Publications

2022

Amna Binte Kamran, Hammad Naveed. GOntoSim: a semantic similarity measure based on LCA and common descendants. Scientific reports, 2022.

Zoya Khalid, Hammad Naveed. Identification of destabilizing SNPs in SARS-CoV2-ACE2 protein and spike glycoprotein: implications for virus entry mechanisms. Journal of Biomolecular Structure and Dynamics, 2022

Salman Ahmed, Haasha bin Atif, Muhammad Bilal Shabbir, Hammad Naveed. PRNet: Progressive Resolution based Network for Radiograph based disease classification 2021 Ethics and Explainability for Responsible Data Science (EE-RDS)

Salman Ahmed, Hammad Naveed. Bias Adjustable Activation Network for Imbalanced Data—Diabetic Foot Ulcer Challenge 2021. Diabetic Foot Ulcers Grand Challenge, 2021

2021

Talha Anwar, Naeem Rehmat, Hammad Naveed. A Generic Approach for Classification of Psychological Disorders Diagnosis using EEG. 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Sana Saleh, Mukhtar Ullah, Hammad Naveed. Role of Cell Morphology in Classical Delta-Notch Pattern Formation. 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)

Muhammad Mushtaq, Hammad Naveed, Zoya Khalid. Computational Prediction of lncRNA-Protein Interactions using Machine learning. 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Sana Saleh, Mukhtar Ullah, Hammad Naveed. Cell fate determination is influenced by Notch heterogeneity. 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Kinaan Aamir Khan, Safyan Aman Memon, Hammad Naveed. A Generic Approach for Classification of Psychological Disorders Diagnosis using EEG. Protein Science, 2021.

Salman Ahmed, Hammad Naveed. OpTorch: Optimized deep learning architectures for resource limited environments. arXiv preprint arXiv:2105.00619, 2021.

Salman Ahmed, Maria Tariq, Hammad Naveed. Pmnet: A probability map based scaled network for breast cancer diagnosis. Computerized Medical Imaging and Graphics, 2021.

Hammad Naveed, Corinna Reglin, Thomas Schubert, Xin Gao, Stefan T Arold, Michael L Maitland. Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors. Genomics, Proteomics & Bioinformatics, 2021.

2020

Umair Ayub, Hammad Naveed, Waseem Shahzad. PRRAT_AM - An Advanced Ant-Miner to Extract Accurate and Comprehensible Classification Rules. Applied Soft Computing, In press.

Hammad Naveed*, Corinna Reglin, 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.

Naeem Rehmat, Hammad Farooq, Sanjay Kumar, Sibt ul Hussain, Hammad Naveed. Predicting the pathogenicity of protein coding mutations using Natural Language Processing. Conf Proc IEEE Eng Med Biol Soc. 2020, Accepted.

Wei Tian, Hammad Naveed, Meishan Lin and Jie Liang. GeTFEP: A general transfer free energy profile of transmembrane proteins. Protein Science, 2020, 29 (2): 469-79.

Thomas Bausewein, Hammad Naveed, Jie Liang, Stephan Nussberger, The structure of the TOM core complex in the mitochondrial outer membrane. Biological Chemistry, In press.

Umair Ayub, Imran Haider, Hammad Naveed. SAlign–a structure aware method for global PPI network alignment. BMC bioinformatics, 2020.

Safyan Aman Memon, Kinaan Aamir Khan, Hammad Naveed. Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors. Genomics, Proteomics & Bioinformatics, 2021.

Hammad Naveed, Corinna Reglin, Thomas Schubert, Xin Gao, Stefan T Arold, Michael L Maitland. HECNet: a hierarchical approach to enzyme function classification using a Siamese Triplet Networks. Bioinformatics, 2020.

Hafsa Iftikhar, Hafiza Nayyer Ali, Sadia Farooq, Hammad Naveed, Syed Shahzad-ul-Hussan. Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach. Computers in biology and medicine, 2020.

Safyan Aman Memon, Kinaan Aamir Khan, Hammad Naveed. Enzyme function prediction using deep learning. Biophysical Journal, 2020.

Hammad Farooq, Junaid Suhail Niaz, Saira Fakhar, Hammad Naveed. Leveraging digital media data for pharmacovigilance. AMIA Annual Symposium Proceedings, 2020.

2019

Hammad Farooq, Hammad Naveed. GPADRlex: Grouped Phrasal Adverse Drug Reaction lexicon. IEEE International Conference on Signal Processing, Communications and Computing (ICSPCC) 2019, 1-6.

Hammad Farooq, Naeem Rehmat, Sanjay Kumar, Hammad Naveed. Genetic Mutation Classification using Machine Learning. Biophysical Journal, 2019.

Hammad Naveed, Corinna Reglin, Thomas Schubert, Xin Gao, Stefan T Arold, Michael L Maitland. Identifying novel targets by using drug-binding site signature: A case study of kinase inhibitors. bioRxiv, 2019.

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

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.

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

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.

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.

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.

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.

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.

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.

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

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.