Shaun Mahony
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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
STAMP: a web tool for exploring DNA-binding motif similarities
S Mahony, PV Benos
Nucleic Acids Research 35 (suppl 2), W253-W258, 2007
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
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), e1002638, 2012
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
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), 1219-1227, 2013
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
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), 1191-1198, 2013
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), e46, 2006
A high-resolution protein architecture of the budding yeast genome
MJ Rossi, PK Kuntala, WKM Lai, N Yamada, N Badjatia, C Mittal, G Kuzu, ...
Nature 592 (7853), 309-314, 2021
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies
S Mahony, PE Auron, PV Benos
PLoS computational biology 3 (3), e61, 2007
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
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), 1046-1054, 2014
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, 1-15, 2011
Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes
B Aydin, A Kakumanu, M Rossillo, M Moreno-Estellés, G Garipler, ...
Nature neuroscience 22 (6), 897-908, 2019
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
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
miniMDS: 3D structural inference from high-resolution Hi-C data
L Rieber, S Mahony
Bioinformatics 33 (14), i261-i266, 2017
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
An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding
S Mahony, MD Edwards, EO Mazzoni, RI Sherwood, A Kakumanu, ...
PLoS computational biology 10 (3), e1003501, 2014
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