Research Topics
Species | Simon N TwiggerSummaryAffiliation: Medical College of Wisconsin Country: USA Publications
| Collaborators
|
Detail Information
Publications
ChromSorter PC: a database of chromosomal regions associated with human prostate cancerAnn Etim
Department of Pathology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
BMC Genomics 5:27. 2004..The input material was based on a broad literature search with subsequent hand annotation of information relevant to prostate cancer...- Of rats and menSimon N Twigger
Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53211, USA
Genome Biol 5:314. 2004 - Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human dataSimon N Twigger
Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
Genome Res 14:651-60. 2004..Integrating rat physiology with mouse genetics and clinical results from human by using the respective genomes provides a novel route to capitalize on comparative genomics and the strengths of model organism biology... - The Rat Genome Database, update 2007--easing the path from disease to data and back againSimon N Twigger
Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
Nucleic Acids Res 35:D658-62. 2007..We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the database... - DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopyBrian D Halligan
Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA
Nucleic Acids Res 33:W376-81. 2005..DeNovoID also uses a geometric indexing scheme that reduces the number of calculations required to determine the best peptide match in the database. DeNovoID is available at http://proteomics.mcw.edu/denovoid... - The Rat Genome Database pathway portalVictoria Petri
Human and Molecular Genetics Center, Medical College of Wisconsin, WI, 53226 3548, USA
Database (Oxford) 2011:bar010. 2011..The Pathway Portal resources at RGD are presented, and future directions are discussed. Database URL: http://rgd.mcw.edu... 
Tools and strategies for physiological genomics: the Rat Genome DatabaseSimon N Twigger
Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
Physiol Genomics 23:246-56. 2005..We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics...- Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant"Wayne A Hicks
National Proteomics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA
J Am Soc Mass Spectrom 16:916-25. 2005..This compares well with data produced from (18)O labeling experiments using time of flight (TOF) and Fourier transform-ion cyclotron resonance (FT-ICR) MS instruments... - Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithmsBrian D Halligan
Biotechnology and Bioengineering Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
J Proteome Res 8:3148-53. 2009..mcw.edu/vipdac )... - The Rat Genome Database 2009: variation, ontologies and pathwaysMelinda R Dwinell
Department of Physiology and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA
Nucleic Acids Res 37:D744-9. 2009..By curating, storing, integrating, visualizing and promoting rat data, RGD ensures that the investment made into rat genomics and genetics can be leveraged by all interested investigators... - What everybody should know about the rat genome and its online resourcesSimon N Twigger
Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
Nat Genet 40:523-7. 2008.... - ZoomQuant: an application for the quantitation of stable isotope labeled peptidesBrian D Halligan
Bioinformatics, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53213, USA
J Am Soc Mass Spectrom 16:302-6. 2005..Finally, ZoomQuant generates a summary report of the relative abundance of the peptides identified in the two samples... - Peptide identification using peptide amino acid attribute vectorsBrian D Halligan
Bioinformatics Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53213, USA
J Proteome Res 3:813-20. 2004..We demonstrate that the amino acid composition of peptides is virtually as informative as the sequence and allows rapid peptide identification more accurately than peptide mass alone... - The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological dataStanley J F Laulederkind
Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226 3548, USA
Database (Oxford) 2011:bar002. 2011..The user interfaces have been adapted to the work routines of the curators, creating a suite of tools that is intuitive and powerful. Database URL: http://rgd.mcw.edu... - Phylogenetics of rat inbred strainsMichael A Thomas
Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
Mamm Genome 14:61-4. 2003 - Exploring phenotypic data at the rat genome databaseSimon N Twigger
Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
Curr Protoc Bioinformatics . 2006..We show how to make associations with the genome and use comparative tools to link the rat with human and mouse in order to integrate results from these three species of critical biomedical importance... - ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gelsBrian D Halligan
Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA
Nucleic Acids Res 32:W638-44. 2004..ProMoST has been implemented as cgi script in Perl available on a WWW server at http://proteomics.mcw.edu/promost... 
Progress and prospects in rat genetics: a community viewTimothy J Aitman
Medical Research Council Clinical Sciences Centre and Imperial College London, Du Cane Road, London W12 0NN, UK
Nat Genet 40:516-22. 2008..Finally, we present a set of principles that justify continuing and strengthening genetic studies in the rat model, and further development of genomic infrastructure for rat research...- A new method for identifying informative genetic markers in selectively bred ratsDavid Weinshenker
Department of Human Genetics, Emory University, Whitehead 301, 615 Michael Street, Atlanta, Georgia 30322, USA
Mamm Genome 16:784-91. 2005..Thus, picking markers based on Het and Unc scores is a valuable method for identifying informative microsatellite markers in selectively bred rodent strains derived from outbred populations... - Structures of proteins of biomedical interest from the Center for Eukaryotic Structural GenomicsGeorge N Phillips
Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
J Struct Funct Genomics 8:73-84. 2007..Many times proteins qualify in more than one of these categories. Here we review some of the structures that have connections to human health and disease...