Hammad Naveed

发表

Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern

S. Kachalo, Hammad Naveed, Youfang Cao, 2015, PloS one.

Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells.

Hammad Naveed, Youfang Cao, Jieling Zhao, 2015, Critical reviews in biomedical engineering.

Structure-based Analysis of VDAC1 Protein

Hammad Naveed, Jie Liang, Shay Geula, 2011, The Journal of Biological Chemistry.

Predicting weakly stable regions, oligomerization state, and protein–protein interfaces in transmembrane domains of outer membrane proteins

Hammad Naveed, Jie Liang, R. Jackups, 2009, Proceedings of the National Academy of Sciences.

Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins.

Hammad Naveed, Jie Liang, R. Jackups, 2012, Journal of the American Chemical Society.

Improving the resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations.

Hammad Naveed, Jie Liang, Dennis Gessmann, 2011, Journal of molecular biology.

GeTFEP: A general transfer free energy profile of transmembrane proteins

Hammad Naveed, Jie Liang, Wei Tian, 2019, Protein science : a publication of the Protein Society.

GeTFEP: A general transfer free energy profile of transmembrane proteins

Hammad Naveed, Jie Liang, Wei Tian, 2017, bioRxiv.

Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis.

Jie Liang, Hammad Naveed, Hammad Naveed, 2011, Biochimica et biophysica acta.

Enzyme Function Prediction using Deep Learning

Safyan Aman Memon, Hammad Naveed, Kinaan Aamir Khan, 2020 .

Multiscale modeling of cellular epigenetic states and tissue patterning : stochasticity in molecular network , chromatin folding in cell nucleus , and cell-cell interactions in tissue patterning

Hammad Naveed, Youfang Cao, Jie Liang, 2016 .

Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding.

Hammad Naveed, Jie Liang, L. Kenney, 2012, 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

Hammad Naveed, Jie Liang, 2012 .

Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale.

Hammad Naveed, Jie Liang, Dennis Gessmann, 2016, Journal of the American Chemical Society.

High-resolution structure prediction of β-barrel membrane proteins

Hammad Naveed, Jie Liang, Wei Tian, 2018, Proceedings of the National Academy of Sciences.

Medical terminology-based computing system: a lightweight post-processing solution for out-of-vocabulary multi-word terms

Hammad Naveed, Nadia Saeed , 2022, Frontiers in Molecular Biosciences.

Leveraging digital media data for pharmacovigilance

Hammad Naveed, Hammad Farooq, Junaid S. Niaz, 2020, AMIA.

Identification of potential inhibitors of three key enzymes of SARS-CoV2 using computational approach

Hammad Naveed, Hafsa Iftikhar, Hafiza Nayyer Ali, 2020, Computers in Biology and Medicine.

Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors

Hammad Naveed, M. Maitland, Xin Gao, 2021, Genom. Proteom. Bioinform..

Predicting the pathogenicity of protein coding mutations using Natural Language Processing

Sanjay Kumar, Hammad Naveed, Naeem Rehmat, 2020, 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Identifying Novel Targets by using Drug-binding Site Signature: A Case Study of Kinase Inhibitors

Hammad Naveed, Thomas Schubert, Corinna Reglin, 2019, bioRxiv.

SAlign–a structure aware method for global PPI network alignment

Hammad Naveed, Umair Ayub, Imran Haider, 2020, BMC Bioinformatics.

Lymphopenia in treatment-naive relapsing multiple sclerosis

Hammad Naveed, I. Galea, E. Elwood, 2016, Neurology: Neuroimmunology & Neuroinflammation.

The effect of systemic inflammation on human brain barrier function

Hammad Naveed, I. Galea, E. Elwood, 2017, Brain, Behavior, and Immunity.

An integrated structure- and system-based framework to identify new targets of metabolites and known drugs

Xin Gao, Hammad Naveed, William Bourguet, 2015, Bioinform..

Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins.

Jie Liang, Hammad Naveed, Hammad Naveed, 2014, Current pharmaceutical design.

Computational studies of membrane proteins: models and predictions for biological understanding.

Jie Liang, Hammad Naveed, Meishan Lin, 2012, Biochimica et biophysica acta.

CoCiter: An Efficient Tool to Infer Gene Function by Assessing the Significance of Literature Co-Citation

Nan Qiao, Christopher D. Green, Hammad Naveed, 2013, PloS one.

Dynamic mechanical finite element model of biological cells for studying cellular pattern formation

Wei Tian, Jie Liang, Youfang Cao, 2013, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

Structure-based protein-protein interaction networks and drug design

Hammad Naveed, Jingdong J. Han, Hammad Naveed, 2013, Quantitative Biology.

GOntoSim: a semantic similarity measure based on LCA and common descendants

Hammad Naveed, Amna Binte Kamran, 2022, Scientific Reports.

Identification of destabilizing SNPs in SARS-CoV2-ACE2 protein and spike glycoprotein: implications for virus entry mechanisms

Hammad Naveed, Z. Khalid, 2020, Journal of biomolecular structure & dynamics.

The structure of the TOM core complex in the mitochondrial outer membrane

Hammad Naveed, Jie Liang, S. Nussberger, 2020, Biological chemistry.

BioAlign: An Accurate Global PPI Network Alignment Algorithm

Hammad Naveed, Umair Ayub, 2022, Evolutionary bioinformatics online.

Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis

Jie Liang, Youfang Cao, Hammad Naveed, 2013, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

Mechanisms of Regulating Cell Topology in Proliferating Epithelia: Impact of Division Plane, Mechanical Forces, and Cell Memory

Jie Liang, Lisa X. Xu, Sema Kachalo, 2012, PloS one.

Biomedical image analysis competitions: The state of current participation practice

Anne L. Martel, Helena R. Torres, Bjoern H Menze, 2022, ArXiv.

HECNet: a hierarchical approach to enzyme function classification using a Siamese Triplet Network

Hammad Naveed, Safyan Aman Memon, Kinaan Aamir Khan, 2020, Bioinform..

Finding optimal interaction interface alignments between biological complexes

Xin Gao, Xuefeng Cui, Hammad Naveed, 2015, Bioinform..

Computational prediction of disease related lncRNAs using machine learning

Hammad Naveed, Z. Khalid, Razia Khalid, 2023, Scientific Reports.

PRRAT_AM - An advanced ant-miner to extract accurate and comprehensible classification rules

Waseem Shahzad, Hammad Naveed, Umair Ayub, 2020, Appl. Soft Comput..

Efficient computation of transfer free energies of amino acids in beta‐barrel membrane proteins

Wei Tian, Jie Liang, Hammad Naveed, 2017, Bioinform..

Mechanisms of Regulating Tissue Elongation in Drosophila Wing: Impact of Oriented Cell Divisions, Oriented Mechanical Forces, and Reduced Cell Size

Jie Liang, Lisa X. Xu, Sema Kachalo, 2014, PloS one.

A hierarchical deep learning based approach for multi‐functional enzyme classification

Safyan Aman Memon, Kinaan Aamir Khan, Hammad Naveed, 2021, Protein science : a publication of the Protein Society.

Bias Adjustable Activation Network for Imbalanced Data - Diabetic Foot Ulcer Challenge 2021

Hammad Naveed, Salman Ahmed, Hammad Naveed, 2021, DFUC@MICCAI.

Cell fate determination is influenced by Notch heterogeneity

Hammad Naveed, Mukhtar Ullah, Sana Saleh, 2021, 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Biomedical image analysis competitions: The state of current participation practice

Anne L. Martel, Helena R. Torres, Bjoern H Menze, 2022, arXiv.org.

Modeling spatial population dynamics of stem cell lineage in tissue growth

Meng Chen, Qing Nie, Yingzi Li, 2012, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

The effect of systemic inflammation on human brain barrier function

Hammad Naveed, I. Galea, E. Elwood, 2017, Brain, Behavior, and Immunity.

Geometric order in proliferating epithelia: Impact of rearrangements and cleavage plane orientation

Jie Liang, Sema Kachalo, Hammad Naveed, 2010, 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology.

Role of Cell Morphology in Classical Delta-Notch Pattern Formation

Hammad Naveed, Mukhtar Ullah, Sana Saleh, 2021, 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC).

Predicting weakly stable regions, oligomerization state, and protein–protein interfaces in transmembrane domains of outer membrane proteins

Hammad Naveed, Jie Liang, R. Jackups, 2009, Proceedings of the National Academy of Sciences.