Eugene Kolker

Summary

Affiliation: The BIATECH Institute
Country: USA

Publications

  1. pmc Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Proc Natl Acad Sci U S A 102:2099-104. 2005
  2. ncbi request reprint Protein identification and expression analysis using mass spectrometry
    Eugene Kolker
    The BIATECH Institute, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Trends Microbiol 14:229-35. 2006
  3. ncbi request reprint H. influenzae Consortium: integrative study of H. influenzae-human interactions
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    OMICS 6:341-8. 2002
  4. pmc Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
    Eugene Kolker
    BIATECH, Bothell, Washington 98011, USA
    J Bacteriol 185:4593-602. 2003
  5. pmc Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Nucleic Acids Res 32:2353-61. 2004
  6. ncbi request reprint LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression
    Roger Higdon
    BIATECH, Bothell, Washington 98011, USA
    OMICS 8:357-69. 2004
  7. ncbi request reprint Charge state estimation for tandem mass spectrometry proteomics
    Jason M Hogan
    BIATECH, Bothell, Washington 98011, USA
    OMICS 9:233-50. 2005
  8. ncbi request reprint Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression
    Eugene Kolker
    The BIATECH Institute, Bothell, WA, USA
    Proteomics 7:3693-8. 2007
  9. ncbi request reprint Randomized sequence databases for tandem mass spectrometry peptide and protein identification
    Roger Higdon
    The BIATECH Institute, 19310 N Creek Parkway South, Suite 115, Bothell, WA 98011, USA
    OMICS 9:364-79. 2005
  10. ncbi request reprint Standard mixtures for proteome studies
    Samuel Purvine
    BIATECH, Bothell, Washington 98011, USA
    OMICS 8:79-92. 2004

Detail Information

Publications27

  1. pmc Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Proc Natl Acad Sci U S A 102:2099-104. 2005
    ..We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome...
  2. ncbi request reprint Protein identification and expression analysis using mass spectrometry
    Eugene Kolker
    The BIATECH Institute, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Trends Microbiol 14:229-35. 2006
    ..The difficulties and bottlenecks of proteome analysis are addressed and the requirements for further improvements are discussed. Several diverse high-throughput proteomics-based studies of microorganisms are described...
  3. ncbi request reprint H. influenzae Consortium: integrative study of H. influenzae-human interactions
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    OMICS 6:341-8. 2002
    ..Data from the HIC will allow greater understanding of cellular behavior, pathogen-host interactions, bacterial infection, and provide future scientific endeavors with a template for studies of other pathogens...
  4. pmc Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
    Eugene Kolker
    BIATECH, Bothell, Washington 98011, USA
    J Bacteriol 185:4593-602. 2003
    ..The direct proteomics approach to studying protein expression in vivo reported here is a powerful method that is applicable to proteome analysis of any (micro)organism...
  5. pmc Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Nucleic Acids Res 32:2353-61. 2004
    ....
  6. ncbi request reprint LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression
    Roger Higdon
    BIATECH, Bothell, Washington 98011, USA
    OMICS 8:357-69. 2004
    ..The LIP Index also incorporates earlier developed statistical models on spectral quality assessment and peptide identification, which further improves sensitivity and specificity...
  7. ncbi request reprint Charge state estimation for tandem mass spectrometry proteomics
    Jason M Hogan
    BIATECH, Bothell, Washington 98011, USA
    OMICS 9:233-50. 2005
    ..Thresholds and parameter estimates can be tailored to specific analysis situations, pipelines, and instrumentations. CHASTE was implemented in Java GUI-based and command-line-based interfaces...
  8. ncbi request reprint Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression
    Eugene Kolker
    The BIATECH Institute, Bothell, WA, USA
    Proteomics 7:3693-8. 2007
    ..Finally, methodology and experimental design developed in this work can be readily applied in future to development of more complex standard mixtures for HTP proteomics studies...
  9. ncbi request reprint Randomized sequence databases for tandem mass spectrometry peptide and protein identification
    Roger Higdon
    The BIATECH Institute, 19310 N Creek Parkway South, Suite 115, Bothell, WA 98011, USA
    OMICS 9:364-79. 2005
    ..quot;..
  10. ncbi request reprint Standard mixtures for proteome studies
    Samuel Purvine
    BIATECH, Bothell, Washington 98011, USA
    OMICS 8:79-92. 2004
    ..These mixtures mimic the complexity seen in large-scale proteomics experiments, and are proposed to serve as quality assessment standards for future proteome studies...
  11. ncbi request reprint A predictive model for identifying proteins by a single peptide match
    Roger Higdon
    The BIATECH Institute, Bothell, WA 98011, USA
    Bioinformatics 23:277-80. 2007
    ..Identifying true single-hit proteins will lead to discovering many crucial regulators, biomarkers and other low abundance proteins. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  12. ncbi request reprint Experimental standards for high-throughput proteomics
    Jason M Hogan
    The BIATECH Institute, Bothell, Washington 98011, USA
    OMICS 10:152-7. 2006
    ..This article discusses such experimental standards and their implementations...
  13. ncbi request reprint Statistical analysis of global gene expression data: some practical considerations
    Ted Holzman
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Curr Opin Biotechnol 15:52-7. 2004
    ....
  14. ncbi request reprint Spectral quality assessment for high-throughput tandem mass spectrometry proteomics
    Samuel Purvine
    BIATECH, Bothell, Washington 98011, USA
    OMICS 8:255-65. 2004
    ..Lastly, SPEQUAL was implemented as Java GUI-based and command-line-based interfaces freely available for both academic and industrial researchers...
  15. doi request reprint A note on the false discovery rate and inconsistent comparisons between experiments
    Roger Higdon
    Seattle Children s Research Institute, Seattle, WA 98101, USA
    Bioinformatics 24:1225-8. 2008
    ..No single error rate or data summary may be appropriate for all of the different objectives...
  16. pmc New metrics for comparative genomics
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Biotechnol 17:440-7. 2006
    ..Several new metrics have recently been used in comparative genome analysis, yet challenges remain in finding an appropriate language for the emerging discipline of systems biology...
  17. ncbi request reprint Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
    Brian Tjaden
    Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
    Bioinformatics 18:S337-44. 2002
    ..The operon elements we identify correspond to documented operons with 99% specificity and 63% sensitivity. Similarly we find that our 5' UTR results accurately coincide with experimentally verified promoter regions for most genes...
  18. ncbi request reprint In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium
    Anu Raghunathan
    Department of Bioengineering, University of California at San Diego, La Jolla, California, USA
    OMICS 8:25-41. 2004
    ..This study demonstrates the significance of an integrated approach to the characterization of H. influenzae metabolism...
  19. pmc Host airway proteins interact with Staphylococcus aureus during early pneumonia
    Christy L Ventura
    Division of Infectious Diseases, Center for Childhood Infections and Prematurity Research, Seattle Children s Hospital Research Institute, 1900 9th Ave, Seattle, WA 98101, USA
    Infect Immun 76:888-98. 2008
    ..aureus in vivo. The data presented here provide novel insights into the host-pathogen interactions that occur when S. aureus enters the airway...
  20. ncbi request reprint Meeting report: the fourth Genomic Standards Consortium (GSC) workshop
    Dawn Field
    NERC Centre for Ecology and Hydrology, Mansfield Road, Oxford, OX1 3SR United Kingdom
    OMICS 12:101-8. 2008
    ..g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org...
  21. pmc Validating annotations for uncharacterized proteins in Shewanella oneidensis
    Brenton Louie
    Department of Medical Education and Biomedical Informatics, Division of Biomedical and Health Informatics, University of Washington, Seattle, Washington 98101 1304, USA
    OMICS 12:211-5. 2008
    ..Our evaluation indicates that these databases readily incorporate new information and are accurate in predicting functions for uncharacterized proteins, provided that experimental function evidence exists...
  22. ncbi request reprint Toward a standards-compliant genomic and metagenomic publication record
    George M Garrity
    Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
    OMICS 12:157-60. 2008
    ....
  23. ncbi request reprint Experiment-specific estimation of peptide identification probabilities using a randomized database
    Roger Higdon
    Seattle Children s Hospital and Regional Medical Center, Seattle, WA 98101, USA
    OMICS 11:351-65. 2007
    ..However, this approach is generally applicable to any search algorithm, peptide scoring, and statistical model when using a randomized database...
  24. ncbi request reprint Experimental protein mixture for validating tandem mass spectral analysis
    Andrew Keller
    Institute for Systems Biology, Seattle, Washington 98103, USA
    OMICS 6:207-12. 2002
    ..We show how the sensitivity and error rate are affected by the use of various filtering criteria based upon SEQUEST scores and the number of tryptic termini of assigned peptides...
  25. ncbi request reprint A statistical model for identifying proteins by tandem mass spectrometry
    Alexey I Nesvizhskii
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:4646-58. 2003
    ..Fast, consistent, and transparent, it provides a standard for publishing large-scale protein identification data sets in the literature and for comparing the results obtained from different experiments...
  26. pmc Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
    Brian Tjaden
    Department of Computer Science, University of Washington, Seattle, WA 98195, USA
    Nucleic Acids Res 30:3732-8. 2002
    ..Through the experimental identification of all RNAs expressed under a specific condition, we gain a more thorough understanding of all cellular processes...
  27. pmc Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
    Chris F Taylor
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nat Biotechnol 26:889-96. 2008

Research Grants2

  1. Experimental Standards and Computational Platform for HTP Proteomics
    Eugene Kolker; Fiscal Year: 2007
    ..1) is well beyond the scope of any single project, the experimental standards and computational platform can provide the basis for development, validation, and comparative analysis of models and methods at each step in the pipeline. ..
  2. Experimental Standards and Computational Platform for HTP Proteomics
    Eugene Kolker; Fiscal Year: 2007
    ..1) is well beyond the scope of any single project, the experimental standards and computational platform can provide the basis for development, validation, and comparative analysis of models and methods at each step in the pipeline. ..