Publications

Google Scholar
Challenging AlphaFold in predicting proteins with large-scale allosteric transitions2025

Brooks H. Perkins-Jechow, Juan Pablo Iglesias Ahualli, Huyen Thuc Nhu, Alireza Omidi, Chunchao Li, Jorge A. Holguin-Cruz, Daeahn Cho, Dokyun Na, Nawar Malhis, Jennifer M. Bui, Jörg Gsponer

Nature Communications Chemistry
Paper
Figure from Challenging AlphaFold in predicting proteins with large-scale allosteric transitions
Integration and Querying of Multimodal Single-Cell Data with PoE-VAE2025

Anastasia Litinetskaya, Maiia Schulman, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, Fabian Theis

Research in Computational Molecular Biology (RECOMB)
PaperCode
Figure from Integration and Querying of Multimodal Single-Cell Data with PoE-VAE
Insulin-dependent and -independent dynamics of insulin receptor trafficking in muscle cells2025

Haoning Howard Cen, Aurora J. Mattison, Alireza Omidi, Jason Rogalski, Libin Abraham, Guang Gao, Michael R. Gold, Leonard J. Foster, Jörg Gsponer, James D. Johnson

bioRxiv
Paper
Figure from Insulin-dependent and -independent dynamics of insulin receptor trafficking in muscle cells
AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions2024

Alireza Omidi, Mads Harder Møller, Nawar Malhis, Jennifer M. Bui, Jörg Gsponer

Proceedings of the National Academy of Sciences (PNAS)
PaperCode
Figure from AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions
Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases2024

Anastasia Litinetskaya, Maiia Shulman, Soroor Hediyeh-zadeh, Amir Ali Moinfar, Fabiola Curion, Artur Szałata, Alireza Omidi, Mohammad Lotfollahi, Fabian J. Theis

bioRxiv
PaperCode
Figure from Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
Learning Cancer Progression Network from Mutation Allele Frequencies2020

Mohammad Sadegh Akhondzadeh, Alireza Omidi, Zeinab Maleki, Kevin Coombes, Amanda E. Toland, Amir Asiaee

ICML Workshop on Computational Biology
PaperCode
Figure from Learning Cancer Progression Network from Mutation Allele Frequencies
View All Publications on Google Scholar
Alireza Omidi
Tiny footprints, big dreams