Research Topics
Genomes and Genes | Eugene KolkerSummaryAffiliation: The BIATECH Institute Country: USA Publications
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Publications
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotationsEugene 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...
Protein identification and expression analysis using mass spectrometryEugene 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...- H. influenzae Consortium: integrative study of H. influenzae-human interactionsEugene 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... - Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20Eugene 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... - Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzaeEugene Kolker
BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
Nucleic Acids Res 32:2353-61. 2004.... - LIP index for peptide classification using MS/MS and SEQUEST search via logistic regressionRoger 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... - Charge state estimation for tandem mass spectrometry proteomicsJason 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... - Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expressionEugene 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... - Randomized sequence databases for tandem mass spectrometry peptide and protein identificationRoger Higdon
The BIATECH Institute, 19310 N. Creek Parkway South, Suite 115, Bothell, WA 98011, USA
OMICS 9:364-79. 2005..quot;.. - Standard mixtures for proteome studiesSamuel 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... - A predictive model for identifying proteins by a single peptide matchRoger 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... - Experimental standards for high-throughput proteomicsJason M Hogan
The BIATECH Institute, Bothell, Washington 98011, USA
OMICS 10:152-7. 2006..This article discusses such experimental standards and their implementations... - Statistical analysis of global gene expression data: some practical considerationsTed Holzman
BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
Curr Opin Biotechnol 15:52-7. 2004.... - Spectral quality assessment for high-throughput tandem mass spectrometry proteomicsSamuel 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... 
A note on the false discovery rate and inconsistent comparisons between experimentsRoger 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...- New metrics for comparative genomicsMichael 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... - Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysisBrian 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... - In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich MediumAnu 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... - Host airway proteins interact with Staphylococcus aureus during early pneumoniaChristy 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... - Meeting report: the fourth Genomic Standards Consortium (GSC) workshopDawn 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... - Validating annotations for uncharacterized proteins in Shewanella oneidensisBrenton 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... - Toward a standards-compliant genomic and metagenomic publication recordGeorge M Garrity
Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
OMICS 12:157-60. 2008.... - Experiment-specific estimation of peptide identification probabilities using a randomized databaseRoger 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... - Experimental protein mixture for validating tandem mass spectral analysisAndrew 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... - A statistical model for identifying proteins by tandem mass spectrometryAlexey 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... - Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arraysBrian 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... - Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI projectChris F Taylor
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
Nat Biotechnol 26:889-96. 2008
Research Grants
- Experimental Standards and Computational Platform for HTP ProteomicsEugene 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. ..