Shaun Mahony

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 10

Top Topics

Programmable Logic

Statistical Inference

Scales Linearly

Top Venues

PLoS Comput. Biol.

J. Comput. Biol.

Publications

Jianyu Yang, Kuangyu Yen, Shaun Mahony
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. RECOMB (2024)
Guanjue Xiang, Belinda Giardine, Shaun Mahony, Yu Zhang, Ross C. Hardison
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. Bioinform. 37 (18) (2021)
Danying Shao, Gretta Kellogg, Shaun Mahony, William K. M. Lai, B. Franklin Pugh
PEGR: a management platform for ChIP-based next generation sequencing pipelines. PEARC (2020)
Naomi Yamada, Prashant Kumar Kuntala, B. Franklin Pugh, Shaun Mahony
ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes. J. Comput. Biol. 27 (3) (2020)
Yu Zhang, Shaun Mahony
Direct prediction of regulatory elements from partial data without imputation. PLoS Comput. Biol. 15 (11) (2019)
Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony
Characterizing protein-DNA binding event subtypes in ChIP-exo data. Bioinform. 35 (6) (2019)
Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony
Characterizing Protein-DNA Binding Event Subtypes in ChIP-Exo Data. RECOMB (2018)
Lila Rieber, Shaun Mahony
miniMDS: 3D structural inference from high-resolution Hi-C data. Bioinform. 33 (14) (2017)
Akshay Kakumanu, Silvia Velasco, Esteban O. Mazzoni, Shaun Mahony
Deconvolving sequence features that discriminate between overlapping regulatory annotations. PLoS Comput. Biol. 13 (10) (2017)
Shefali S. Verma, Alex T. Frase, Anurag Verma, Sarah A. Pendergrass, Shaun Mahony, David W. Haas, Marylyn D. Ritchie
Phenome-Wide Interaction Study (PheWIS) in Aids Clinical Trials Group Data (ACTG). PSB (2016)
Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. PLoS Comput. Biol. 10 (3) (2014)
Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. RECOMB (2014)
Yuchun Guo, Shaun Mahony, David K. Gifford
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints. PLoS Comput. Biol. 8 (8) (2012)
Yuchun Guo, Georgios Papachristoudis, Robert C. Altshuler, Georg K. Gerber, Tommi S. Jaakkola, David K. Gifford, Shaun Mahony
Discovering homotypic binding events at high spatial resolution. Bioinform. 26 (24) (2010)
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
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36 (Database-Issue) (2008)
Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
Inferring protein-DNA dependencies using motif alignments and mutual information. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Shaun Mahony, Panayiotis V. Benos
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Shaun Mahony, Philip E. Auron, Panayiotis V. Benos
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies. PLoS Comput. Biol. 3 (3) (2007)
Nigel McCoy, Shaun Mahony, Aaron Golden
Gene Prediction in Metagenomic Libraries Using the Self Organising Map and High Performance Computing Techniques. GCCB (2006)
Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden
Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Networks 19 (6-7) (2006)
Shaun Mahony, Aaron Golden, Terry J. Smith, Panayiotis V. Benos
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. ISMB (Supplement of Bioinformatics) (2005)
Shaun Mahony, David Hendrix, Aaron Golden, Terry J. Smith, Daniel S. Rokhsar
Transcription factor binding site identification using the self-organizing map. Bioinform. 21 (9) (2005)
Shaun Mahony, David Hendrix, Terry J. Smith, Aaron Golden
Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences. Artif. Intell. Rev. 24 (3-4) (2005)
Shaun Mahony, James O. McInerney, Terry J. Smith, Aaron Golden
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. BMC Bioinform. 5 (2004)
Shaun Mahony, Terry J. Smith, James O. McInerney, Aaron Golden
A New Approach to Gene Prediction Using the Self-Organizing Map. CSB (2003)