Shaun Mahony's Publications

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 De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones, The Open Regulatory Annotation Consortium, (2008) ORegAnno: an open-access community-driven resource for regulatory annotation., D107-13. In Nucleic acids research 36 (Database issue).

Yong Lu, Shaun Mahony, Panayiotis Benos, Roni Rosenfeld, Itamar Simon, Linda Breeden, Ziv Bar-Joseph (2007) Combined analysis reveals a core set of cycling genes., R146. In Genome biology 8 (7).

Shaun Mahony, Philip E Auron, Panayiotis V Benos (2007) DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies, e61. In PLoS Comput Biol 3 (3).

Tarjei S Mikkelsen, Matthew J Wakefield, Bronwen Aken, Chris T Amemiya, Jean L Chang, Shannon Duke, Manuel Garber, Andrew J Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen M J Searle, Ted Sharpe, Michelle L Baker, Mark A Batzer, Panayiotis V Benos, Katherine Belov, Michele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E Deakin, Melissa J Fazzari, Jacob L Glass, Manfred Grabherr, John M Greally, Wanjun Gu, Timothy A Hore, Gavin A Huttley, Michael Kleber, Randy L Jirtle, Edda Koina, Jeannie T Lee, Shaun Mahony, Marco A Marra, Robert D Miller, Robert D Nicholls, Mayumi Oda, Anthony T Papenfuss, Zuly E Parra, David D Pollock, David A Ray, Jacqueline E Schein, Terence P Speed, Katherine Thompson, John L VandeBerg, Claire M Wade, Jerilyn A Walker, Paul D Waters, Caleb Webber, Jennifer R Weidman, Xiaohui Xie, Michael C Zody, Jennifer A Marshall Graves, , Chris P Ponting, Matthew Breen, Paul B Samollow, Eric S Lander, Kerstin Lindblad-Toh (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences., 167-77. In Nature 447 (7141).

Shaun. Mahony, P.E. Auron, P.V. Benos (2007) Inferring protein DNA dependencies using motif alignments and mutual information, i297. In Bioinformatics 23 (13).

Shaun Mahony, Panayiotis V Benos, Eleanor Feingold, David L Corcoran (2007) Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome, R84. In Genome Biol 8 (5).

Shaun. Mahony, P.V. Benos (2007) STAMP: a web tool for exploring DNA-binding motif similarities, W253-258. In Nucleic acids research 35 (suppl_2).

Katherine Belov, Janine E Deakin, Anthony T Papenfuss, Michelle L Baker, Sandra D Melman, Hannah V Siddle, Nicolas Gouin, David L Goode, Tobias J Sargeant, Mark D Robinson, Matthew J Wakefield, Shaun Mahony, Joseph G. R Cross, Panayiotis V Benos, Paul B Samollow, Terence P Speed, Jennifer A. Marshall Graves, Robert D Miller (2006) Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex., e46. In PLoS biology 4 (3).

Shaun Mahony, Panayiotis V Benos, Aaron Golden, Terry J Smith (2006) Self-organizing neural networks to support the discovery of DNA-binding motifs, 950–62. In Neural networks : the official journal of the International Neural Network Society 19 (6-7).

Shaun Mahony, Panayiotis V Benos, Aaron Golden, Terry J Smith (2005) Improved detection of DNA motifs using a self-organized clustering of familial binding profiles, i283–91. In Bioinformatics.

Shaun Mahony, David Hendrix, Daniel S Rokhsar, Aaron Golden, Terry J Smith (2005) Transcription factor binding site identification using the self-organizing map, 1807–14. In Bioinformatics 21 (9).

Shaun Mahony, Aaron Golden, James O McInerney, Terry J Smith (2004) Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models, 23. In BMC Bioinformatics.