hammad.naveed@nu.edu.pk
Associate Professor

Department of Computer Science

National University of Computer & Emerging Sciences, Pakistan

Google Scholar Profile

Publications

  1. Wei Tian, Meishan Lin, Ke Tang, Jie Liang and Hammad Naveed. Towards high resolution structure prediction of Beta-barrel membrane proteins . Proc National Academy of Sciences. 2018, In press.
  2. 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.
  3. 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.
  4. 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.
  5. Jie Liang, Youfang Cao, Gamze Gursoy, Hammad Naveed, Anna Terebus, and Jieling Zhao. Multiscale modeling of cellular epigenetic states: stochasticity in molecular networks, chromatin folding in cell nuclei, and tissue pattern formation of cells. Critical Reviews in Biomedical Engineering, 2015. 43(4): 323-346.
  6. Hammad Naveed, Umar S Hameed, Deborah Harrus, William Bourguet, Stefan T 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. Highlighted in Nature Middle East
  7. Sema 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)
  8. Xuefeng Cui, Hammad Naveed, and Xin Gao. Finding Optimal Interaction Interface Alignments between Biological Complexes. Bioinformatics 2015, 31 (12), i133-i141.
  9. Yingzi Li, Hammad Naveed, Lisa X. Xu, and Jie Liang. Effects of mechanical properties on tumor invasion: Insights from a cellular Model. Conf Proc IEEE Eng Med Biol Soc. 2014, 2014:6818-21.
  10. Hammad Naveed and Jie Liang. Weakly Stable Regions and Protein-Protein Interactions in Beta-Barrel Membrane Proteins. Current Pharmaceutical Design 2014, 20(8):1268-73.
  11. Yingzi Li, Hammad Naveed, Sema 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.
  12. Hammad Naveed and Jing-Dong J. Han. Structure-based Protein-Protein Interaction Networks and Drug Design. Quantitative Biology 2013, 1(3), 183-191.
  13. 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.
  14. 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, 2013, pg 5550-5553.
  15. Jieling Zhao, Hammad Naveed, Sema Kachalo, Youfang Cao, Tian Wei, and Jie Liang. Dynamic mechanical finite element model of biological cells for studying cellular pattern formation. Conf Proc IEEE Eng Med Biol Soc. 2013, pg 4517-4520.
  16. 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 Molecular Biology. 2012, 419: 89-101.
  17. Hammad Naveed, Yun Xu, Ronald Jackups Jr., and Jie Liang. Predicting three-dimensional structures of transmembrane domains of beta-barrel membrane proteins. J American Chemical Society. 2012, 134(3):1775-81.
  18. Shay Geula, Hammad Naveed, Jie Liang, and Varda Shoshan-Barmatz. Structure-based Analysis of VDAC1 Protein: Defining Oligomer Contact Sites. J Biological Chemistry. 2012, 287(3):2179-2190.
  19. Yingzi Li, Hammad Naveed, Sema 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.
  20. Jie Liang, Hammad Naveed, David Jimenez-Morales, Larisa Adamian, Meishan Lin. Computational Studies of Membrane Proteins: Models and Predictions for Biological Understanding. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2012, 1818(4):927-941.
  21. Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, Meng Chen, and Qing Nie. Modeling Spatial Population Dynamics of Stem Cell Lineage in Tissue Growth. Conf Proc IEEE Eng Med Biol Soc. 2012, pg 5502-5.
  22. 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 Molecular Biology. 2011, 413:150-161.
  23. Yingzi Li, Hammad Naveed, Sema 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.
  24. Larisa Adamian, Hammad Naveed, and Jie Liang. Lipid-binding surfaces of membrane proteins: Evidence from evolutionary and structural analysis. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011, 1808:1092-1102.
  25. Hammad Naveed, Yingzi Li, Sema 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.
  26. 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 National Academy of Sciences. 2009, 106(31):12735-12740.

    27. Commentery on my work

    • Modeling workshops and methods. PSI-Nature Structural Biology Knowledgebase. August 2010. Link to Article