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2020 – today
- 2024
[c9]Jianyu Yang, Kuangyu Yen, Shaun Mahony:
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. RECOMB 2024: 320-323- 2021
- [j16]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): 3011-3013 (2021) - 2020
- [j15]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): 429-435 (2020) - [c8]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: 285-292
2010 – 2019
- 2019
- [j14]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): 903-913 (2019) - [j13]Yu Zhang, Shaun Mahony:
Direct prediction of regulatory elements from partial data without imputation. PLoS Comput. Biol. 15(11) (2019) - 2018
- [c7]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: 291-292 - 2017
- [j12]Lila Rieber, Shaun Mahony:
miniMDS: 3D structural inference from high-resolution Hi-C data. Bioinform. 33(14): i261-i266 (2017) - [j11]Akshay Kakumanu, Silvia Velasco, Esteban O. Mazzoni, Shaun Mahony:
Deconvolving sequence features that discriminate between overlapping regulatory annotations. PLoS Comput. Biol. 13(10) (2017) - 2016
- [c6]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: 57-68 - 2014
- [j10]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) - [c5]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: 175-176 - 2012
- [j9]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) - 2010
- [j8]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): 3028-3034 (2010)
2000 – 2009
- 2008
- [j7]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): 107-113 (2008) - 2007
- [j6]Shaun Mahony, Panayiotis V. Benos:
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 35(Web-Server-Issue): 253-258 (2007) - [j5]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) - [c4]Shaun Mahony, Philip E. Auron, Panayiotis V. Benos:
Inferring protein-DNA dependencies using motif alignments and mutual information. ISMB/ECCB (Supplement of Bioinformatics) 2007: 297-304 - 2006
- [j4]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): 950-962 (2006) - [c3]Nigel McCoy, Shaun Mahony, Aaron Golden:
Gene Prediction in Metagenomic Libraries Using the Self Organising Map and High Performance Computing Techniques. GCCB 2006: 99-109 - 2005
- [j3]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): 397-413 (2005) - [j2]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): 1807-1814 (2005) - [c2]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: 283-291 - 2004
- [j1]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: 23 (2004) - 2003
- [c1]Shaun Mahony, Terry J. Smith, James O. McInerney, Aaron Golden:
A New Approach to Gene Prediction Using the Self-Organizing Map. CSB 2003: 444-445
Coauthor Index
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