SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes - Jianyu Yang; Kuangyu Yen; Shaun Mahony (Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29 - May 2, 2024, Proceedings, 2024)

S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types - Guanjue Xiang; Belinda Giardine; Shaun Mahony; Yu Zhang; Ross C. Hardison (Bioinform., 2021)

ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes - Naomi Yamada; Prashant Kumar Kuntala; B. Franklin Pugh; Shaun Mahony (J. Comput. Biol., 2020)

PEGR: a management platform for ChIP-based next generation sequencing pipelines - Danying Shao; Gretta Kellogg; Shaun Mahony; William K. M. Lai; B. Franklin Pugh (PEARC '20: Practice and Experience in Advanced Research Computing, Portland, OR, USA, July 27-31, 2020, 2020)

Characterizing protein-DNA binding event subtypes in ChIP-exo data - Naomi Yamada; William K. M. Lai; Nina Farrell; B. Franklin Pugh; Shaun Mahony (Bioinform., 2019)

Direct prediction of regulatory elements from partial data without imputation - Yu Zhang; Shaun Mahony (PLoS Comput. Biol., 2019)

Characterizing Protein-DNA Binding Event Subtypes in ChIP-Exo Data - Naomi Yamada; William K. M. Lai; Nina Farrell; B. Franklin Pugh; Shaun Mahony (Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings, 2018)

miniMDS: 3D structural inference from high-resolution Hi-C data - Lila Rieber; Shaun Mahony (Bioinform., 2017)

Deconvolving sequence features that discriminate between overlapping regulatory annotations - Akshay Kakumanu; Silvia Velasco; Esteban O. Mazzoni; Shaun Mahony (PLoS Comput. Biol., 2017)

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 (Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast, Hawaii, USA, January 4-8, 2016, 2016)

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding - Shaun Mahony; Matthew D. Edwards; Esteban O. Mazzoni; Richard I. Sherwood; Akshay Kakumanu; Carolyn A. Morrison; Hynek Wichterle; David K. Gifford (PLoS Comput. Biol., 2014)

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 (Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings, 2014)

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints - Yuchun Guo; Shaun Mahony; David K. Gifford (PLoS Comput. Biol., 2012)

Discovering homotypic binding events at high spatial resolution - Yuchun Guo; Georgios Papachristoudis; Robert C. Altshuler; Georg K. Gerber; Tommi S. Jaakkola; David K. Gifford; Shaun Mahony (Bioinform., 2010)

ORegAnno: an open-access community-driven resource for regulatory annotation - Obi L. Griffith; Stephen B. Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica C. Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M. Gallo; et al. (Nucleic Acids Res., 2008)

STAMP: a web tool for exploring DNA-binding motif similarities - Shaun Mahony; Panayiotis V. Benos (Nucleic Acids Res., 2007)

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies - Shaun Mahony; Philip E. Auron; Panayiotis V. Benos (PLoS Comput. Biol., 2007)

Inferring protein-DNA dependencies using motif alignments and mutual information - Shaun Mahony; Philip E. Auron; Panayiotis V. Benos (Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007, 2007)

Self-organizing neural networks to support the discovery of DNA-binding motifs - Shaun Mahony; Panayiotis V. Benos; Terry J. Smith; Aaron Golden (Neural Networks, 2006)

Gene Prediction in Metagenomic Libraries Using the Self Organising Map and High Performance Computing Techniques - Nigel McCoy; Shaun Mahony; Aaron Golden (Distributed, High-Performance and Grid Computing in Computational Biology , International Workshop, GCCB 2006, Eilat, Israel, January 21, 2007, Proceeding, 2006)

Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences - Shaun Mahony; David Hendrix; Terry J. Smith; Aaron Golden (Artif. Intell. Rev., 2005)

Transcription factor binding site identification using the self-organizing map - Shaun Mahony; David Hendrix; Aaron Golden; Terry J. Smith; Daniel S. Rokhsar (Bioinform., 2005)

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles - Shaun Mahony; Aaron Golden; Terry J. Smith; Panayiotis V. Benos (Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005, 2005)

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models - Shaun Mahony; James O. McInerney; Terry J. Smith; Aaron Golden (BMC Bioinform., 2004)

A New Approach to Gene Prediction Using the Self-Organizing Map - Shaun Mahony; Terry J. Smith; James O. McInerney; Aaron Golden (2nd IEEE Computer Society Bioinformatics Conference, CSB 2003, Stanford, CA, USA, August 11-14, 2003, 2003)