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Hammad Naveed

Associate Professor, Ph.D.

National University of Computer and Emerging Sciences, A.K. Brohi Road, H-11, Islamabad

  hammad.naveed@nu.edu.pk

   

Education

  • 2007 - 2012: Ph.D. (Bioinformatics). University of Illinois at Chicago - Chicago, IL, USA

  • 2001 - 2005: B.S (Computer Science). National University of Computer and Emerging Sciences - Islamabad, Pakistan

Employment

  • Jul 2017 - Present: Associate Professor at National University of Computer and Emerging Sciences, Islamabad, Pakistan

  • Nov 2014 - Aug 2017: Research Assistant Professor at Toyota Technological Institute at Chicago (TTIC)

  • Aug 2013 - Nov 2014: Postdoctoral Fellow at KAUST (King Abdullah University of Science and Technology), Saudi Arabia

  • Aug 2012 - Jun 2013: Postdoctoral Fellow at CAS-MPG Partner Institute of Computational Biology, Shanghai, China

Publications

  • Hammad Naveed*, Corinna Kuttenberger, Thomas Schubert, Xin Gao, Stefan T. Arold and Michael L. Maitland. Identifying novel targets by using drug-binding site signature: a case study of kinase inhibitors. Genomics, Proteomics & Bioinformatics, In press. *Corresponding Author.

  • Wei Tian, Hammad Naveed, Meishan Lin, Jie Liang. GeTFEP: A general transfer free energy profile of transmembraneproteins. Protein Science, In press.

  • Hammad Farooq, Hammad Naveed. GPADRlex: Grouped Phrasal Adverse Drug Reaction lexicon. IEEE International Conference on Signal Processing, Communications and Computing (ICSPCC) 2019, In press.

  • High-resolution structure prediction of β-barrel membrane proteins W Tian, M Lin, K Tang, J Liang, H Naveed Proceedings of the National Academy of Sciences 115 (7), 1511-1516

  • Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins W Tian, M Lin, H Naveed, J Liang Bioinformatics 33 (11), 1664-1671

  • ModuleAlign: module-based global alignment of protein–protein interaction networks S Hashemifar, J Ma, H Naveed, S Canzar, J Xu Bioinformatics 32 (17), i658-i664

  • Outer membrane protein folding and topology from a computational transfer free energy scale M Lin, D Gessmann, H Naveed, J Liang Journal of the American Chemical Society 138 (8), 2592-2601

  • Multiscale modeling of cellular epigenetic states: stochasticity in molecular networks, chromatin folding in cell nuclei, and tissue pattern formation of cells J Liang, Y Cao, G Gursoy, H Naveed, A Terebus, J Zhao Critical Reviews™ in Biomedical Engineering

  • Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces X Cui, H Naveed, X Gao Proceedings of the 6th ACM Conference on Bioinformatics, Computational …

  • An integrated structure-and system-based framework to identify new targets of metabolites and known drugs H Naveed, US Hameed, D Harrus, W Bourguet, ST Arold, X Gao Bioinformatics 31 (24), 3922-3929

  • An integrated structure-and system-based framework to identify new targets of metabolites and known drugs H Naveed, US Hameed, D Harrus, W Bourguet, ST Arold, X Gao Bioinformatics 31 (24), 3922-3929

  • Finding optimal interaction interface alignments between biological complexes X Cui, H Naveed, X Gao Bioinformatics 31 (12), i133-i141

  • Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern S Kachalo, H Naveed, Y Cao, J Zhao, J Liang PLOS One

  • Effects of Mechanical Properties on Tumor Invasion: Insights from a Cellular Model Y Li, H Naveed, J Liang, LX Xu

  • Mechanisms of Regulating Tissue Elongation in Drosophila Wing: Impact of Oriented Cell Divisions, Oriented Mechanical Forces, and Reduced Cell Size Y Li, H Naveed, S Kachalo, LX Xu, J Liang PLoS ONE

  • Weakly Stable Regions and Protein-Protein Interactions in Beta-Barrel Membrane Proteins H Naveed, J Liang Current Pharmaceutical Design

  • CoCiter: An Efficient Tool to Infer Gene Function by Assessing the Significance of Literature Co-Citation N Qiao, Y Huang, H Naveed, CD Green, JDJ Han PLoS ONE 8 (9), e74074

  • Structure-based protein-protein interaction networks and drug design H Naveed, JJ Han Quantitative Biology, 1-9

  • Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis Y Cao, H Naveed, C Liang, J Liang Engineering in Medicine and Biology Society, EMBC, 2013 Annual International Conference of the IEEE

  • Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis Y Cao, H Naveed, C Liang, J Liang Engineering in Medicine and Biology Society, EMBC, 2013 Annual International Conference of the IEEE

  • Modeling spatial population dynamics of stem cell lineage in tissue growth Y Cao, C Liang, H Naveed, Y Li, M Chen, Q Nie Engineering in Medicine and Biology Society, EMBC, 2012 Annual International Conference of the IEEE

  • Mechanisms of Regulating Cell Topology in Proliferating Epithelia: Impact of Division Plane, Mechanical Forces, and Cell Memory Y Li, H Naveed, S Kachalo, LX Xu, J Liang PLoS ONE 7 (8), e43108

  • Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. H Naveed, D Jimenez-Morales, J Tian, V Pasupuleti, LJ Kenney, J Liang Journal of molecular biology

  • TMBB-Explorer: A Webserver to Predict the Structure, Oligomerization State, Ppi Interface, and Thermodynamic Properties of the Transmembrane Domains of Outer Membrane Proteins H Naveed, J Liang Biophysical Journal 102 (3), 469a

  • Structure-based Analysis of VDAC1 Protein S Geula, H Naveed, J Liang, V Shoshan-Barmatz Journal of Biological Chemistry 287 (3), 2179-2190

  • Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins H Naveed, Y Xu, R Jackups Jr, J Liang Journal of the American Chemical Society 134 (3), 1775-1781

  • Computational Characterization of Structural and Thermodynamic Properties of β-barrel Membrane Proteins H Naveed University of Illinois at Chicago

  • Computational Studies of Membrane Proteins: Models and Predictions for Biological Understanding J Liang, H Naveed, D Jimenez-Morales, L Adamian, M Lin Biochimica et Biophysica Acta (BBA)-Biomembranes

  • Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations Dennis Gessmann, Frauke Mager, Hammad Naveed, Thomas Arnold, Sara Weirich, Dirk Linke, Jie Liang, Stephan Nussberger Journal of molecular biology 413 (1), 150-161

  • Mechanical forces mediate localized topological change in epithelia Y Li, H Naveed, S Kachalo, LX Xu, J Liang 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society

  • Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis L Adamian, H Naveed, J Liang Biochimica et Biophysica Acta (BBA)-Biomembranes 1808 (4), 1092-1102

  • Geometric order in proliferating epithelia: impact of rearrangements and cleavage plane orientation H Naveed, Y Li, S Kachalo, J Liang 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology

  • Predicting weakly stable regions, oligomerization state, and protein–protein interfaces in transmembrane domains of outer membrane proteins H Naveed, R Jackups, J Liang Proceedings of the National Academy of Sciences 106 (31), 12735-12740



Computational Biology Research Lab

Precision Medicine Lab, National Center in Big Data and Cloud Computing

Phone: +92 51 111 128 128 Ext. 394

Email: hammad.naveed@nu.edu.pk