Shaun Mahony

According to our database, Shaun Mahony authored at least 23 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes.

Jianyu Yang, Kuangyu Yen, Shaun Mahony

Proceedings of the Research in Computational Molecular Biology, 2024

2021

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

2020

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

Proceedings of the PEARC '20: Practice and Experience in Advanced Research Computing, 2020

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

Bioinform., 2019

2017

Deconvolving sequence features that discriminate between overlapping regulatory annotations.

Akshay Kakumanu, Silvia Velasco, Esteban O. Mazzoni, Shaun Mahony

PLoS Comput. Biol., 2017

miniMDS: 3D structural inference from high-resolution Hi-C data.

Lila Rieber, Shaun Mahony

Bioinform., 2017

2016

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

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2014

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

2012

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

2010

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

2008

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, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, Steven J. M. Jones

Nucleic Acids Res., 2008

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

STAMP: a web tool for exploring DNA-binding motif similarities.

Shaun Mahony, Panayiotis V. Benos

Nucleic Acids Res., 2007

Inferring protein-DNA dependencies using motif alignments and mutual information.

Shaun Mahony, Philip E. Auron, Panayiotis V. Benos

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

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

Proceedings of the Distributed, 2006

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

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

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 of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004

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

2003

A New Approach to Gene Prediction Using the Self-Organizing Map.

Shaun Mahony, Terry J. Smith, James O. McInerney, Aaron Golden

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003