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Eugene Kolker, PhD

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Eugene Kolker, PhD

Children's Title: Chief Data Officer

Academic Title: Head, Bioinformatics and High-throughput Analysis Lab, Seattle Children's Research Institute

Research Center: Center for Developmental Therapeutics

Overview

Research Description

In his role as Chief Data Officer of Seattle Children's, Eugene Kolker and members of his research group have been developing advanced data analytics to sift through massive volumes of complex data to identify methods for more efficient and effective management of patients with complex diseases, such as diabetes. In addition, by creating and leading an international non-profit (Data-Enabled Life Sciences Alliance), the Kolker lab is building collaborations to advance the frontiers of science and address complex challenges in improving human health.
Research Focus: A substantial part of our research focuses on data-enabled science, biomedical and proteomics analyses for disease states (diabetes and cardiac), bioinformatics, statistical models, and software applications. In addition, our team's work in predictive analytics includes exploring factors that influence the health and care of our patients, strategic development and resource management of the hospital, the national levels of support for the sciences as well as economic modeling of Seattle.

Lab URL

http://www.seattlechildrens.org/research/developmental-therapeutics/labs-programs/kolker-lab/

Research Focus Area

Biomedical Research, OMICS, Proteomics, Predictive Analytics, Data Analysis

Awards and Honors

Award NameAward DescriptionAwarded ByAward Date
U.S.A. permanent residency as "alien of exceptional ability" 2000
Ph.D. in Structural Molecular Biology (Bioinformatics) 1996
M.S. in Applied Mathematics and Computer Sciences, summa cum laude 1986

Publications

MOPED Enables Discoveries through Consistently Processed Proteomics Data.
Journal of proteome research , 2014 Jan 3: 13(1)107-13
Reproducibility: In praise of open research measures.
Nature , 2013 Jun 13: 498(7453)170
Reproducibility: In praise of open research measures.
Nature , 2013 Jun 13: 498(7453)170
Differential expression analysis for pathways.
PLoS computational biology , 2013: 9(3)e1002967
Differential expression analysis for pathways.
PLoS computational biology , 2013: 9(3)e1002967
Designing a post-genomics knowledge ecosystem to translate pharmacogenomics into public health action.
Genome medicine , 2012 Nov 29: 4(11)91
Designing a post-genomics knowledge ecosystem to translate pharmacogenomics into public health action.
Genome medicine , 2012 Nov 29: 4(11)91
Collective theranostics and postgenomics entrepreneurship: rethinking innovations as knowledge ecosystems built by complex collaboration.
Expert review of molecular diagnostics , 2012 Nov: 12(8)787-90
Collective theranostics and postgenomics entrepreneurship: rethinking innovations as knowledge ecosystems built by complex collaboration.
Expert review of molecular diagnostics , 2012 Nov: 12(8)787-90
Opportunities and challenges for the life sciences community.
Omics : a journal of integrative biology , 2012 Mar: 16(3)138-47
Opportunities and challenges for the life sciences community.
Omics : a journal of integrative biology , 2012 Mar: 16(3)138-47
Statistical Methods in Systems Biology
Encyclopedia of Systems Biology , 2012
MOPED: Model Organism Protein Expression Database.
Nucleic acids research , Jan. 2012: 40(Database issue)D1093-9
SPIRE: Systematic protein investigative research environment.
Journal of proteomics , Dec. 2011: 75(1)122-6
MOPED: Model Organism Protein Expression Database.
Nucleic acids research , 2012 Jan: 40(Database issue)D1093-9
IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
Journal of proteomics , 2011 Dec 10: 75(1)116-21
Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010.
Journal of proteomics , 2011 Dec 10: 75(1)4-17
IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
Journal of proteomics , 2011 Dec 10: 75(1)116-21
SPIRE: Systematic protein investigative research environment.
Journal of proteomics , 2011 Dec 10: 75(1)122-6
Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010.
Journal of proteomics , 2011 Dec 10: 75(1)4-17
Towards an Ecology of Collective Innovation: Human Variome Project (HVP), Rare Disease Consortium for Autosomal Loci (RaDiCAL) and Data-Enabled Life Sciences Alliance (DELSA).
Current pharmacogenomics and personalized medicine , 2011 Dec 1: 9(4)243-251
In-silico human genomics with GeneCards.
Human genomics , 2011 Oct: 5(6)709-17
In-silico human genomics with GeneCards.
Human genomics , 2011 Oct: 5(6)709-17
Vaccines of the 21st century and vaccinomics: data-enabled science meets global health to spark collective action for vaccine innovation.
Omics : a journal of integrative biology , 2011 Sep: 15(9)523-7
Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins.
Omics : a journal of integrative biology , 2011 Jul-Aug: 15(7-8)513-21
Policy and data-intensive scientific discovery in the beginning of the 21st century.
Omics : a journal of integrative biology , 2011 Apr: 15(4)221-5
Education and data-intensive science in the beginning of the 21st century.
Omics : a journal of integrative biology , 2011 Apr: 15(4)217-9
Communication and data-intensive science in the beginning of the 21st century.
Omics : a journal of integrative biology , 2011 Apr: 15(4)213-5
Biology and data-intensive scientific discovery in the beginning of the 21st century.
Omics : a journal of integrative biology , 2011 Apr: 15(4)209-12
Technology and data-intensive science in the beginning of the 21st century.
Omics : a journal of integrative biology , 2011 Apr: 15(4)203-7
Bioinformatics and data-intensive scientific discovery in the beginning of the 21st century.
Omics : a journal of integrative biology , 2011 Apr: 15(4)199-201
Special issue on data-intensive science.
Omics : a journal of integrative biology , 2011 Apr: 15(4)197-8
Design and initial characterization of the SC-200 proteomics standard mixture.
Omics : a journal of integrative biology , 2011 Jan-Feb: 15(1-2)73-82
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project.
Standards in genomic sciences , 2010 Dec 25: 3(3)243-8
The necessity of adjusting tests of protein category enrichment in discovery proteomics.
Bioinformatics (Oxford, England) , 2010 Dec 15: 26(24)3007-11
Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.
Standards in genomic sciences , 2010 Dec 4: 3(3)216-24
The United States of America and scientific research.
PloS one , 2010 Aug 16: 5(8)e12203
A vision for 21st century U.S. Policy to support sustainable advancement of scientific discovery and technological innovation.
Omics : a journal of integrative biology , 2010 Aug: 14(4)333-5
Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
Standards in genomic sciences , 2010 Jun 15: 2(3)357-60
Meta-analysis for protein identification: a case study on yeast data.
Omics : a journal of integrative biology , 2010 Jun: 14(3)309-14
Editorial: global issues.
Omics : a journal of integrative biology , 2010 Jun: 14(3)229
Estimating false discovery rates for peptide and protein identification using randomized databases.
Proteomics , 2010 Jun: 10(12)2369-76
Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.
Molecular bioSystems , 2010 Apr: 6(4)721-8
Quantifying protein function specificity in the gene ontology.
Standards in genomic sciences , 2010 Mar 30: 2(2)238-44
OMICS: 2009, 2010, and Beyond.
Omics : a journal of integrative biology , 2009 Dec: 13(6)451
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions.
PloS one , 2009 Oct 21: 4(10)e7546
Megascience. 'Omics data sharing.
Science (New York, N.Y.) , 2009 Oct 9: 326(5950)234-6
Meeting report: the 2009 Westlake International Conference on Personalized Medicine.
Omics : a journal of integrative biology , 2009 Aug: 13(4)285-9
Modeling sequence and function similarity between proteins for protein functional annotation
HPDC '10 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing , 2009: 499-502
Risk assessment and communication tools for genotype associations with multifactorial phenotypes: the concept of "edge effect" and cultivating an ethical bridge between omics innovations and society.
Omics : a journal of integrative biology , 2009 Feb: 13(1)43-61
Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.
Omics : a journal of integrative biology , 2009 Feb: 13(1)1-6
Staphylococcus aureus elicits marked alterations in the airway proteome during early pneumonia.
Infection and immunity , 2008 Dec: 76(12)5862-72
Validating annotations for uncharacterized proteins in Shewanella oneidensis.
Omics : a journal of integrative biology , 2008 Sep: 12(3)211-5
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Nature biotechnology , 2008 Aug: 26(8)889-96
Toward a standards-compliant genomic and metagenomic publication record.
Omics : a journal of integrative biology , 2008 Jun: 12(2)157-60
Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.
Omics : a journal of integrative biology , 2008 Jun: 12(2)101-8
A note on the false discovery rate and inconsistent comparisons between experiments.
Bioinformatics (Oxford, England) , 2008 May 15: 24(10)1225-8
The minimum information about a genome sequence (MIGS) specification.
Nature biotechnology , 2008 May: 26(5)541-7
Host airway proteins interact with Staphylococcus aureus during early pneumonia.
Infection and immunity , 2008 Mar: 76(3)888-98
Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression.
Proteomics , 2007 Oct: 7(20)3693-8
A predictive model for identifying proteins by a single peptide match.
Bioinformatics (Oxford, England) , 2007 Feb 1: 23(3)277-80
Experiment-specific estimation of peptide identification probabilities using a randomized database.
Omics : a journal of integrative biology , 2007 Winter: 11(4)351-65
New metrics for comparative genomics.
Current opinion in biotechnology , 2006 Oct: 17(5)440-7
Protein identification and expression analysis using mass spectrometry.
Trends in microbiology , 2006 May: 14(5)229-35
Experimental standards for high-throughput proteomics.
Omics : a journal of integrative biology , 2006 Summer: 10(2)152-7
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.
Proceedings of the National Academy of Sciences of the United States of America , 2005 Feb 8: 102(6)2099-104
Integration of data for gene annotation using the BioMediator system
AMIA Annual Symposium Proceedings , 2005: 1036
Charge state estimation for tandem mass spectrometry proteomics.
Omics : a journal of integrative biology , 2005 Fall: 9(3)233-50
Randomized sequence databases for tandem mass spectrometry peptide and protein identification.
Omics : a journal of integrative biology , 2005 Winter: 9(4)364-79
Statistical analysis of global gene expression data: some practical considerations.
Current opinion in biotechnology , 2004 Feb: 15(1)52-7
Spectral quality assessment for high-throughput tandem mass spectrometry proteomics.
Omics : a journal of integrative biology , 2004 Fall: 8(3)255-65
Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.
Nucleic acids research , 2004: 32(8)2353-61
Standard mixtures for proteome studies.
Omics : a journal of integrative biology , 2004 Spring: 8(1)79-92
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
Omics : a journal of integrative biology , 2004 Spring: 8(1)25-41
LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression.
Omics : a journal of integrative biology , 2004 Winter: 8(4)357-69
Initial proteome analysis of model microorganism Haemophilus influenzae Rd KW20
Journal of Bacteriology , 2003: 185(15)
Annotating and re-annotating genomes
OMICS , 2003: 7(2)141
Statistical analysis of global gene expression data: Some practical considerations
Current Opinion in Biotechnology , 2003: 15(1)52-57
Spectral analysis of distributions: finding periodic component in eukaryotic enzyme length data
OMICS , 2002: 6(1)123-130
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
Nucleic Acids Research , 2002: 30(17)3737-3738
Experimental protein mixture for validating tandem mass spectrometry analysis
OMICS , 2002: 6(2)207-212
Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
Bioinformatics , 2002: 18(S1)337-344
Integrative Microbiology
OMICS , 2002: 6(4)285
H. influenzae consortium: Integrative study of H. influenzae-Human interactions
OMICS , 2002: 6(4)341-348
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
Analytical Chemistry , 2002: 74(20)5383-5392
Differential isotopic labeling of peptides for quantitation and de novo sequence derivation
Rapid Communications in Mass Spectrometry , 2001: 15(14)1214-1221
Sequence sizes of eukaryotic enzymes
Pacific Symposium on Biocomputing '96 , 1996: 351-361
Segments, folds and overall protein structure
Biological Structure and Dynamics , 1996: 257-265
Periodic recurrence of methionines: Fossil of gene fusion?
Proceedings of the National Academy of Sciences of USA , 1995: 92(2)557-560
Sequence markers of segmented protein structure
Modeling of Biomolecular Structures and Mechanisms , 1995: 461-471
Underlying order in protein sequence organization
Proceedings of the National Academy of Sciences of USA , 1994: 91(9)4044-4047
Peptide_Prophet, Protein_Prophet and Proteomics Standards
,
SPIRE: Systematic Protein Investigative Research Environment
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MOPED: Model Organism Protein Expression Database
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Research Funding

Grant TitleGrantorAmountAward Date
Metabolism during Mechanical Circulatory Support in the Developing Heart.NHLBI, NIH, Co-PI, PI: Portman
Mechanical support of children with end-stage cardiac failure.McMillen Foundation, PI $, $
Community Driven Proteomics Analysis EnvironmentNSF, PI $, $
PASS: Transformative Collaborative ProjectNIDDK, NIH, Co-PI, PI: Hebrok
Analysis of best practices for Childrens and Adult Hospitals SCRI-NEU
Investigation of Childhood CancerSCRI/NEU

Primary Office

Seattle Children's Research Institute
JMB - 9 - Developmental Therapeutics
1900 - 9th Ave
Seattle, WA 98101
206-884-7170

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