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ORCIDMohammad R. K. Mofrad
Person information
- affiliation: University of California Berkeley, Departments of Bioengineering and Mechanical Engineering, CA, USA
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2020 – today
- 2024
[j17]Andrew Dickson
, Mohammad R. K. Mofrad:
Fine-tuning protein embeddings for functional similarity evaluation. Bioinform. 40(8) (2024)- [j16]Salmonn Talebi, Elizabeth Tong, Anna Li, Ghiam Yamin, Greg Zaharchuk, Mohammad R. K. Mofrad:
Exploring the performance and explainability of fine-tuned BERT models for neuroradiology protocol assignment. BMC Medical Informatics Decis. Mak. 24(1): 40 (2024) - 2023
- [j15]Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad:
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations. Bioinform. 39(2) (2023) - [j14]Mohammad Khavani, Aliyeh Mehranfar, Mohammad R. K. Mofrad:
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study. J. Chem. Inf. Model. 63(4): 1276-1292 (2023) - [i7]Salmonn Talebi, Elizabeth Tong, Mohammad R. K. Mofrad:
Beyond the Hype: Assessing the Performance, Trustworthiness, and Clinical Suitability of GPT3.5. CoRR abs/2306.15887 (2023) - 2022
- [j13]Esmaeil Nourani, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad:
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3744-3753 (2022) - 2021
- [j12]Akash Bahai, Ehsaneddin Asgari, Mohammad R. K. Mofrad, Andreas Kloetgen, Alice C. McHardy:
EpitopeVec: linear epitope prediction using deep protein sequence embeddings. Bioinform. 37(23): 4517-4525 (2021) - 2020
- [j11]Ali Lesani, Somaieh Kazemnejad, Mahdi Moghimi Zand, Mojtaba Azadi, Hassan Jafari, Mohammad R. K. Mofrad, Reza Nosrati:
Quantification of human sperm concentration using machine learning-based spectrophotometry. Comput. Biol. Medicine 127: 104061 (2020) - [c4]Ehsaneddin Asgari, Fabienne Braune, Benjamin Roth, Christoph Ringlstetter, Mohammad R. K. Mofrad:
UniSent: Universal Adaptable Sentiment Lexica for 1000+ Languages. LREC 2020: 4113-4120
2010 – 2019
- 2019
- [j10]Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy, Mohammad R. K. Mofrad:
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. Bioinform. 35(6): 1082 (2019) - [j9]Ehsaneddin Asgari, Philipp C. Münch, Till R. Lesker, Alice C. McHardy, Mohammad R. K. Mofrad:
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. Bioinform. 35(14): 2498-2500 (2019) - [i6]Ehsaneddin Asgari, Fabienne Braune, Christoph Ringlstetter, Mohammad R. K. Mofrad:
UniSent: Universal Adaptable Sentiment Lexica for 1000+ Languages. CoRR abs/1904.09678 (2019) - [i5]Ali Madani, Cyna Shirazinejad, Jia Rui Ong, Hengameh Shams, Mohammad R. K. Mofrad:
ProDyn0: Inferring calponin homology domain stretching behavior using graph neural networks. CoRR abs/1910.09738 (2019) - 2018
- [j8]Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy, Mohammad R. K. Mofrad:
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. Bioinform. 34(13): i32-i42 (2018) - [j7]Ali Madani, Ramy Arnaout, Mohammad R. K. Mofrad, Rima Arnaout:
Fast and accurate view classification of echocardiograms using deep learning. npj Digit. Medicine 1 (2018) - [j6]Ali Madani, Jia Rui Ong, Anshul Tibrewal, Mohammad R. K. Mofrad:
Deep echocardiography: data-efficient supervised and semi-supervised deep learning towards automated diagnosis of cardiac disease. npj Digit. Medicine 1 (2018) - 2017
- [i4]Ali Madani, Ramy Arnaout, Mohammad R. K. Mofrad, Rima Arnaout:
Fast and accurate classification of echocardiograms using deep learning. CoRR abs/1706.08658 (2017) - 2016
- [c3]Ehsaneddin Asgari, Soroush Nasiriany, Mohammad R. K. Mofrad:
Text Analysis and Automatic Triage of Posts in a Mental Health Forum. CLPsych@HLT-NAACL 2016: 153-157 - [i3]Ehsaneddin Asgari, Mohammad R. K. Mofrad:
Comparing Fifty Natural Languages and Twelve Genetic Languages Using Word Embedding Language Divergence (WELD) as a Quantitative Measure of Language Distance. CoRR abs/1604.08561 (2016) - 2015
- [i2]Ehsaneddin Asgari, Mohammad R. K. Mofrad:
ProtVec: A Continuous Distributed Representation of Biological Sequences. CoRR abs/1503.05140 (2015) - [i1]Ehsaneddin Asgari, Kiavash Garakani, Mohammad R. K. Mofrad:
A New Approach for Scalable Analysis of Microbial Communities. CoRR abs/1512.00397 (2015) - 2013
- [j5]Yousef Jamali, Tahereh Jamali, Mohammad R. Kaazempur Mofrad:
An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homo-oligomerization, integrin-ligand affinity, membrane crowdedness and ligand mobility. J. Comput. Phys. 244: 264-278 (2013) - [j4]Mehrdad Mehrbod, Mohammad R. K. Mofrad:
Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering. PLoS Comput. Biol. 9(3) (2013) - [j3]Javad Golji, Mohammad R. K. Mofrad:
The Interaction of Vinculin with Actin. PLoS Comput. Biol. 9(4) (2013) - 2011
- [j2]Ruhollah Moussavi-Baygi, Yousef Jamali, Reza Karimi, Mohammad R. Kaazempur Mofrad:
Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex. PLoS Comput. Biol. 7(6) (2011)
2000 – 2009
- 2009
- [j1]Javad Golji, Robert Collins, Mohammad R. K. Mofrad:
Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior. PLoS Comput. Biol. 5(5) (2009) - 2006
- [c2]Reza Karimi, Raymond R. Chan, Stuart L. Houser, Brett E. Bouma, Mohammad R. Kaazempur Mofrad:
A novel framework for elastography and modulus estimation: integration of tissue mechanics with imaging. ISBI 2006: 602-605 - [c1]R. C. Chan, Sham Sokka, D. Hinton, Robert Manzke, Annemarie Hanekamp, Vivek Y. Reddy, Mohammad R. Kaazempur Mofrad, Volker Rasche:
Non-rigid registration for fusion of carotid vascular ultrasound and MRI volumetric datasets. Image Processing 2006: 61442E
Coauthor Index
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