A novel framework for elastography and modulus estimation: integration of tissue mechanics with imaging. - Reza Karimi; Raymond R. Chan; Stuart L. Houser; Brett E. Bouma; Mohammad R. Kaazempur Mofrad (ISBI, 2006)

Non-rigid registration for fusion of carotid vascular ultrasound and MRI volumetric datasets. - R. C. Chan; Sham Sokka; D. Hinton; Robert Manzke; Annemarie Hanekamp; Vivek Y. Reddy; Mohammad R. Kaazempur Mofrad; Volker Rasche (Image Processing, 2006)

Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior. - Javad Golji; Robert Collins; Mohammad R. K. Mofrad (PLoS Comput. Biol., 2009)

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex. - Ruhollah Moussavi-Baygi; Yousef Jamali; Reza Karimi; Mohammad R. Kaazempur Mofrad (PLoS Comput. Biol., 2011)

An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homo-oligomerization, integrin-ligand affinity, membrane crowdedness and ligand mobility. - Yousef Jamali; Tahereh Jamali; Mohammad R. Kaazempur Mofrad (J. Comput. Phys., 2013)

The Interaction of Vinculin with Actin. - Javad Golji; Mohammad R. K. Mofrad (PLoS Comput. Biol., 2013)

Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering. - Mehrdad Mehrbod; Mohammad R. K. Mofrad (PLoS Comput. Biol., 2013)

A New Approach for Scalable Analysis of Microbial Communities. - Ehsaneddin Asgari; Kiavash Garakani; Mohammad R. K. Mofrad (CoRR, 2015)

ProtVec: A Continuous Distributed Representation of Biological Sequences. - Ehsaneddin Asgari; Mohammad R. K. Mofrad (CoRR, 2015)

Text Analysis and Automatic Triage of Posts in a Mental Health Forum. - Ehsaneddin Asgari; Soroush Nasiriany; Mohammad R. K. Mofrad (CLPsych@HLT-NAACL, 2016)

Comparing Fifty Natural Languages and Twelve Genetic Languages Using Word Embedding Language Divergence (WELD) as a Quantitative Measure of Language Distance. - Ehsaneddin Asgari; Mohammad R. K. Mofrad (CoRR, 2016)

Fast and accurate classification of echocardiograms using deep learning. - Ali Madani; Ramy Arnaout; Mohammad R. K. Mofrad; Rima Arnaout (CoRR, 2017)

Fast and accurate view classification of echocardiograms using deep learning. - Ali Madani; Ramy Arnaout; Mohammad R. K. Mofrad; Rima Arnaout (npj Digit. Medicine, 2018)

Deep echocardiography: data-efficient supervised and semi-supervised deep learning towards automated diagnosis of cardiac disease. - Ali Madani; Jia Rui Ong; Anshul Tibrewal; Mohammad R. K. Mofrad (npj Digit. Medicine, 2018)

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. - Ehsaneddin Asgari; Kiavash Garakani; Alice C. McHardy; Mohammad R. K. Mofrad (Bioinform., 2019)

DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. - Ehsaneddin Asgari; Philipp C. Münch; Till R. Lesker; Alice C. McHardy; Mohammad R. K. Mofrad (Bioinform., 2019)

UniSent: Universal Adaptable Sentiment Lexica for 1000+ Languages. - Ehsaneddin Asgari; Fabienne Braune; Christoph Ringlstetter; Mohammad R. K. Mofrad (CoRR, 2019)

ProDyn0: Inferring calponin homology domain stretching behavior using graph neural networks. - Ali Madani; Cyna Shirazinejad; Jia Rui Ong; Hengameh Shams; Mohammad R. K. Mofrad (CoRR, 2019)

UniSent: Universal Adaptable Sentiment Lexica for 1000+ Languages. - Ehsaneddin Asgari; Fabienne Braune; Benjamin Roth 001; Christoph Ringlstetter; Mohammad R. K. Mofrad (LREC, 2020)

Quantification of human sperm concentration using machine learning-based spectrophotometry. - Ali Lesani; Somaieh Kazemnejad; Mahdi Moghimi Zand; Mojtaba Azadi; Hassan Jafari; Mohammad R. K. Mofrad; Reza Nosrati (Comput. Biol. Medicine, 2020)

EpitopeVec: linear epitope prediction using deep protein sequence embeddings. - Akash Bahai; Ehsaneddin Asgari; Mohammad R. K. Mofrad; Andreas Kloetgen; Alice C. McHardy (Bioinform., 2021)

TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks. - Esmaeil Nourani; Ehsaneddin Asgari; Alice C. McHardy; Mohammad R. K. Mofrad (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Beyond the Hype: Assessing the Performance, Trustworthiness, and Clinical Suitability of GPT3.5. - Salmonn Talebi; Elizabeth Tong; Mohammad R. K. Mofrad (CoRR, 2023)

GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations. - Andrew Dickson; Ehsaneddin Asgari; Alice C. McHardy; Mohammad R. K. Mofrad (Bioinform., 2023)

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study. - Mohammad Khavani; Aliyeh Mehranfar; Mohammad R. K. Mofrad (J. Chem. Inf. Model., 2023)

Fine-tuning protein embeddings for functional similarity evaluation. - Andrew Dickson; Mohammad R. K. Mofrad (Bioinform., 2024)

Exploring the performance and explainability of fine-tuned BERT models for neuroradiology protocol assignment. - Salmonn Talebi; Elizabeth Tong; Anna Li; Ghiam Yamin; Greg Zaharchuk; Mohammad R. K. Mofrad (BMC Medical Informatics Decis. Mak., 2024)

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory. - Atsushi Matsuda; Mohammad R. K. Mofrad (PLoS Comput. Biol., 2025)