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

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

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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

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

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