. Keeble-Gagnère G., Nyström-Persson J., et al.
    “An Open Framework for Extensible Multi-Stage Bioinformatics Software. “
    Proceedings of the 7th International Conference on Pattern Recognition inBioinformatics (PRIB) , 2012 Arxiv
  • 6. Morita M.,Igarashi Y., et al.
    “Sagace: A web-based search engine for biomedical databases in Japan. “
    BMC Res Notes, 5(1): 604, 2012 Pubmed
  • 7. Tripathi L. P., and K. Mizuguchi.
    “A combined proteomics and computational approach provides a better understanding of HCV-induced liver disease. “
    Expert Rev Proteomics 9(5): 493-496, 2012 Pubmed
2011
  • 1. Morita M., Katta AV., Ahmad S., Mori T., Sugita Y., Mizuguchi K.
    “Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data. “
    BMC Biophys, 4(1):21, 2011 PubMed
  • 2. Ahmad S., Mizuguchi K.
    “Partner-aware prediction of interacting residues in protein-protein complexes from sequence data. “
    PLoS One, 6(12):e29104, 2011 PubMed
  • 3. Williams SG., Madan R., Norris MG., Archer J., Mizuguchi K., Robertson DL., Lovell SC.
    “Using Knowledge of Protein Structural Constraints to Predict the Evolution of HIV-1. “
    Molecular Biology, 410(5):1023-34, 2011 PubMed
  • 4. Kahali B., Ashmad S., Ghosh TC.
    “Selective constraints in yeast genes with differential expressivity: Codon pair usage and mRNA stability perspectives. “
    Gene, 481(2):76-82, 2011 PubMed
  • 5. Firoz A., Malik A., Jpolin KH., Ahmad Z., Jha V., Ahmad S.
    “Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. “
    BMC Biochem, 12:20, 2011 PubMed
  • 6. Chen YA., Tripathi L.P., Mizuguchi K.
    “TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery. “
    PLoS One, 8;6(3):e17844, 2011 PubMed
  • 7. Schwarz UI., Meyer Zu Schwabedissen HE., Tirona RG., Suzuki A., Leake BF., Mokrab Y., Mizuguchi K., Ho RH., Kim RB.
    “Identification of novel functional organic anion-transporting polypeptide 1B3 polymorphisms and assessment of substrate specificity. “
    Pharmacogenet Genomics, 21(3):103-114, 2011 PubMed
  • 8. Ahmad S., Sarai A.
    “Analysis of electric moments of RNA-binding proteins: Implications for mechanism and prediction. “
    BMC Structure Biology, 11:8, 2011 PubMed
  • 9. Fernandez M., Kumagai Y., Standley M. D., Sarai A., Mizuguchi K., and Ahmad S.
    “Prediction of dinucleotide-specific RNA-binding sites in proteins. “
    BMC Bioinformatics 2011, 12(13):S5, 2011 PubMed
  • 10. Hirata M., Ahamad S., Fujiki A., Matsumura H., Wakabayashi M., Ueda N., Liu K., Hayashada M., Hirayama T., Kohara A., Yanagihara K., Mizuguchi K. and Furue K. M.
    “日本におけるヒト ES,iPS 細胞研究標準化:その3 品質管理 “
    Tiss. Cult. Res. Commun., 30:137-149, 2011
2010
  • 1. Mondal S., Nagao C., Mizuguchi K.
    “Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores. “
    Protein Engineering, Design and Selection, 23(11): 859-869, 2010 PubMed
  • 2. Nagao C., Nagano N., Mizuguchi K.
    “Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies. “
    Proteins:structure, function, and bioinformatics, 78(10):2369-2384, 2010 PubMed
  • 3. Ahmad S., Singh YH., Paudel Y., Mori T., Sugita Y., Mizuguchi K.
    “Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. “
    BMC Bioinformatics, 11:533, 2010 PubMed
  • 4. Ahmad S., Keskin O., Mizuguchi K., Sarai A., Nussinov R.
    “CCRXP: exploring clusters of conserved residues in protein structures. “
    Nucleic Acids Research, 38:W398-401, 2010 PubMed
  • 5. Singh YH., Andrabi M., Kahali B., Ghosh TC., Mizuguchi K., Kochetov AV., Ahmad S.
    “On nucleotide solvent accessibility in RNA strucyure. “
    Gene, 463:41-48, 2010 PubMed
  • 6. Fernandez M., Ahmad S., Sarai A.
    “Proteometric recognition of stable kinase inhibition complexes using topological autocorrelation and support vector machines. “
    J Chem Inf Model, 50(6):1179-1188, 2010 PubMed
  • 7. Murakami Y.,Mizuguchi K.
    “Applying the Naive Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. “
    Bioinformatics, 26(15):1841-1848, 2010 PubMed
  • 8. Murakami Y., Spriggs, RV., Nakamura H., Jones S.
    “PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences. “
    Nucleic Acids Res, 38: W412-416, 2010 PubMed
  • 9. Someya S., Kakuta M., Morita M., Sumikoshi K., Cao W., Ge Z., Hirose O., Nakamura S., Terada T., Shimizu K.
    “Prediction of carbohydrate-binding proteins from sequences using support vector machines. “
    Adv Bioinformatics, 2010: 289301, 2010 PubMed
  • 10. Tripathi LP., Kataoka C., Taguwa S., Moriishi K., Mori Y., Matsuura Y., Mizuguchi K.
    “Network based analysis of hepatitis C virus Core and NS4B protein interactions. “
    Molecular BioSystems, 6(12): 2539-2553, 2010 PubMed
  • 11. Mokrab Y., Stevens TJ., Mizuguchi K.
    “A structural dissection of amino acid substitutions in helical transmembrane proteins has been published in Proteins. “
    Proteins: Structure, Function, and Bioinformatics, 78(14):2895-2907, 2010 PubMed
  • 12. Yoshioka Y., Watanabe H., Morishige T., Yao X., Ikemizu S., Nagao C., Ahmad S., Mizuguchi K., Tsunoda S., Tsutsumi Y., Mukai Y., Okada N., Nakagawa S.
    “Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using a phage display system. “
    Biomaterials, 31(7):1935-1943, 2010 PubMed
2009
  • 1. Andrabi M., Mizuguchi K., Sarai A. and Ahmad S.
    “Prediction of mono- and di-nucleotide specific contacts in DNA-binding proteins using neural networks. “
    BMC Structural Biology, 9:30, 2009 PubMed
  • 2. Singh H., Ahmad S.
    “Context-dependent reference state of solvent accessibility derived from native protein structure, s and assessed by predictability analysis. “
    BMC Structural Biology, 9:25, 2009 PubMed
  • 3. Spriggs VR., Murakami Y., Nakamura H., Jones S.
    “Protein function annotation from sequence: prediction of residues interacting with RNA. “
    Bioinformatics, 25(12):1492-1497, 2009 PubMed
  • 4. Morita M., Saito S., Ikeda K., Ohno K., Sugawara K., Suzuki T., Togawa T., Sakuraba H.
    “Structural bases of GM1 gangliosidosis and Morquio B disease. “
    J Hum Genet, 54(9):510-515, 2009 PubMed
  • 5. Furusawa H., Ozeki T., Morita M., Okahata Y.
    “Added Mass Effect on Immobilizations of Proteins on a 27 MHz Quartz Crystal Microbalance in Aqueous Solution. “
    Anal Chem, 81(6):2268-2273, 2009 PubMed
  • 6. Mondal S., Mizuguchi K.
    “Structural insights into the enzyme mechanism of a new family of d-2-hydroxyacid dehydrogenases, a close homolog of 2-ketopantoate reductase. “
    Genome Informatics, 23:98-105, 2009 PubMed
  • 7. Tateishi Y, Ariyoshi M, Igarashi R, Hara H, Mizuguchi K., Seto A, Nakai A, Kokubo T, Tochio H, Shirakawa M.
    “Molecular Basis for SUMOylation-dependent Regulation of DNA Binding Activity of Heat Shock Factor 2. “
    J Biol Chem, 284:2435-47, 2009 PubMed
  • 8. Shandar Ahmad
    “Sequence dependence and prediction of nucleotide solvent accessibility in double stranded DNA. “
    Gene, 428: 25-30, 2009 PubMed
  • 9. Bratati Kahali, Shandar Ahmad and Tapash C. Ghosh
    “Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network. “
    Gene 429: 18-22, 2009 PubMed
2008
  • 1. Zhu B., et al.
    “Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation. “
    PLoS Biol 6, e284.,2008 PubMed
  • 2. Tateishi Y., et al.
    “Molecular basis for SUMOylation-dependent regulation of DNA binding activity of heat shock factor 2. “
    J Biol Chem. 2008 PubMed
  • 3. Mokrab Y., Stevens T.J. and Mizuguchi K.
    “Lipophobicity and the residue environments of the transmembrane alpha-helical bundle. “
    Proteins 74, 32-49., 2008 PubMed
  • 4. Hart S.E., Howe C.J., Mizuguchi K. and Fernandez-Recio J.
    “Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum. “
    Protein Eng Des Sel 21, 689-98., 2008 PubMed
  • 5. Bailly X., Vanin S., Chabasse C., Mizuguchi K. and Vinogradov S.N.
    “A Phylogenomic Profile of Hemerythrins, the Nonheme Diiron Binding Respiratory Proteins. “
    BMC Evol Biol 8, 244., 2008 PubMed
  • 6. Zhu B., Pennack J.A., McQuilton P., Forero M.G., Mizuguchi K., Sutcliffe B., Gu C.J., Fenton J.C., Hidalgo A.
    “Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation. “
    PLoS Biol, 6:e284, 2008 PubMed
  • 7. Shandar Ahmad, Ozlem Keskin, Akinori Sarai and Ruth Nussinov
    “Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. “
    Nucleic Acids Research. 36: 5922-5932, 2008 PubMed
  • 8. Naqvi RA, Hussain A, Raish M, Noor A, Shahid M, Sarin R, Kukreti H, Khan NJ, Ahmad S, Deo VS, Husain SA, Pasha ST, Basir SF, Shukla NK.
    “Specific 50′CpG island methylation signatures of FHIT and p16 genes and their potential diagnostic relevance in Indian breast cancer patients. “
    DNA Cell Biology 27: 517-525, 2008 PubMed
  • 9. Ritu Singh, Shandar Ahmad, A. Mossavi and Faizan Ahmad
    “A new method for determining the constant pressure heat-capacity change associated with the transition between the native and random coil state of the proteins. “
    Biophysical Chemistry 133: 81-89, 2008 PubMed
  • 10. Kochetov AV, Ahmad S, Ivanisenko V, Volkova OA, Kolchanov NA, Sarai A.
    “uORFs, reinitiation and alternative translation start sites in human mRNAs. “
    FEBS Lett. 582(9): 1293-1297, 2008 PubMed
  • 11. Malik A., Arif S. M., Ahmad S., Sunderasan E.
    “A molecular and in-silico characterization of Hev b 4, a glycosylated latex allergen. “
    Int. J. Biol. Macromol. 42: 185-190, 2008 PubMed
2007
  • 1. Wang J.Y., Lee H.M. and Ahmad S.
    “SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine. “
    Proteins 68, 82-91, 2007 PubMed
  • 2. Vinogradov S.N., Hoogewijs D., Bailly X., Mizuguchi K., Dewilde S., Moens L. and Vanfleteren J.R.
    “A model of globin evolution. “
    Gene 398, 132-42, 2007 DOI:10.1016/j.gene.2007.02.041
  • 3. Mokrab Y., Bavro V.N., Mizuguchi K., Todorov N.P., Martin I.L., Dunn S.M., Chan S.L. and Chau P.L.
    “Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor. “
    J Mol Graph Model 26, 760-74 PubMed
  • 4. Mizuguchi K., Sele M. and Cubellis M.V.
    “Environment specific substitution tables for thermophilic proteins. “
    BMC Bioinformatics 8 Suppl 1, S15, 2007 PubMed
  • 5. Lyne R. et al.
    “FlyMine: an integrated database for Drosophila and Anopheles genomics. “
    Genome Biol 8, R129, 2007 PubMed
  • 6. Camargo L.M. et al.
    “Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia. “
    Mol Psychiatry 12, 74-86, 2007 PubMed
  • 7. Ahmad S., Singh Y.H., Arauzo-Bravo M.J. and Sarai A.
    “Sequence-based prediction of residue-level properties in proteins. “
    In Machine Learning in Bioinformatics (Zhang and Rajpakse, ed.^eds), pp. 143-169. Wiley USA, 2007
2006
  • 1. Shiozawa K., Goda N., Shimizu T., Mizuguchi K., Kondo N., Shimozawa N., Shirakawa M. and Hiroaki H.
    “The common phospholipid binding activity of the N-terminal domains of PEX1 and VCP/p97. “
    FEBS J 273, 4959-4971, 2006 PubMed
  • 2. Shirai H., Mokrab Y., Mizuguchi K.
    “The guanidino-group modifying enzymes: Structural basis for their diversity and commonality. “
    Proteins: Structure, Function, and Bioinformatics;64:1010-1023, 2006 PubMed