Formation of Regulatory Modules by Local Sequence Duplication. - Armita Nourmohammad; Michael Lässig (PLoS Comput. Biol., 2011)

SOS: online probability estimation and generation of T-and B-cell receptors. - Giulio Isacchini; Carlos Olivares; Armita Nourmohammad; Aleksandra M. Walczak; Thierry Mora (Bioinform., 2020)

Information-Geometric Optimization with Natural Selection. - Jakub Otwinowski; Colin H. LaMont; Armita Nourmohammad (Entropy, 2020)

MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories. - Giulio Isacchini; Natanael Spisak; Armita Nourmohammad; Thierry Mora; Aleksandra M. Walczak (CoRR, 2021)

Holographic-(V)AE: an end-to-end SO(3)-Equivariant (Variational) Autoencoder in Fourier Space. - Gian Marco Visani; Michael N. Pun; Armita Nourmohammad (CoRR, 2022)

Learning the shape of protein micro-environments with a holographic convolutional neural network. - Michael N. Pun; Andrew Ivanov; Quinn Bellamy; Zachary Montague; Colin H. LaMont; Philip Bradley; Jakub Otwinowski; Armita Nourmohammad (CoRR, 2022)

H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing. - Gian Marco Visani; William Galvin; Michael N. Pun; Armita Nourmohammad (MLCB, 2023)

HERMES: Holographic Equivariant neuRal network model for Mutational Effect and Stability prediction. - Gian Marco Visani; Michael N. Pun; William Galvin; Eric Daniel; Kevin Borisiak; Utheri Wagura; Armita Nourmohammad (CoRR, 2024)

Loop-Diffusion: an equivariant diffusion model for designing and scoring protein loops. - Kevin Borisiak; Gian Marco Visani; Armita Nourmohammad (CoRR, 2024)

T-cell receptor specificity landscape revealed through de novo peptide design. - Gian Marco Visani; Michael N. Pun; Anastasia A. Minervina; Philip Bradley; Paul Thomas; Armita Nourmohammad (CoRR, 2025)