FACULTY LIST
 Simon N. Twigger, Ph.D.
Assistant Professor
Phone: (414) 456-8802
Email: simont@mcw.edu
B.S. University of Nottingham, UK, 1990
Ph.D. University of Nottingham, UK, 1994
Computational biology consumes and generates data, and managing this effectively is a key thrust of much of my current work. As part of the NHGRI funded component of the Generic Model Organism Database project (GMOD, http://www.gmod.org) we have created PubFetch, a web service that provides standardized access to popular literature databases PubMed and Agricola. Access to literature is vital for model organism database curation, and the BioMOBY web service approach we have used makes this data accessible to any BioMOBY-compatible system (http://www.biomoby.org). PubTrack, another component of the GMOD project is a data tracking package that allows researchers to follow their data and analyses as they progress through the heterogeneous web lab and computational environments.
The NHLBI-funded Rat Genome Database has established itself as a primary source of rat genomic data. Our goal is to assist rat researchers in relating their results in the rat, to facilitate the development of disease treatments. However, this is a moving target and our latest challenge is to integrate the rat genomic sequence and provide the database users with effective ways to integrate the sequence with their own experimental research.
The NHLBI National Proteomics Center ties together many elements of computational biology. We are developing a novel proteomic analysis algorithm that is significantly faster than the existing state of the art. We will be extending this package and adapting it to run in a parallel architecture. Effective use of high performance computer clusters is another area of emphasis, and we will be making use of BioMOBY and the PubTrack projects to assist in data management and tracking in this distributed environment.
Recent Publications:
Hicks WA, Halligan BD, Slyper RY, Twigger SN, Greene AS, Olivier M. Simultaneous quantification and identification using (18)O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant." J Am Soc Mass Spectrom. 2005 Jun;16(6):916-25.
Halligan BD, Slyper RY, Twigger SN, Hicks W, Olivier M, Greene AS. ZoomQuant: an application for the quantitation of stable isotope labeled peptides. J Am Soc Mass Spectrom. 2005 Mar;16(3):302-6.
Halligan BD, Dratz EA, Feng X, Twigger SN, Tonellato PJ, Greene AS. Peptide identification using peptide amino acid attribute vectors. J Proteome Res. 2004 Jul-Aug;3(4):813-20.
Halligan BD, Ruotti V, Jin W, Laffoon S, Twigger SN, Dratz EA. ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels. Nucleic Acids Res. 2004 Jul 1;32:W638-44.
Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ. Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res. 2004 Apr;14(4):651-60.
Gibbs, R.A. et.al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 428:493-521.
Twigger SN. Of rats and men. Genome Biol. 2004;5(3):314.
Thomas MA, Chen C-F. Jensen-Seaman MI, Tonellato PJ and Twigger SN. Phylogenetics of rat inbred strains, Mammalian Genome, 2003 14:1-4.
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