Kenneth R Williams

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint YPED: a web-accessible database system for protein expression analysis
    Mark A Shifman
    Center for Medical Informatics, Department of Anesthesiology, Yale University, New Haven, Connecticut 06520, USA
    J Proteome Res 6:4019-24. 2007
  2. ncbi request reprint Enzymatic cleavage and HPLC peptide mapping of proteins
    K R Williams
    W M Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
    Mol Biotechnol 8:155-67. 1997
  3. pmc Comparing protein abundance and mRNA expression levels on a genomic scale
    Dov Greenbaum
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Genome Biol 4:117. 2003
  4. ncbi request reprint Identification of proteins based on MS/MS spectra and location of posttranslational modifications
    Kathryn L Stone
    WM Keck Foundation Biotechnology Resource Laboratory, Mass Spectrometry and Protomic Resources, Yale University, New Haven, CT, USA
    Methods Mol Biol 386:57-77. 2007
  5. doi request reprint Enzymatic digestion of proteins in gels for mass spectrometric identification and structural analysis
    Kathryn L Stone
    W M Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, Connecticut, USA
    Curr Protoc Protein Sci . 2004
  6. pmc KARMA: a web server application for comparing and annotating heterogeneous microarray platforms
    Kei Hoi Cheung
    Center for Medical Informatics, Department of Anesthesiology, Yale University, New Haven, CT, USA
    Nucleic Acids Res 32:W441-4. 2004
  7. ncbi request reprint A dynamic approach to mapping coordinates between microplates and microarrays
    Kei Hoi Cheung
    Department of Anesthesiology, Center for Medical Informatics, Yale University, New Haven, CT 06520, USA
    J Biomed Inform 35:306-12. 2002
  8. pmc A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies
    Nicholas Carriero
    Department of Computer Science, Yale University, New Haven, CT 06520 8285, USA
    J Am Med Inform Assoc 12:90-8. 2005
  9. ncbi request reprint Detecting and aligning peaks in mass spectrometry data with applications to MALDI
    Weichuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, Suite 503, 300 George Street, New Haven, CT 06520, USA
    Comput Biol Chem 30:27-38. 2006
  10. ncbi request reprint X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers
    Robert D Bjornson
    Yale University, Department of Computer Science, P O Box 208285, New Haven, Connecticut 06520 8285, USA
    J Proteome Res 7:293-9. 2008

Research Grants

  1. STRUCTURE/FUNCTION OF EUKARYOTIC RNA BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 1993
  2. HIGH THROUGHPUT MALDI MASS SPECTROMETER SYSTEM
    Kenneth Williams; Fiscal Year: 2001
  3. STRUCTURE/FUNCTION OF EUKARYOTIC RNA BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 2001
  4. YALE MICROARRAY RESOURCE
    Kenneth Williams; Fiscal Year: 2002
  5. FTICR Mass Spectrometer
    Kenneth Williams; Fiscal Year: 2003
  6. Yale Biomedical Supercomputer
    Kenneth Williams; Fiscal Year: 2004
  7. STRUCTURE/FUNCTION OF EUKARYOTIC DNA BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 1990

Collaborators

Detail Information

Publications18

  1. ncbi request reprint YPED: a web-accessible database system for protein expression analysis
    Mark A Shifman
    Center for Medical Informatics, Department of Anesthesiology, Yale University, New Haven, Connecticut 06520, USA
    J Proteome Res 6:4019-24. 2007
    ..A summary report with PANTHER Classification System annotations is also available to aid in biological interpretation of the results. The source code is open-source and is available from http://yped.med.yale.edu/yped_dist...
  2. ncbi request reprint Enzymatic cleavage and HPLC peptide mapping of proteins
    K R Williams
    W M Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
    Mol Biotechnol 8:155-67. 1997
    ....
  3. pmc Comparing protein abundance and mRNA expression levels on a genomic scale
    Dov Greenbaum
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Genome Biol 4:117. 2003
    ..We also merge many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories...
  4. ncbi request reprint Identification of proteins based on MS/MS spectra and location of posttranslational modifications
    Kathryn L Stone
    WM Keck Foundation Biotechnology Resource Laboratory, Mass Spectrometry and Protomic Resources, Yale University, New Haven, CT, USA
    Methods Mol Biol 386:57-77. 2007
    ..Additionally, multiple techniques will be described for identifying sites of protein posttranslational modification, with emphasis on phosphorylation and Arg methylation...
  5. doi request reprint Enzymatic digestion of proteins in gels for mass spectrometric identification and structural analysis
    Kathryn L Stone
    W M Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, Connecticut, USA
    Curr Protoc Protein Sci . 2004
    ..In each case, an in-gel digestion, usually tryptic, is used with mass spectrometry to identify these proteins of interest. For large numbers of gel spots, robotic digestion can save time and money...
  6. pmc KARMA: a web server application for comparing and annotating heterogeneous microarray platforms
    Kei Hoi Cheung
    Center for Medical Informatics, Department of Anesthesiology, Yale University, New Haven, CT, USA
    Nucleic Acids Res 32:W441-4. 2004
    ..The KARMA database, which is updated periodically, is available on line at the following URL: http://ymd.med.yale.edu/karma/cgi-bin/karma.pl...
  7. ncbi request reprint A dynamic approach to mapping coordinates between microplates and microarrays
    Kei Hoi Cheung
    Department of Anesthesiology, Center for Medical Informatics, Yale University, New Haven, CT 06520, USA
    J Biomed Inform 35:306-12. 2002
    ..MAC and its source code can be accessed via the following Web address: http://ymd.med.yale.edu/kei-cgi/kc_mac_dev8.pl...
  8. pmc A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies
    Nicholas Carriero
    Department of Computer Science, Yale University, New Haven, CT 06520 8285, USA
    J Am Med Inform Assoc 12:90-8. 2005
    ....
  9. ncbi request reprint Detecting and aligning peaks in mass spectrometry data with applications to MALDI
    Weichuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, Suite 503, 300 George Street, New Haven, CT 06520, USA
    Comput Biol Chem 30:27-38. 2006
    ..Additional comparisons also demonstrate that our method has a similar performance as the hierarchical clustering method, although the implementations of these methods are different...
  10. ncbi request reprint X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers
    Robert D Bjornson
    Yale University, Department of Computer Science, P O Box 208285, New Haven, Connecticut 06520 8285, USA
    J Proteome Res 7:293-9. 2008
    ..Furthermore, the parallelization technique used is unusual and potentially useful for parallelizing other complex programs...
  11. pmc Keck Foundation Biotechnology Resource Laboratory, Yale University
    Kathryn L Stone
    Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut, USA
    Yale J Biol Med 80:195-211. 2007
  12. doi request reprint Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies
    Erol E Gulcicek
    Yale University, New Haven, Connecticut, USA
    Curr Protoc Bioinformatics . 2005
    ..In this unit, some of the common protein-profiling technologies are reviewed, along with the accompanying data-analysis tools...
  13. ncbi request reprint MALDI-MS data analysis for disease biomarker discovery
    Weichuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
    Methods Mol Biol 328:199-216. 2006
    ..After that, we show some application examples using an ovarian sera cancer dataset. Finally, we discuss the limitations of current approaches and possible future research directions...
  14. ncbi request reprint Isotope-coded affinity tags for protein quantification
    Christopher M Colangelo
    W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA
    Methods Mol Biol 328:151-8. 2006
    ..The results are then database searched and a list of hundreds of proteins and their heavy:light ratio is obtained...
  15. ncbi request reprint Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas
    Keith Hoek
    Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 15 York Street, New Haven, CT 06520 8059, USA
    Cancer Res 64:5270-82. 2004
    ..These results provide a comprehensive view of changes in advanced melanoma relative to normal melanocytes and reveal new targets that can be used in assessing prognosis, staging, and therapy of melanoma patients...
  16. ncbi request reprint Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
    Baolin Wu
    Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, USA
    Bioinformatics 19:1636-43. 2003
    ..Although various statistical methods have been utilized to identify biomarkers from MS data, there has been no systematic comparison among these approaches in their relative ability to analyze MS data...
  17. ncbi request reprint Recent advances in neuroproteomics and potential application to studies of drug addiction
    Kenneth Williams
    Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536 0812, USA
    Neuropharmacology 47:148-66. 2004
    ....
  18. ncbi request reprint Multiple peak alignment in sequential data analysis: a scale-space-based approach
    Weichuan Yu
    Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Sai Kung, Kowloon, Hong Kong
    IEEE/ACM Trans Comput Biol Bioinform 3:208-19. 2006
    ..e., a candidate is considered either as a peak or as a nonpeak) with a quantitative scoring measure-based approach (i.e., we assign to each candidate a possibility of being a peak)...

Research Grants23

  1. STRUCTURE/FUNCTION OF EUKARYOTIC RNA BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 1993
    ..These studies are basic to understanding structure/function relationships in a family of eukaryotic, single-stranded RNA binding proteins that are intimately involved in RNA metabolism...
  2. HIGH THROUGHPUT MALDI MASS SPECTROMETER SYSTEM
    Kenneth Williams; Fiscal Year: 2001
    ..abstract_text> ..
  3. STRUCTURE/FUNCTION OF EUKARYOTIC RNA BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 2001
    ..Some conclusions may be relevant to the more than 100 other RNA binding proteins that use the same RNA binding motif as A1. ..
  4. YALE MICROARRAY RESOURCE
    Kenneth Williams; Fiscal Year: 2002
    ....
  5. FTICR Mass Spectrometer
    Kenneth Williams; Fiscal Year: 2003
    ..We believe the requested instrument would make a major contribution to biomedical research that would extend far beyond Yale University. ..
  6. Yale Biomedical Supercomputer
    Kenneth Williams; Fiscal Year: 2004
    ....
  7. STRUCTURE/FUNCTION OF EUKARYOTIC DNA BINDING PROTEINS
    Kenneth Williams; Fiscal Year: 1990
    ..These proposed studies are basic to our understanding of those physiological processes that require a single-stranded nucleic acid template...