Prof. Shandar Ahmad

    Publication Philosophy

    Publications

    Selected papers:

    Protein-DNA interactions

    Enabling full‐length evolutionary profiles based Deep Convolutional Neural Network for predicting DNA‐binding proteins from sequence, Sucheta Chauhan and  Shandar Ahmad, Proteins: Structure, Function, and Bioinformatics (2019)

    read here

     

    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 (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. read here


    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. read here


    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. read here


    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 read here


    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 read here


    Selected Papers

    Other topics

    ECG anomaly class identification using LSTM and error profile modeling, Sucheta Chauhan, Lovekesh Vig, Shandar Ahmad, Computers in Biology and Medicine (2019) read here

    A comparison of shallow and deep learning methods for predicting cognitive performance of stroke patients from MRI lesion images, S Chauhan, L Vig, MDFD Grazia, M Corbetta, S Ahmad*, M Zorzi*, Frontiers in Neuroinformatics (2019)

    read here

     

    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 read here

    ECG anomaly class identification using LSTM and error profile modeling, Sucheta Chauhan, Lovekesh Vig, Shandar Ahmad


    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 read here

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