Shaun Mahony

Department: National Centre for Biomedical Engineering Science

Contact:
I moved to the University of Pittsburgh in 2005.
See here for new contact details: http://biodev.hgen.pitt.edu/shaun

Bioinformatics Research Interests:
My PhD project is entitled "Neural networks to identify patterns in genomic data". The first part of this project involved implementing the codon usage analysis software package RescueNet. The program is written in C++ and is based on a neural network algorithm named the Self-Organizing Map. While it is a useful tool in studying the sources of synonymous codon usage diversity, RescueNet was also developed as an automatic gene recognition tool.

I participated in the University of California Education Abroad Program, which allowed me to join the Rokhsar group at UC Berkeley from August until December in 2003. While working with the group, I became involved in developing software to predict the location of transcription factor binding sites in promoter sequences. This software, also based on the Self-Organizing Map, is named SOMBRERO.

I also was fortunate enough to be allowed to spend three months at the University of Pittsburgh in the Autumn of 2004. While there, I studied with Takis Benos, and we explored the advantageous performance that results from biasing the SOMBRERO motif finder with the binding constraints of known transcription factor families.

My research interests span such fields as:

• Neural networks, in particular the Self-Organizing Map, and their applications in biosequence analysis.
• Motif identification.
• Transcription factor evolution.
• Marsupial genomics.
• Gene prediction.

Publications:

• S Mahony, A Golden, TJ Smith, PV Benos: "Improved detection of DNA motifs using a self-organized clustering of familial binding profiles." (2005) Bioinformatics 21(Suppl 1):i283-i291 ( Proc. ISMB). Abstract, Full Text, Supporting Information .
• S Mahony, D Hendrix, TJ Smith, A Golden: "Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences." (2005) AI Review (accepted)
• S Mahony, D Hendrix, A Golden, TJ Smith, DS Rokhsar: "Transcription factor binding site identification using the Self-Organizing Map." (2005) Bioinformatics 21(9):1807-14. Abstract, Full Text, Supporting Information.
• S Mahony, JO McInerney, TJ Smith, A Golden: "Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models." (2004) BMC Bioinformatics 5:23. Abstract, Full Text

CONFERENCES AND EVENTS:

• Workshop on Self-Organizing Maps, 2005, Paris, France (oral presentation accepted: "SOMBRERO: Integrating self-organizing neural networks in the search for DNA binding motifs").
• ISMB 2005, Detroit, MI (oral presentation: "Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.").
• Annual symposium of the Virtual Institute for Bioinformatics, Èireann, 2005 (oral presentation: "Clustering PSSMs and Applications for Familial Binding Profiles").
• Royal Academy of Medicine in Ireland, Biomedical Sciences Section Meeting 2005 (oral presentation: "Bioinformatic Identification of Human Labour-Related Genes Using Regulatory Module Scanning").
• Artificial Intelligence and Cognitive Science 2004 (oral presentation: "Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences").
• ISMB 2004, Glasgow, Scotland (poster presentation: "A Self-Organizing Map of Probability Weight Matrices for Motif Identification").
• Annual symposium of the Virtual Institute for Bioinformatics, Èireann, 2004 (oral presentation: "Finding Biological Regulatory Elements Using the Self-Organizing Map").
• Genomes 2004, Cambridge, UK (poster presentation: "Identifying Multiple Gene Models Using the Self-Organizing Map").
• IEEE Computational Systems Bioinformatics Conference 2003 at Stanford University, CA (poster presentation: "A New Approach to Gene Prediction Using the Self-Organizing Map").
• Annual symposium of the Virtual Institute for Bioinformatics, Èireann, 2002 (oral presentation: "Analysis of Codon Usage Patterns Using the Self-Organizing Map")
• European Conference on Computational Biology, 2002 (poster presentation: "Interpreting Patterns of Codon Usage in Bacterial Genomes Using the Self-Organizing Map").
• Annual symposium of the Irish Society for Scientific and Engineering Computation, 2002 (oral presentation: "Gene Prediction in Neisseria meningitidis Using Artificial Intelligence Methods").

Professional Organization Memberships:
I am a member of the International Society for Computational Biology and I am currently serving as a member of the inaugural ISCB Student Council.

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