Simon N Twigger

Summary

Affiliation: Medical College of Wisconsin
Country: USA

Publications

  1. pmc ChromSorter PC: a database of chromosomal regions associated with human prostate cancer
    Ann Etim
    Department of Pathology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
    BMC Genomics 5:27. 2004
  2. pmc Of rats and men
    Simon N Twigger
    Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53211, USA
    Genome Biol 5:314. 2004
  3. pmc Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data
    Simon N Twigger
    Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
    Genome Res 14:651-60. 2004
  4. pmc The Rat Genome Database, update 2007--easing the path from disease to data and back again
    Simon N Twigger
    Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
    Nucleic Acids Res 35:D658-62. 2007
  5. pmc DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
    Brian D Halligan
    Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA
    Nucleic Acids Res 33:W376-81. 2005
  6. pmc The Rat Genome Database pathway portal
    Victoria Petri
    Human and Molecular Genetics Center, Medical College of Wisconsin, WI, 53226 3548, USA
    Database (Oxford) 2011:bar010. 2011
  7. pmc 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
  8. ncbi request reprint Tools and strategies for physiological genomics: the Rat Genome Database
    Simon N Twigger
    Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
    Physiol Genomics 23:246-56. 2005
  9. pmc Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms
    Brian 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
  10. pmc What everybody should know about the rat genome and its online resources
    Simon N Twigger
    Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
    Nat Genet 40:523-7. 2008

Detail Information

Publications20

  1. pmc ChromSorter PC: a database of chromosomal regions associated with human prostate cancer
    Ann 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...
  2. pmc Of rats and men
    Simon N Twigger
    Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53211, USA
    Genome Biol 5:314. 2004
  3. pmc Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data
    Simon 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...
  4. pmc The Rat Genome Database, update 2007--easing the path from disease to data and back again
    Simon 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...
  5. pmc DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
    Brian 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...
  6. pmc The Rat Genome Database pathway portal
    Victoria 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...
  7. pmc 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...
  8. ncbi request reprint Tools and strategies for physiological genomics: the Rat Genome Database
    Simon 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...
  9. pmc Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms
    Brian 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 )...
  10. pmc What everybody should know about the rat genome and its online resources
    Simon N Twigger
    Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
    Nat Genet 40:523-7. 2008
    ....
  11. pmc The Rat Genome Database 2009: variation, ontologies and pathways
    Melinda 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...
  12. pmc ZoomQuant: an application for the quantitation of stable isotope labeled peptides
    Brian 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...
  13. ncbi request reprint Peptide identification using peptide amino acid attribute vectors
    Brian 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...
  14. pmc The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data
    Stanley 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...
  15. ncbi request reprint Phylogenetics of rat inbred strains
    Michael A Thomas
    Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
    Mamm Genome 14:61-4. 2003
  16. doi request reprint Exploring phenotypic data at the rat genome database
    Simon 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...
  17. pmc ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels
    Brian 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...
  18. doi request reprint Progress and prospects in rat genetics: a community view
    Timothy 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...
  19. ncbi request reprint A new method for identifying informative genetic markers in selectively bred rats
    David 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...
  20. ncbi request reprint Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics
    George 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...