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Publications

2019

  • 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.

Upto 2018

  • Wei Tian, Meishan Lin, Ke Tang, Jie Liang and Hammad Naveed. Towards high resolution structure prediction of β-barrel membrane proteins. Proceedings of the National Academy Sciences USA, 2018, 115 (7): 1511-1516.

  • 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.

  • 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.

  • Meishan Lin, Dennis Gessmann, Hammad Naveed and Jie Liang. Outer membrane protein folding and topology from a computational transfer free energy scale. Journal of the American Chemical Society, 2016, 138(8): 2592–2601

  • 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

  • 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

  • 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.

  • 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. Journal of Molecular Biology, 2012, 419(1-2), 89-101.

  • Hammad Naveed, Yun Xu, Ronald Jackups Jr. and Jie Liang. Predicting three-dimensional atomic structures of transmembrane domains of β-barrel membrane proteins. Journal of the American Chemical Society, 2012, 134(3), 1775-81.

  • Shay Geula, Hammad Naveed, Jie Liang and Varda Shoshan-Barmatz. Structure-Based Analysis of VDAC1: Defining Oligomer Contact Sites. Journal of Biological Chemistry, 2012, 287(3), 2179-2190.

  • 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.

  • 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.

  • 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. Journal of Molecular Biology, 2011, 413(1), pg 150-161.

  • 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.

  • 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. Proceedings of the National Academy Sciences USA, 2009, 106(31), pg 12735-12740.

  • 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


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