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

by Mahony, Shaun, Benos, Panayiotis V.
Published 2007

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

by Guo, Yuchun, Mahony, Shaun, Gifford, David K.
Published 2012

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies

by Mahony, Shaun, Auron, Philip E, Benos, Panayiotis V
Published 2007

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

by Mahony, Shaun, Corcoran, David L, Feingold, Eleanor, Benos, Panayiotis V
Published 2007

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

by Mahony, Shaun, Mazzoni, Esteban O, McCuine, Scott, Young, Richard A, Wichterle, Hynek, Gifford, David K
Published 2011

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models

by Mahony, Shaun, McInerney, James O, Smith, Terry J, Golden, Aaron
Published 2004

Embryonic stem cell-based system for mapping developmental transcriptional programs

by Mazzoni, Esteban O., Mahony, Shaun, Iacovino, Michelina, Morrison, Carolyn A., Mountoufaris, George, Closser, Michael, Whyte, Warren A., Young, Richard A., Kyba, Michael, Gifford, David K., Wichterle, Hynek
Published 2011

Saltatory remodeling of Hox chromatin in response to rostro-caudal patterning signals

by Mazzoni, Esteban O., Mahony, Shaun, Peljto, Mirza, Patel, Tulsi, Thornton, Seraphim R., McCuine, Scott, Reeder, Christopher, Boyer, Laurie A., Young, Richard A., Gifford, David K., Wichterle, Hynek
Published 2013

A Cdx4-Sall4 Regulatory Module Controls the Transition from Mesoderm Formation to Embryonic Hematopoiesis

by Paik, Elizabeth J., Mahony, Shaun, White, Richard M., Price, Emily N., DiBiase, Anthony, Dorjsuren, Bilguujin, Mosimann, Christian, Davidson, Alan J., Gifford, David, Zon, Leonard I.
Published 2013

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

by Mahony, Shaun, Edwards, Matthew D., Mazzoni, Esteban O., Sherwood, Richard I., Kakumanu, Akshay, Morrison, Carolyn A., Wichterle, Hynek, Gifford, David K.
Published 2014

Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution

by Han, G. Celine, Vinayachandran, Vinesh, Bataille, Alain R., Park, Bongsoo, Chan-Salis, Ka Yim, Keller, Cheryl A., Long, Maria, Mahony, Shaun, Hardison, Ross C., Pugh, B. Franklin
Published 2015

A multi-parametric flow cytometric assay to analyze DNA–protein interactions

by Arbab, Mandana, Mahony, Shaun, Cho, Hyunjii, Chick, Joel M., Rolfe, P. Alexander, van Hoff, John Peter, Morris, Viveca W.S., Gygi, Steven P., Maas, Richard L., Gifford, David K., Sherwood, Richard I.
Published 2013

Large Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and Macaque

by Zinman, Guy, Brower-Sinning, Rachel, Emeche, Chineye H., Ernst, Jason, Huang, Grace Tzu-Wei, Mahony, Shaun, Myers, Amy J., O'Dee, Dawn M., Flynn, JoAnne L., Nau, Gerard J., Ross, Ted M., Salter, Russell D., Benos, Panayiotis V., Bar Joseph, Ziv, Morel, Penelope A.
Published 2011

Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex

by Belov, Katherine, Deakin, Janine E, Papenfuss, Anthony T, Baker, Michelle L, Melman, Sandra D, Siddle, Hannah V, Gouin, Nicolas, Goode, David L, Sargeant, Tobias J, Robinson, Mark D, Wakefield, Matthew J, Mahony, Shaun, Cross, Joseph G. R, Benos, Panayiotis V, Samollow, Paul B, Speed, Terence P, Graves, Jennifer A. Marshall, Miller, Robert D
Published 2006

ORegAnno: an open-access community-driven resource for regulatory annotation

by Griffith, Obi L., Montgomery, Stephen B., Bernier, Bridget, Chu, Bryan, Kasaian, Katayoon, Aerts, Stein, Mahony, Shaun, Sleumer, Monica C., Bilenky, Mikhail, Haeussler, Maximilian, Griffith, Malachi, Gallo, Steven M., Giardine, Belinda, Hooghe, Bart, Van Loo, Peter, Blanco, Enrique, Ticoll, Amy, Lithwick, Stuart, Portales-Casamar, Elodie, Donaldson, Ian J., Robertson, Gordon, Wadelius, Claes, De Bleser, Pieter, Vlieghe, Dominique, Halfon, Marc S., Wasserman, Wyeth, Hardison, Ross, Bergman, Casey M., Jones, Steven J.M.
Published 2008