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Paul Shannon
Area of Expertise
Software engineering, bioinformatics
Current Position
Senior Software Engineer
Degree
B.A. Mathematics, University of Virginia, 1984
Research Interests
Mr Shannon works closely with biologists exploring data, inferring mechanism where possible, generating hypotheses for the next round of experimentation; writing software for these pursuits as needed, of whatever scale and complexity the problem requires.
Selected Publications
Roach JC,* Glusman G,* Smit AFA,* Huff CD,* Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ. 2010. Analysis of genetic inheritance in a family quartet by whole genome sequencing. Science 328(5978):636-9. *Equal contributions.
Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. 2010. Exome sequencing identified the cause of a mendelian disorder. Nat Genet. Jan;42(1):30-5. Epub 2009 Nov 13.
Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V. 2006. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology 7: R36 (2006)
Shannon PT, Reiss DJ, Bonneau R, Baliga NS. 2006. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics. Mar 28;7:176
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. Nov;13(11):2498-504
Relevant Links
http://gaggle.systemsbiology.net
http://cytoscape.org
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