Kenneth R Williams
Affiliation: Yale University
- YPED: a web-accessible database system for protein expression analysisMark 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...
- Keck Foundation Biotechnology Resource Laboratory, Yale UniversityKathryn L Stone
Keck Foundation Biotechnology Resource Laboratory, Yale University, 300 George Street, New Haven, Connecticut, USA
Yale J Biol Med 80:195-211. 2007
- Enzymatic cleavage and HPLC peptide mapping of proteinsK R Williams
W M Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
Mol Biotechnol 8:155-67. 1997..A compilation of data from nearly 200 "unknown" samples is used to help provide realistic expectations with respect to the results that are likely to be obtained from carrying out in-gel proteolytic digests on large numbers of proteins...
- Comparing protein abundance and mRNA expression levels on a genomic scaleDov 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...
- YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics researchChristopher M Colangelo
W M Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA Electronic address
Genomics Proteomics Bioinformatics 13:25-35. 2015..In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. ..
- Identification of proteins based on MS/MS spectra and location of posttranslational modificationsKathryn 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...
- Development of a Targeted Urine Proteome Assay for kidney diseasesLloyd G Cantley
Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
Proteomics Clin Appl 10:58-74. 2016..Since human urine is the most readily available biofluid whose proteome changes in response to disease, it is a logical sample for identifying protein biomarkers for kidney diseases...
- Enzymatic digestion of proteins in gels for mass spectrometric identification and structural analysisKathryn 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...
- KARMA: a web server application for comparing and annotating heterogeneous microarray platformsKei 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...
- X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computersRobert 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...
- A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studiesNicholas Carriero
Department of Computer Science, Yale University, New Haven, CT 06520 8285, USA
J Am Med Inform Assoc 12:90-8. 2005....
- Detecting and aligning peaks in mass spectrometry data with applications to MALDIWeichuan 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...
- A dynamic approach to mapping coordinates between microplates and microarraysKei 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...
- Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologiesErol 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...
- MALDI-MS data analysis for disease biomarker discoveryWeichuan 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...
- Isotope-coded affinity tags for protein quantificationChristopher 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...
- Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteinsChristopher M Colangelo
Yale NIDA Neuroproteomics Center, New Haven, CT, USA W M Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
Proteomics 15:1202-14. 2015..Overall, our method achieved a technical CV of 11.4% with >97.5% of the 1697 transitions being quantified without user intervention, resulting in a highly efficient, robust, and single injection LC-MRM assay. ..
- Expression profiling reveals novel pathways in the transformation of melanocytes to melanomasKeith 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...
- Comparison of statistical methods for classification of ovarian cancer using mass spectrometry dataBaolin 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...
- Recent advances in neuroproteomics and potential application to studies of drug addictionKenneth 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....
- Multiple peak alignment in sequential data analysis: a scale-space-based approachWeichuan 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)...
- HIGH THROUGHPUT MALDI MASS SPECTROMETER SYSTEMKenneth Williams; Fiscal Year: 2001..abstract_text> ..
- STRUCTURE/FUNCTION OF EUKARYOTIC RNA BINDING PROTEINSKenneth 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. ..
- YALE MICROARRAY RESOURCEKenneth Williams; Fiscal Year: 2002....
- FTICR Mass SpectrometerKenneth Williams; Fiscal Year: 2003..We believe the requested instrument would make a major contribution to biomedical research that would extend far beyond Yale University. ..
- Yale Biomedical SupercomputerKenneth Williams; Fiscal Year: 2004....