| 2024 | RECOMB | SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. | Jianyu Yang, Kuangyu Yen, Shaun Mahony |
| 2018 | RECOMB | Characterizing Protein-DNA Binding Event Subtypes in ChIP-Exo Data. | Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony |
| 2016 | PSB | Phenome-Wide Interaction Study (PheWIS) in Aids Clinical Trials Group Data (ACTG). | Shefali S. Verma, Alex T. Frase, Anurag Verma, Sarah A. Pendergrass, Shaun Mahony, David W. Haas, Marylyn D. Ritchie |
| 2014 | RECOMB | An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. | Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford |
| 2007 | ISMB | Inferring protein-DNA dependencies using motif alignments and mutual information. | Shaun Mahony, Philip E. Auron, Panayiotis V. Benos |
| 2005 | ISMB | Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. | Shaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos |