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Shandar Ahmad  シャンダー アハマド

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シャンダー アハマド  シャンダー アハマド

SHANDAR Ahmad  シャンダー アハマド

AHMAD Shandar  アハマド シヤンダー

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Researcher Number 80463298
Affiliation (Current) 2025: 国立研究開発法人医薬基盤・健康・栄養研究所, 医薬基盤研究所 AI健康・医薬研究センター, 客員研究員
Affiliation (based on the past Project Information) *help 2015: 国立研究開発法人医薬基盤・健康・栄養研究所, その他部局等, 研究員
2011 – 2012: 独立行政法人医薬基盤研究所, 創薬基盤研究部, 研究員
2010: 独立行政法人医薬基盤研究所, 研究員
Review Section/Research Field
Principal Investigator
Life / Health / Medical informatics / Bioinformatics/Life informatics
Keywords
Principal Investigator
Machine learning / Protein-DNA interactions / Transcription / DNA dynamics / DNA structure / protein function / Protein structure / Amino acids / Protein function / Binding site … More / Protein-protein interaction / Residue-pair / Protein complex / Transfer of training / Neural network / Partner-aware prediction / Evolutionary profiles / Protein interactions / Binding sites / Prediction / バイオインフォマティクス Less
  • Research Projects

    (2 results)
  • Research Products

    (22 results)
  •  Genome-wide DNA and protein conformational dynamics: sequence-based prediction and tissue-specific profilingPrincipal Investigator

    • Principal Investigator
      シャンダー アハマド
    • Project Period (FY)
      2015
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Life / Health / Medical informatics
    • Research Institution
      National Institutes of Biomedical Innovation, Health and Nutrition
  •  Prediction of protein-protein interactions from residue-pair interaction predictionPrincipal Investigator

    • Principal Investigator
      SHANDAR Ahmad
    • Project Period (FY)
      2010 – 2012
    • Research Category
      Grant-in-Aid for Scientific Research (C)
    • Research Field
      Bioinformatics/Life informatics
    • Research Institution
      独立行政法人医薬基盤研究所

All 2015 2013 2012 2011 2010

All Journal Article Presentation

  • [Journal Article] Genome-wide transcription factor activities are explained by intrinsic conformational dynamics of binding-sites and distal flanking-regions2015

    • Author(s)
      Munazah Andrabi, Andrew Paul Hutchins, Diego Miranda-Saavedra, Hidetoshi Kono, Ruth Nussinov, Kenji Mizuguchi, Shandar Ahmad
    • Journal Title

      bioRxiv

      Volume: June 9

    • DOI

      10.1101/020602

    • Acknowledgement Compliant / Open Access
    • Data Source
      KAKENHI-PROJECT-15K00419
  • [Journal Article] Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins2013

    • Author(s)
      Nagarajan R, Ahmad S, GromihaM
    • Journal Title

      Nucleic Acids Research

      Volume: (In Press)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions2013

    • Author(s)
      Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay ML, Miranda-Saavedra D
    • Journal Title

      Nucleic Acids Res

      Volume: 41(4) Pages: 2155-70

    • URL

      http://dx.doi.org/10.1093/nar/gks1

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in Serum amyloid A gene promoter2013

    • Author(s)
      Prabha Tiwari, Lokesh P Tripathi, Teppei Nishikawa-Matsumura, Shandar Ahmad, Soken-Nakazawa J Song, Tomoyasu Isobe, Kenji Mizuguchi, Kazuyuki Yoshizaki
    • Journal Title

      Biochimica et Biophysica Acta (BBA)-General Subjects

      Volume: 1830 Issue: 6 Pages: 3650-3655

    • DOI

      10.1016/j.bbagen.2013.01.024

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions2013

    • Author(s)
      Andrew Paul Hutchins, Diego Diez, Yoshiko Takahashi, Shandar Ahmad, Ralf Jauch, Michel Lucien Tremblay, Diego Miranda-Saavedra
    • Journal Title

      Nucleic Acids Research

      Volume: 41 Issue: 4 Pages: 2155-2170

    • DOI

      10.1093/nar/gks1300

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277, KAKENHI-PROJECT-23710235
  • [Journal Article] Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter2012

    • Author(s)
      Tiwari P, Tripathi LP, Nishikawa-Matsumura T, Ahmad S, Song SN, Isobe T, Mizuguchi K, Yoshizaki K
    • Journal Title

      Biochim Biophys Acta

      Volume: 1830(6) Pages: 3650-5

    • URL

      http://dx.doi.org/10.1016/j.bbagen.2013.01.024

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Prediction of dinucleotide-specific RNA-binding sites in proteins2011

    • Author(s)
      Fernandez M, Kumagai Y, Standley DM, Sarai A, Mizuguchi K, Ahmad S
    • Journal Title

      BMC Bioinformatics

      Volume: Nov 30

    • URL

      http://doi.org/10.1186/1471-2105-12-S13-S5

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Partner-aware prediction of interacting residues in protein-protein complexes from sequence data2011

    • Author(s)
      Shandar Ahmad, Kenji Mizuguchi
    • Journal Title

      PLoS One

      Volume: VOL.6 Issue: 12 Pages: e29104-e29104

    • DOI

      10.1371/journal.pone.0029104

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction2011

    • Author(s)
      Ahmad S, Sarai A
    • Journal Title

      BMC Struct Biol

      Volume: 11 Pages: 8-8

    • URL

      http://doi.org/10.1186/1472-6807-11-8

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates2011

    • Author(s)
      Firoz A, Malik A, Joplin KH, Ahmad Z, Jha V, Ahmad S
    • Journal Title

      BMC Biochem

      Volume: 12 Pages: 20-20

    • URL

      http://doi.org/10.1186/1471-2091-12-20

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Residue propensities, discrimination and binding site prediction of adenine and guanine phosohates2011

    • Author(s)
      Ahmad Firoz, et al
    • Journal Title

      BMC Biochemistry

      Volume: VOL.12 Issue: 1

    • DOI

      10.1186/1471-2091-12-20

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Analysis of electric moments of RNA-binding proteins : Implications for mechanism and prediction.2011

    • Author(s)
      Shandar Ahmad, Akinori Sarai
    • Journal Title

      BMC Structural Biology

      Volume: 11

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Journal Article] Partner-aware prediction of interacting residues in protein-protein complexes from sequence data2011

    • Author(s)
      Ahmad S, Mizuguchi K
    • Journal Title

      PLoS One

      Volume: 6(12)

    • Peer Reviewed
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] A meta-analysis of public microarray datasets to detect differential expression of heat shock proteins in children2012

    • Author(s)
      Shandar Ahmad
    • Organizer
      Biomarker discovery conference
    • Place of Presentation
      Shoal Bay, Australia
    • Year and Date
      2012-11-13
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] A sliding-probe model for predicting partner aware protein-protein interaction sites2012

    • Author(s)
      Shandar Ahmad, Kenji Mizuguchi
    • Organizer
      Geneome Informatics Conference (GIW2012)
    • Place of Presentation
      Taiwan
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] (1) A meta-analysis of public microarray datasets to detect differential expression of heat shock proteins in children2012

    • Author(s)
      Shandar Ahmad
    • Organizer
      Biomarker discovery conference (BDC2012)
    • Place of Presentation
      Shoal Bay, Australia
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] A sliding-probe model for predicting partner aware protein-protein interaction sites2012

    • Author(s)
      Shandar Ahmad, Kenji Mizuguchi
    • Organizer
      Genome Informatics Conference (GIW2012)
    • Place of Presentation
      Taiwan
    • Year and Date
      2012-11-06
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] Predicting Bio-molecular interactions in proteins and nucleic acids, International2011

    • Author(s)
      Shandar Ahmad
    • Organizer
      Interdisciplinary science conference
    • Place of Presentation
      Jamia Millia Islamia University, New Delhi, India (invited talk by Shandar Ahmad)
    • Year and Date
      2011-11-16
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] Predicting Bio-molecular interactions in proteins and nucleic acids2011

    • Author(s)
      Shandar Ahmad
    • Organizer
      International Interdisciplinary science conference
    • Place of Presentation
      Jamia Millia Islamia University(インド、ニューデリ)(招待講演)
    • Year and Date
      2011-11-16
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] Sequence-to-structure prediction errors can reveal conformational flexibility in helical membrane proteins2010

    • Author(s)
      Shandar Ahmad, Hemjit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita and Kenji Mizuguchi
    • Organizer
      Intelligent Systems in Molecular Biology (ISMB 2010)
    • Place of Presentation
      Boston, USA
    • Year and Date
      2010-07-11
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] Statistical analysis and prediction of kinked residue positions in helical membrane proteins2010

    • Author(s)
      Shandar Ahmad, Kenji Mizuguchi
    • Organizer
      Japanese Society of Bioinformatics (JSBI) annual meeting 2010
    • Place of Presentation
      Kyushu University, Fukuoka
    • Year and Date
      2010-11-13
    • Data Source
      KAKENHI-PROJECT-22500277
  • [Presentation] Prediction of dinucleotide-specific RNA-binding sites in proteins using sequence and evolutionary information2010

    • Author(s)
      Michael Llamosa Fernandez, Yutaro Kumagai, Daron Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad
    • Organizer
      Intelligent Systems in Molecular Biology (ISMB 2010)
    • Place of Presentation
      Boston, USA
    • Year and Date
      2010-07-11
    • Data Source
      KAKENHI-PROJECT-22500277

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