Faculty Members

Education

• Ph.D. (Bioengineering), The University of Illinois at Chicago, USA (2012)
• BS (CS), National University of Computer & Emerging Sciences, Islamabad Pakistan (2005)

Profile

Hammad Naveed received his Ph.D. in Bioinformatics from University of Illinois at Chicago in 2012. He spent the following two and half years as a Postdoctoral Fellow at the CAS-MPG Partner institute for Computational Biology, Shanghai China and the Computational Biology Research Centre at KAUST, Saudi Arabia. He was a Research Assistant Professor at the Toyota Technological Institute at Chicago from 2014-2017. His research interests lie in several areas of Computational Structural Biology. He is particularly interested in computational identification of novel drug targets, drug repositioning, biophysical modelling of tissues and computational characterization of membrane proteins.
Research Papers

• Wei Tian, Meishan Lin, Hammad Naveed and Jie Liang. Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins. Bioinformatics, 2017, 33 (11), 1664-1671. IF: 7.307
• Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar and Jinbo Xu. ModuleAlign: Module-based global alignment of protein-protein interaction networks. Bioinformatics, 2016, 32(17): i658-i664. IF:7.307
• Meishan Lin, Dennis Gessmann, Hammad Naveed, and Jie Liang. Outer membrane protein folding and topology from a computational transfer free energy scale. J American Chemical Society. 2016, 138(8): 2592–2601. IF:13.858
• Jie Liang, Youfang Cao, Gamze Gursoy, Hammad Naveed, Anna Terebus, and Jieling Zhao. Multiscale modeling of cellular epigenetic state and cell patterning: stochastic network, chromatin folding and tissue formation. Critical Reviews in Biomedical Engineering, 2015. 43(4):323-346.
• Hammad Naveed, Umar Hameed, Deborrah Harrus, William Bourguet, Stefan Arold and Xin Gao. An integrated structure- and system-based framework to identify new targets of metabolites and known drugs. Bioinformatics. 2015, 31(24): 3922-3929. IF: 7.307 Highlighted in Nature Middle East (doi:10.1038/nmiddleeast.2015.153)
• Sëma Kachalo*, Hammad Naveed*, Youfang Cao, Jieling Zhao and Jie Liang. Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern. PLoS One. 2015, 10(5): e0126484. (* Equal Contribution) IF: 2.806
• Xuefeng Cui, Hammad Naveed, and Xin Gao. Finding Optimal Interaction Interface Alignments between Biological Complexes. Bioinformatics. 2015, 31(12): i133-i141. IF: 7.307
• Hammad Naveed and Jie Liang. Weakly Stable Regions and Protein-Protein Interactions in Beta-Barrel Membrane Proteins. Current Pharmaceutical Design. 2014, 20(8) 1268-1273. IF: 3.052
• Yingzi Li, Hammad Naveed, Sëma Kachalo, Lisa X. Xu, and Jie Liang. Mechanisms of Regulating Tissue Elongation in Drosophila Wing: Impact of Oriented Cell Divisions, Oriented Mechanical Forces, and Reduced Cell Size. PLoS One. 2014, 9(2), e86725. IF: 2.806
• Hammad Naveed and Jing-Dong J. Han. Structure-based Protein-Protein Interaction Networks and Drug Design. Quantitative Biology, 2013, 1(3), 183-191.
• Nan Qiao, Yi Huang, Hammad Naveed, Christopher D. Green, and Jing-Dong J. Han. CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation. PLoS One, 2013, 8(9), e74074. IF: 2.806
• Hammad Naveed, David Jimenez-Morales, Jun Tian, Volga Pasupuleti, Linda J. Kenney, and Jie Liang. Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding. J Mol Biol. 2012, 419(1-2), 89-101. IF: 4.333
• Hammad Naveed, Yun Xu, Ronald Jackups Jr., and Jie Liang. Predicting three-dimensional atomic structures of transmembrane domains of ß-barrel membrane proteins. J American Chemical Society. 2012, 134(3), 1775-81. IF: 13.858
• Shay Geula, Hammad Naveed, Jie Liang, and Varda Shoshan-Barmatz. Structure-Based Analysis of VDAC1: Defining Oligomer Contact Sites. J Biol Chem. 2012, 287(3), 2179-2190. IF: 4.573
• Jie Liang, Hammad Naveed, David Jimenez-Morales, Larisa Adamian, and Meishan Lin. Computational Studies of Membrane Proteins: Models and Predictions for Biological Understanding. BBA-Biomembranes. 2012, 1818(4), 927-941. IF: 3.498
• Yingzi Li, Hammad Naveed, Sëma Kachalo, Lisa X. Xu, and Jie Liang. Mechanisms of Regulating Cell Topology in Proliferating Epithelia: Impact of Division Plane, Mechanical Forces, and Cell Memory. PLoS One. 2012, 7(8), e43108. IF: 2.806
• Dennis Gessmann, Frauke Mager, Hammad Naveed, Thomas Arnold, Sara Weirich, Dirk Linke, Jie Liang, and Stephan Nussberger. Improving the Resistance of a Eukaryotic Beta-Barrel Protein to Thermal and Chemical Perturbation. J Mol Biol. 2011, 413(1), pg 150-161. IF: 4.333
• Larisa Adamian, Hammad Naveed, and Jie Liang. Lipid-binding surfaces of membrane proteins: Evidence from evolutionary and structural analysis. BBA-Biomembranes. 2011, 1808, pg 1092-1102. IF: 3.498
• Hammad Naveed, Ronald Jackups Jr., and Jie Liang. Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins. Proc. Nat. Aca. Sci. 2009, 106(31), pg 12735-12740. IF: 9.661 Highlighted in Modeling Workshops and Methods. PSI-Nature Structural Biology Knowledgebase, August 2010.

Conference Publications

• Xuefeng Cui, Hammad Naveed, and Xin Gao. Pairwise Structure Alignment Specifically Tuned for Surface Pockets and Interaction Interfaces. BCB '15 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, 507-508.
• Yingzi Li, Hammad Naveed, Jie Liang, and Lisa X. Xu. Effects of Mechanical Properties on Tumor Invasion: Insights from a Cellular Model. Conf Proc IEEE Eng Med Biol Soc. 2014, 6818-21.
• Youfang Cao, Hammad Naveed, Claire Liang, and Jie Liang. Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis. Conf Proc IEEE Eng Med Biol Soc. 2013, 5550-5553.
• Jieling Zhao, Hammad Naveed, Sema Kachalo, Youfang Cao, Wei Tian, and Jie Liang. Dynamic mechanical finite element model of biological cells for studying cellular pattern formation. Conf Proc IEEE Eng Med Biol Soc. 2013, 4517-4520.
• Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, and Qing Nie. Modeling spatial population dynamics of stem cells in tissue growth. Conf Proc IEEE Eng Med Biol Soc. 2012, 5502-5.
• Yingzi Li, Hammad Naveed, Sëma Kachalo, Lisa X. Xu, and Jie Liang. Mechanical Forces Mediate Localized Topological Change in Epithelia. Conf Proc IEEE Eng Med Biol Soc. 2011, 178-81.
• Hammad Naveed, Yingzi Li, Sëma Kachalo, and Jie Liang. Geometric order in proliferating epithelia: Impact of rearrangements and cleavage plane orientation. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2010, 3808-11.