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Publications
For a full publication list, see my CV.
Journal Articles:
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OL Griffith, SB Montgomery, ..., S Mahony (7th of 29 authors), ..., CM Bergman, SJM Jones:
"ORegAnno: an open-access community-driven resource for regulatory annotation."
Nucleic Acids Research, (2008) Accepted for publication
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Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden, Z Bar-Joseph:
"Combined analysis reveals a core set of cycling genes."
Genome Biology, (2007) 8(7):R146
Abstract Free Full Text
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S Mahony, PE Auron, PV Benos:
"Inferring protein-DNA dependencies using motif alignments and mutual information."
Bioinformatics, (2007) 23(13):i297-i304
Abstract Free Full Text
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S Mahony, DL Corcoran, E Feingold, PV Benos:
"Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome."
Genome Biology, (2007) 8(5):R84
Abstract Free Full Text
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TS Mikkelsen, MJ Wakefield, ..., S Mahony (37 of 64), ..., ES Lander, K Lindblad-Toh:
"Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequence."
Nature, (2007) 447:167-177
Abstract Full Text
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S Mahony, PV Benos:
"STAMP: a web tool for exploring DNA-binding motif similarities."
Nucleic Acids Research, Webserver Issue, (2007) 35(Web Server issue):W253-W258
Abstract Free Full Text
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S Mahony, P Auron, PV Benos:
"DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies."
PLoS Computational Biology, (2007) 3(3):e61
Abstract Free Full Text
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N McCoy, S Mahony, A Golden:
"Gene prediction in metagenomic libraries using the self-organising map and high performance computing techniques."
Springer Lecture Notes in Bioinformatics, (2007) 4360:99-110. (Proc. GCCB 2006)
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S Mahony, PV Benos, TJ Smith, A Golden:
"Self-organizing neural networks to support the discovery of
DNA-binding motifs." Neural Networks, (2006) 19(6-7):950-962.
Abstract
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K Belov, JE Deakin, AT Papenfuss, ML Baker, HV Siddle, N Gouin,
DL Goode, TJ Sargeant, MD Robinson, MJ Wakefield, S
Mahony, JGR Cross, PV Benos, PB Samollow, TP Speed, JA
Marshall Graves, RD Miller: "Reconstructing an Ancestral
Mammalian Immune Supercomplex from a Marsupial MHC."
PLoS Biology, (2006) 4(3):e46.
Abstract
Free Full Text
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S Mahony, A Golden, TJ Smith, PV Benos: "Improved
detection of DNA motifs using a self-organized clustering of
familial binding profiles." Bioinformatics, (2005)
21(Suppl 1):i283-i291 (Proc. ISMB 2005).
Abstract
Free Full Text
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S Mahony, D Hendrix, TJ Smith, A Golden:
"Self-Organizing Maps of Position Weight Matrices for Motif
Discovery in Biological Sequences." AI
Review, (2005) 24:397-413 (Proc. AICS 2004).
Abstract
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S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar:
"Transcription factor binding site identification using the
Self-Organizing Map." Bioinformatics, (2005)
21(9):1807-14.
Abstract
Free Full Text
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S Mahony, JO McInerney, TJ Smith, A Golden:
"Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models."
BMC Bioinformatics, (2004) 5:23.
Abstract
Free Full Text
PhD Thesis:
S Mahony:
"Self-organizing neural networks for biological sequence analysis"
(2005) Ph.D. Thesis, National University of Ireland, Galway.
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