Prof. Shandar Ahmad

    Publication Philosophy


    Selected papers:

    Protein-DNA interactions

    Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism, Shandar Ahmad*, Philip Prathipati, Lokesh P Tripathi, Yi-An Chen, Ajay Arya, Yoichi Murakami and Kenji Mizuguchi, Nucleic Acids Research (In Press; 2018) read here


    Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences, Munazah Andrabi, Andrew Paul Hutchins, Diego Miranda-Saavedra, Hidetoshi Kono, Ruth Nussinov, Kenji Mizuguchi and Shandar Ahmad*, Scientific Reports (2017) 7,4071 read here


    Analysis and Prediction of DNA-binding proteins and their binding residues based on Composition, Sequence and Structural Information, Shandar Ahmad*, M. Michael Gromiha and Akinori Sarai, Bioinformatics 20 (2004), 477-486.

    ReadOut: Structure-based Calculation of Direct and Indirect Readout Energies and Specificities for Protein-DNA Recognition, Shandar Ahmad, Hidetoshi Kono, Marcos J. Araœzo-Bravo, Akinori Sarai*, Nucleic Acids Res. 34 (2006), W124-W127.

    DNA-binding proteins: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins, Shandar Ahmad, Ozlem Keskin, Akinori Sarai* and Ruth Nussinov, Nucleic Acids Res. 36 (2008), 5922-5932.

    Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. Andrew Paul Hutchins, Diego Diez, Yoshiko Takahashi, Shandar Ahmad, Ralf Jauch, Michel Tremblay, Diego Miranda-Saavedra*, Nucleic Acids Research (2013) 41 (4), 2155-2170

    Conformational changes in DNA-binding proteins: relationships with pre-complex features and contributions to specificity and stability, Munazah Andrabi, Kenji Mizuguchi and Shandar Ahmad*, Proteins: Structure, function and bioinformatics (2014) 82(5), 841–857

    Selected Papers

    Other topics

    Partner-aware prediction of interacting residues in protein-protein complexes from sequence data, Shandar Ahmad* and Kenji Mizuguchi, PLoS One 6(12) e29104. (2011): doi:10.1371/journal.pone.0029104

    Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation, YA Chen, LP Tripathi, BH Dessailly, J Nyström-Persson, Shandar Ahmad, Kenji Mizuguchi, PloS one (2014) 9 (6), e99030 

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