Shandar Ahmad
Professor
Centre/School/Special Centre
School of Computational and Integrative Sciences
Room No
09
Email
shandar[at]jnu[dot]ac[dot]in
Personal Webpage
Qualifications
Ph.D.
Areas of Interest/Specialization
Protein-DNA interactions
Genome-wide DNA conformation
Microbrial genome assembly and genome-phenome association
Algorthims for Computational Biology
Machine Learning and Integrative analysis of biological data; Neural networks, deep learning and big data analytics
Experience
Lecturer/Reader/Professor at Jamia Millia Islamia, New Delhi (Aug 1994-Jan 2007)
Visiting Scientist at RIKEN Tsukuba Institute, Tsukuba, Japan (2001)
Visiting Lecturer at Universiti Putra Malaysia, Malaysia (2000-2001)
Senior Scientist at Kyushu Institute of Technology, Japan (2003-2005)
Research Scientist at National Institute of Biomedical Innovation, Osaka, Japan (Jan 2007-March 2016)
Adjunct Associate Professor at Graduate School of Frontier Bioscience, Osaka University, Japan (April 2008-March 2016)
Awards & Honours
Appointed Visiting Scientist at National Institute of Biomedical Innovation, Health and Nutrition, Japan w.e.f. April 2016-March 2017
Best Peer Reviewed Publications
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information, S Ahmad, MM Gromiha, A Sarai, Bioinformatics (2004) 20 (4), 477-486
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition, S Ahmad, H Kono, MJ Arauzo-Bravo, A Sarai, Nucleic acids research (2006) 34 (suppl 2), W124-W127
Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins, S Ahmad, O Keskin, A Sarai, R Nussinov. Nucleic acids research (2008) 36 (18), 5922-5932
CCRXP: exploring clusters of conserved residues in protein structures Shandar Ahmad,Ozlem Keskin, Kenji Mizuguchi, Akinori Sarai, and Ruth Nussinov, Nucl. Acids Res. (2010) 38 (suppl 2): W398-W401
Prediction of dinucleotide-specific RNA-binding sites in proteins, M Fernandez, Y Kumagai, DM Standley, A Sarai, K Mizuguchi, S Ahmad BMC bioinformatics (2011) 12 (Suppl 13), S5
Recent Peer Reviewed Journals/Books
Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis Juneyoung Lee, Eun Jeong Park, Yoshikazu Yuki, Shandar Ahmad, Kenji Mizuguchi, Ken J Ishii, Motomu Shimaoka, Hiroshi Kiyono, Scientific reports (2015) 5
Genome-wide transcription factor activities are explained by intrinsic conformational dynamics of binding-sites and distal flanking-regions, Munazah Andrabi, Andrew Paul Hutchins, Diego Miranda-Saavedra, Hidetoshi Kono, Ruth Nussinov, Kenji Mizuguchi, Shandar Ahmad (2015) bioRxiv, 020602
Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability, M Andrabi, K Mizuguchi, S Ahmad, Proteins: Structure, Function, and Bioinformatics (2014) 82 (5), 841-857