Shaun Mahony
Title
Cited by
Cited by
Year
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
TS Mikkelsen, MJ Wakefield, B Aken, CT Amemiya, JL Chang, S Duke, ...
Nature 447 (7141), 167-177, 2007
6802007
STAMP: a web tool for exploring DNA-binding motif similarities
S Mahony, PV Benos
Nucleic Acids Research 35 (suppl 2), W253-W258, 2007
4692007
ORegAnno: an open-access community-driven resource for regulatory annotation
OL Griffith, SB Montgomery, B Bernier, B Chu, K Kasaian, S Aerts, ...
Nucleic acids research 36 (suppl_1), D107-D113, 2007
2642007
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
Y Guo, S Mahony, DK Gifford
PLoS computational biology 8 (8), 2012
1902012
The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation
M Iwafuchi-Doi, G Donahue, A Kakumanu, JA Watts, S Mahony, BF Pugh, ...
Molecular cell 62 (1), 79-91, 2016
1592016
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex
K Belov, JE Deakin, AT Papenfuss, ML Baker, SD Melman, HV Siddle, ...
PLoS biology 4 (3), 2006
1402006
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies
S Mahony, PE Auron, PV Benos
PLoS Comput Biol 3 (3), e61, 2007
1362007
Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity
EO Mazzoni, S Mahony, M Closser, CA Morrison, S Nedelec, DJ Williams, ...
Nature neuroscience 16 (9), 1219, 2013
1302013
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
S Mahony, EO Mazzoni, S McCuine, RA Young, H Wichterle, DK Gifford
Genome biology 12 (1), R2, 2011
1052011
Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene
H Jung, J Lacombe, EO Mazzoni, KF Liem Jr, J Grinstein, S Mahony, ...
Neuron 67 (5), 781-796, 2010
1012010
Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals
EO Mazzoni, S Mahony, M Peljto, T Patel, SR Thornton, S McCuine, ...
Nature neuroscience 16 (9), 1191, 2013
952013
Reprogrammed stomach tissue as a renewable source of functional β cells for blood glucose regulation
C Ariyachet, A Tovaglieri, G Xiang, J Lu, MS Shah, CA Richmond, ...
Cell Stem Cell 18 (3), 410-421, 2016
812016
Transcription factor binding site identification using the self-organizing map
S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar
Bioinformatics 21 (9), 1807-1814, 2005
812005
Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons
S Lodato, BJ Molyneaux, E Zuccaro, LA Goff, HH Chen, W Yuan, ...
Nature neuroscience 17 (8), 1046, 2014
662014
Embryonic stem cell–based mapping of developmental transcriptional programs
EO Mazzoni, S Mahony, M Iacovino, CA Morrison, G Mountoufaris, ...
Nature methods 8 (12), 1056-1058, 2011
642011
Discovering homotypic binding events at high spatial resolution
Y Guo, G Papachristoudis, RC Altshuler, GK Gerber, TS Jaakkola, ...
Bioinformatics 26 (24), 3028-3034, 2010
512010
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles
S Mahony, A Golden, TJ Smith, PV Benos
Bioinformatics 21 (suppl_1), i283-i291, 2005
462005
An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding
S Mahony, MD Edwards, EO Mazzoni, RI Sherwood, A Kakumanu, ...
International Conference on Research in Computational Molecular Biology, 175-176, 2014
452014
A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells
S Velasco, MM Ibrahim, A Kakumanu, G Garipler, B Aydin, MA Al-Sayegh, ...
Cell Stem Cell 20 (2), 205–217, 2017
422017
Combined analysis reveals a core set of cycling genes
Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden, ...
Genome biology 8 (7), R146, 2007
422007
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