Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network. - Jinyuan Yan; Maxime Deforet; Kerry E. Boyle; Rayees Rahman; Raymond Liang; Chinweike Okegbe; Lars E. P. Dietrich; Weigang Qiu; João B. Xavier (PLoS Comput. Biol., 2017)

KinaMetrix: a web resource to investigate kinase conformations and inhibitor space. - Rayees Rahman; Peter Man-Un Ung; Avner Schlessinger (Nucleic Acids Res., 2019)

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. - Jinyuan Yan; Henri Estanbouli; Chen Liao; Wook Kim; Jonathan M. Monk; Rayees Rahman; Mini Kamboj; Bernhard O. Palsson; Weigang Qiu; João B. Xavier (PLoS Comput. Biol., 2019)

Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues. - Nicole Zatorski; David Stein 003; Rayees Rahman; Ravi Iyengar; Avner Schlessinger (Database J. Biol. Databases Curation, 2022)

Preference Optimization for Molecular Language Models. - Ryan Park; Ryan Theisen; Navriti Sahni; Marcel Patek; Anna Cichonska; Rayees Rahman (CoRR, 2023)