Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. - Sayed-Amir Marashi; Hani Goodarzi; Mehdi Sadeghi; Changiz Eslahchi; Hamid Pezeshk (Comput. Biol. Chem., 2006)

Artificial Intelligence for COVID-19 Drug Discovery and Vaccine Development. - Arash Keshavarzi Arshadi; Julia Webb; Milad Salem; Emmanuel Cruz; Stacie Calad-Thomson; Niloofar Ghadirian; Jennifer Collins; Elena Diez-Cecilia; Brendan Kelly; Hani Goodarzi; Jiann-Shiun Yuan (Frontiers Artif. Intell., 2020)

To Transformers and Beyond: Large Language Models for the Genome. - Micaela E. Consens; Cameron Dufault; Michael Wainberg; Duncan Forster; Mehran Karimzadeh; Hani Goodarzi; Fabian J. Theis; Alan Moses; Bo Wang 044 (CoRR, 2023)

pyPAGE: A framework for Addressing biases in gene-set enrichment analysis - A case study on Alzheimer's disease. - Artemy Bakulin; Noam B. Teyssier; Martin Kampmann; Matvei Khoroshkin; Hani Goodarzi (PLoS Comput. Biol., 2024)

Functional microRNA-targeting drug discovery by graph-based deep learning. - Arash Keshavarzi Arshadi; Milad Salem; Heather Karner; Kristle Garcia; Abolfazl Arab; Jiann-Shiun Yuan; Hani Goodarzi (Patterns, 2024)

Transformers and genome language models. - Micaela E. Consens; Cameron Dufault; Michael Wainberg; Duncan Forster; Mehran Karimzadeh; Hani Goodarzi; Fabian J. Theis; Alan Moses; Bo Wang 044 (Nat. Mac. Intell., 2025)

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model. - Adibvafa Fallahpour; Andrew Magnuson; Purav Gupta; Shihao Ma; Jack Naimer; Arnav Shah; Haonan Duan 002; Omar Ibrahim; Hani Goodarzi; Chris J. Maddison; Bo Wang 044 (CoRR, 2025)