Shaun Mahony

25 papers B 3Misc 1Journal 16Unranked 5
YearRankTypeTitle / Venue / Authors
2024 B conf
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes.
RECOMB
Jianyu Yang, Kuangyu Yen, Shaun Mahony
2021 J jnl
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types.
Bioinform.
Guanjue Xiang, Belinda Giardine, Shaun Mahony, Yu Zhang, Ross C. Hardison
2020 J jnl
ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes.
J. Comput. Biol.
Naomi Yamada, Prashant Kumar Kuntala, B. Franklin Pugh, Shaun Mahony
2020 — conf
PEGR: a management platform for ChIP-based next generation sequencing pipelines.
PEARC
Danying Shao, Gretta Kellogg, Shaun Mahony, William K. M. Lai, B. Franklin Pugh
2019 J jnl
Characterizing protein-DNA binding event subtypes in ChIP-exo data.
Bioinform.
Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony
2019 J jnl
Direct prediction of regulatory elements from partial data without imputation.
PLoS Comput. Biol.
Yu Zhang, Shaun Mahony
2018 B conf
Characterizing Protein-DNA Binding Event Subtypes in ChIP-Exo Data.
RECOMB
Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony
2017 J jnl
Deconvolving sequence features that discriminate between overlapping regulatory annotations.
PLoS Comput. Biol.
Akshay Kakumanu, Silvia Velasco, Esteban O. Mazzoni, Shaun Mahony
2017 J jnl
miniMDS: 3D structural inference from high-resolution Hi-C data.
Bioinform.
Lila Rieber, Shaun Mahony
2016 Misc conf
Phenome-Wide Interaction Study (PheWIS) in Aids Clinical Trials Group Data (ACTG).
PSB
Shefali S. Verma, Alex T. Frase, Anurag Verma, Sarah A. Pendergrass, Shaun Mahony, David W. Haas, Marylyn D. Ritchie
2014 B conf
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.
RECOMB
Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
2014 J jnl
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.
PLoS Comput. Biol.
Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
2012 J jnl
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints.
PLoS Comput. Biol.
Yuchun Guo, Shaun Mahony, David K. Gifford
2010 J jnl
Discovering homotypic binding events at high spatial resolution.
Bioinform.
Yuchun Guo, Georgios Papachristoudis, Robert C. Altshuler, Georg K. Gerber, Tommi S. Jaakkola, David K. Gifford, Shaun Mahony
2008 J jnl
ORegAnno: an open-access community-driven resource for regulatory annotation.
Nucleic Acids Res.
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
2007 J jnl
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies.
PLoS Comput. Biol.
Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
2007 — conf
Inferring protein-DNA dependencies using motif alignments and mutual information.
ISMB/ECCB (Supplement of Bioinformatics)
Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
2007 J jnl
STAMP: a web tool for exploring DNA-binding motif similarities.
Nucleic Acids Res.
Shaun Mahony, Panayiotis V. Benos
2006 — conf
Gene Prediction in Metagenomic Libraries Using the Self Organising Map and High Performance Computing Techniques.
GCCB
Nigel McCoy, Shaun Mahony, Aaron Golden
2006 J jnl
Self-organizing neural networks to support the discovery of DNA-binding motifs.
Neural Networks
Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden
2005 — conf
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.
ISMB (Supplement of Bioinformatics)
Shaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos
2005 J jnl
Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences.
Artif. Intell. Rev.
Shaun Mahony, David Hendrix, Terry J. Smith, Aaron Golden
2005 J jnl
Transcription factor binding site identification using the self-organizing map.
Bioinform.
Shaun Mahony, David Hendrix, Aaron Golden, Terry J. Smith, Daniel S. Rokhsar
2004 J jnl
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.
BMC Bioinform.
Shaun Mahony, James O. McInerney, Terry J. Smith, Aaron Golden
2003 — conf
A New Approach to Gene Prediction Using the Self-Organizing Map.
CSB
Shaun Mahony, Terry J. Smith, James O. McInerney, Aaron Golden