Publications

Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions
Rao J, Wang M, Howard MK, Coyote-Maestas W*, Pimentel H*
Biorxiv, 2025
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Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilaces
Freudenberg J, Rao J, Howard MK, Macdonald CB, Greenwald NF, Coyote-Maestas W*, Pimentel H*
Biorxiv, 2025
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dotears: Scalable, consistent DAG estimation using observational and interventional data
Xue A, Rao J, Sankararaman S*, Pimentel H*
iScience, 2025
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Rosace-AA: Enhancing Interpretation of Deep Mutational Scanning Data with Amino Acid Substitution and Position-Specific Insights
Rao J*, Wang M, Howard MK, Macdonald CB, Fraser JS, Coyote-Maestas W*, Pimentel H*
Biorxiv, 2025
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Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage
Rao J, Xin R, Macdonald CB, Howard M, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W*, Pimentel H*
Genome Biology, 2024
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