Publications

Upto 2018

• 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

• GeTFEP: A general transfer free energy profile of transmembrane proteins W Tian, H Naveed, M Lin, J Liang BioRxiv, 191650

• 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