Research Topics
| Shaun MahonySummaryAffiliation: University of Pittsburgh Country: USA Publications
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Detail Information
Publications
Inferring protein-DNA dependencies using motif alignments and mutual informationShaun Mahony
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, USA
Bioinformatics 23:i297-304. 2007..Such inference of protein-DNA contacting positions may guide future experimental studies of DNA recognition...- Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genomeShaun Mahony
Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA
Genome Biol 8:R84. 2007..This study focuses on the evolutionary relationships between conservation of noncoding sequences, cis-regulatory elements, and biologic functions of regulated genes in opossum and eight vertebrate species... - Self-organizing neural networks to support the discovery of DNA-binding motifsShaun Mahony
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
Neural Netw 19:950-62. 2006..The performance of the three self-organizing neural networks is evaluated here using various datasets... - STAMP: a web tool for exploring DNA-binding motif similaritiesShaun Mahony
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
Nucleic Acids Res 35:W253-8. 2007..STAMP also directly accepts the output files from 12 supported motif-finders, enabling quick interpretation of motif-discovery analyses. STAMP is available at http://www.benoslab.pitt.edu/stamp... - DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategiesShaun Mahony
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
PLoS Comput Biol 3:e61. 2007..Detecting similarities between DNA motifs is a key step in the comparative study of transcriptional regulation, and the work presented here will form the basis for tool and method development for future transcriptional modeling studies... - Combined analysis reveals a core set of cycling genesYong Lu
Department of Computer Science, Carnegie Mellon University, Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
Genome Biol 8:R146. 2007..Combining and comparing data from multiple species is challenging because of noise in expression data, the different synchronization and scoring methods used, and the need to determine an accurate set of homologs... - Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequencesTarjei S Mikkelsen
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 447:167-77. 2007..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation... - ORegAnno: an open-access community-driven resource for regulatory annotationObi L Griffith
Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
Nucleic Acids Res 36:D107-13. 2008..All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org... - Improved detection of DNA motifs using a self-organized clustering of familial binding profilesShaun Mahony
National Centre for Biomedical Engineering Science, NUI Galway Galway, Ireland
Bioinformatics 21:i283-91. 2005..This assumption is not true, at least not for some TF families. Automatic PSSM clustering methods are thus required for augmenting the usefulness of FBPs... - Transcription factor binding site identification using the self-organizing mapShaun Mahony
National Centre for Biomedical Engineering Science, NUI Galway, Ireland
Bioinformatics 21:1807-14. 2005..Features identified are ranked in terms of over-representation relative to a background model... - Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complexKatherine Belov
Centre for Advanced Technologies in Animal Genetics and Reproduction, Faculty of Veterinary Science, The University of Sydney, Camden, Australia
PLoS Biol 4:e46. 2006.... - Gene prediction using the Self-Organizing Map: automatic generation of multiple gene modelsShaun Mahony
National Centre for Biomedical Engineering Science, NUI, Galway, Galway, Ireland
BMC Bioinformatics 5:23. 2004..It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation...