Shandar Ahmad シャンダーアハマド

… Alternative Names

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

Shandar Ahmad シャンダー アハマド

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

Research Projects

Research Products

Genome-wide DNA and protein conformational dynamics: sequence-based prediction and tissue-specific profilingPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Prediction of protein-protein interactions from residue-pair interaction predictionPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

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

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins2013

Author(s)

Journal Title

Data Source

[Journal Article] Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions2013

Author(s)

Journal Title

URL

Data Source

[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)

Journal Title

DOI

Data Source

[Journal Article] Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions2013

Author(s)

Journal Title

DOI

Data Source

[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)

Journal Title

URL

Data Source

[Journal Article] Prediction of dinucleotide-specific RNA-binding sites in proteins2011

Author(s)

Journal Title

URL

Data Source

[Journal Article] Partner-aware prediction of interacting residues in protein-protein complexes from sequence data2011

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction2011

Author(s)

Journal Title

URL

Data Source

[Journal Article] Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates2011

Author(s)

Journal Title

URL

Data Source

[Journal Article] Residue propensities, discrimination and binding site prediction of adenine and guanine phosohates2011

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Analysis of electric moments of RNA-binding proteins : Implications for mechanism and prediction.2011

Author(s)

Journal Title

Data Source

[Journal Article] Partner-aware prediction of interacting residues in protein-protein complexes from sequence data2011

Author(s)

Journal Title

Data Source

Shandar Ahmad シャンダーアハマド

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