Associate Professor of Computational Biology

Associate Professor of Biomedical Informatics

Contact Info:

Publications

S. Kadri, V. Hinman, P.V. Benos, “HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models”, Proc Asian- Pacific Bioinformatics Conference published in BMC Bioinformatics, (2009) to appear.

S. Mahony, P.E. Auron and P.V. Benos “Inferring protein-DNA dependencies using motif alignments and mutual information”, Bioinformatics (Proc ISMB), (2007) 23:i297-i304.

S. Mahony, D.L. Corcoran, E. Feingold, P.V. Benos “Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome”, Genome Biol, (2007) 8:R84.

S. Mahony, P.V. Benos “STAMP: a web tool for exploring DNA-binding motif similarities”, Nucl Acids Res, (2007) 35:W253-258. Abstract

T.S. Mikkelsen et al. “Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences”, Nature, (2007) 447:167-177. Abstract

S. Mahony, P.E. Auron, P.V. Benos “DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies”, PLoS Comput Biol, (2007) 3:e61. Abstract

S. Mahony, P.V. Benos, T.J. Smith, and A. Golden “Self-Organizing Neural Networks to Support the Discovery of DNA-Binding Motifs”, Neural Networks, (2006) 19:950-962. Abstract

K. Belov, J.E. Deakin, A.T. Papenfuss, M.L. Baker, S.D. Melman, H.V. Siddle, N. Gouin, D.L. Goode, T.J. Sargeant, MD Robinson, M.J. Wakefield, S. Mahony, J.G.R. Cross, P.V. Benos, P.B. Samollow, T.P. Speed, J.A.M. Graves, and R.D. Miller “Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial MHC”, PLoS Biology, (2006) 4:e46.