Profile

Eugene Kolker, PhD

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.

About My Work

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 Name Award Description Awarded By Award 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

  • Higdon R, Stewart E, Stanberry L, Haynes W, Choiniere J, Montague E, Anderson N, Yandl G, Janko I, Broomall W, Fishilevich S, Lancet D, Kolker N, Kolker E
    MOPED Enables Discoveries through Consistently Processed Proteomics Data.
    24350770 Journal of proteome research , 2014 Jan. 3 : 13(1)107-13
  • Kolker E, Altintas I, Bourne P, Faris J, Fox G, Frishman D, Geraci C, Hancock W, Lin B, Lancet D, Lisitsa A, Knight R, Martens L, Mesirov J, Özdemir V, Schultes E, Smith T, Snyder M, Srivastava S, Toppo S, Wilmes P
    Reproducibility: In praise of open research measures.
    23765483 Nature , 2013 June 13 : 498(7453)170
  • Kolker E
    Reproducibility: In praise of open research measures.
    23765483 Nature , 2013 June 13 : 498(7453)170
  • Haynes WA, Higdon R, Stanberry L, Collins D, Kolker E
    Differential expression analysis for pathways.
    23516350 PLoS computational biology , 2013 : 9(3)e1002967 PMCID: PMC3597535
  • Haynes WA, Higdon R, Stanberry L, Collins D, Kolker E
    Differential expression analysis for pathways.
    23516350 PLoS computational biology , 2013 : 9(3)e1002967 PMCID: PMC3597535
  • Dove ES, Faraj SA, Kolker E, Ozdemir V
    Designing a post-genomics knowledge ecosystem to translate pharmacogenomics into public health action.
    23194449 Genome medicine , 2012 Nov. 29 : 4(11)91 PMCID: PMC3580424
  • Dove ES, Faraj SA, Kolker E, Ozdemir V
    Designing a post-genomics knowledge ecosystem to translate pharmacogenomics into public health action.
    23194449 Genome medicine , 2012 Nov. 29 : 4(11)91 PMCID: PMC3580424
  • Faraj SA, Kolker E, Bevilacqua L, Özdemir V
    Collective theranostics and postgenomics entrepreneurship: rethinking innovations as knowledge ecosystems built by complex collaboration.
    23249193 Expert review of molecular diagnostics , 2012 Nov. : 12(8)787-90
  • Faraj SA, Kolker E, Bevilacqua L, Özdemir V
    Collective theranostics and postgenomics entrepreneurship: rethinking innovations as knowledge ecosystems built by complex collaboration.
    23249193 Expert review of molecular diagnostics , 2012 Nov. : 12(8)787-90
  • Kolker E, Stewart E, Ozdemir V
    Opportunities and challenges for the life sciences community.
    22401659 Omics : a journal of integrative biology , 2012 Mar. : 16(3)138-47 PMCID: PMC3300061
  • Kolker E, Stewart E, Ozdemir V
    Opportunities and challenges for the life sciences community.
    22401659 Omics : a journal of integrative biology , 2012 Mar. : 16(3)138-47 PMCID: PMC3300061
  • Kolker E, Higdon R, Haynes W, Welch D, Broomall W, Lancet D, Stanberry L, Kolker N
    MOPED: Model Organism Protein Expression Database.
    22139914 Nucleic acids research , 2012 Jan. : 40(Database issue)D1093-9 PMCID: PMC3245040
  • Kolker E, Higdon R, Haynes W, Welch D, Broomall W, Lancet D, Stanberry L, Kolker N
    MOPED: Model Organism Protein Expression Database.
    22139914 Nucleic acids research , 2012 Jan. : 40(Database issue)D1093-9 PMCID: PMC3245040
    https://www.proteinspire.org/SPIRE/startviews/proteinExpressionDatabase.jsf?goToTab=about
  • Eugene Kolker, PhD
    Statistical Methods in Systems Biology
    Encyclopedia of Systems Biology , 2012
  • Cox J, Heeren RM, James P, Jorrin-Novo JV, Kolker E, Levander F, Morrice N, Picotti P, Righetti PG, Sánchez JC, Turck CW, Zubarev R, Alexandre BM, Corrales FJ, Marko-Varga G, O'Donovan S, O'Neil S, Prechl J, Simões T, Weckwerth W, Penque D
    Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010.
    21571109 Journal of proteomics , 2011 Dec. 10 : 75(1)4-17
  • Kolker E, Higdon R, Morgan P, Sedensky M, Welch D, Bauman A, Stewart E, Haynes W, Broomall W, Kolker N
    SPIRE: Systematic protein investigative research environment.
    21609792 Journal of proteomics , 2011 Dec. 10 : 75(1)122-6
  • Higdon R, Reiter L, Hather G, Haynes W, Kolker N, Stewart E, Bauman AT, Picotti P, Schmidt A, van Belle G, Aebersold R, Kolker E
    IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
    21718813 Journal of proteomics , 2011 Dec. 10 : 75(1)116-21
  • Cox J, Heeren RM, James P, Jorrin-Novo JV, Kolker E, Levander F, Morrice N, Picotti P, Righetti PG, Sánchez JC, Turck CW, Zubarev R, Alexandre BM, Corrales FJ, Marko-Varga G, O'Donovan S, O'Neil S, Prechl J, Simões T, Weckwerth W, Penque D
    Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010.
    21571109 Journal of proteomics , 2011 Dec. 10 : 75(1)4-17
  • Higdon R, Reiter L, Hather G, Haynes W, Kolker N, Stewart E, Bauman AT, Picotti P, Schmidt A, van Belle G, Aebersold R, Kolker E
    IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.
    21718813 Journal of proteomics , 2011 Dec. 10 : 75(1)116-21
  • Ozdemir V, Rosenblatt DS, Warnich L, Srivastava S, Tadmouri GO, Aziz RK, Reddy PJ, Manamperi A, Dove ES, Joly Y, Zawati MH, Hzel C, Yazan Y, John L, Vaast E, Ptolemy AS, Faraj SA, Kolker E, Cotton RG
    Towards an Ecology of Collective Innovation: Human Variome Project (HVP), Rare Disease Consortium for Autosomal Loci (RaDiCAL) and Data-Enabled Life Sciences Alliance (DELSA).
    22523528 Current pharmacogenomics and personalized medicine , 2011 Dec. 1 : 9(4)243-251 PMCID: PMC3329442
  • Kolker E, Higdon R, Welch D, Bauman A, Stewart E, Haynes W, Broomall W, Kolker N
    SPIRE: Systematic protein investigative research environment.
    21609792 Journal of proteomics , 2011 Dec. : 75(1)122-6
    https://www.proteinspire.org/SPIRE/startviews/welcome.jsf
  • Stelzer G, Dalah I, Stein TI, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, Krug H, Perco P, Mayer B, Kolker E, Safran M, Lancet D
    In-silico human genomics with GeneCards.
    22155609 Human genomics , 2011 Oct. : 5(6)709-17 PMCID: PMC3525253
  • Stelzer G, Dalah I, Stein TI, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, Krug H, Perco P, Mayer B, Kolker E, Safran M, Lancet D
    In-silico human genomics with GeneCards.
    22155609 Human genomics , 2011 Oct. : 5(6)709-17
  • Ozdemir V, Pang T, Knoppers BM, Avard D, Faraj SA, Zawati MH, Kolker E
    Vaccines of the 21st century and vaccinomics: data-enabled science meets global health to spark collective action for vaccine innovation.
    21848418 Omics : a journal of integrative biology , 2011 Sept. : 15(9)523-7
  • Kolker N, Higdon R, Broomall W, Stanberry L, Welch D, Lu W, Haynes W, Barga R, Kolker E
    Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins.
    21809957 Omics : a journal of integrative biology , 2011 July : 15(7-8)513-21
  • Kolker E
    Special issue on data-intensive science.
    21476839 Omics : a journal of integrative biology , 2011 Apr, : 15(4)197-8
  • Barga R, Howe B, Beck D, Bowers S, Dobyns W, Haynes W, Higdon R, Howard C, Roth C, Stewart E, Welch D, Kolker E
    Bioinformatics and data-intensive scientific discovery in the beginning of the 21st century.
    21476840 Omics : a journal of integrative biology , 2011 Apr, : 15(4)199-201
  • Bernstein PA, Wecker D, Krishnamurthy A, Manocha D, Gardner J, Kolker N, Reschke C, Stombaugh J, Vagata P, Stewart E, Welch D, Kolker E
    Technology and data-intensive science in the beginning of the 21st century.
    21476841 Omics : a journal of integrative biology , 2011 Apr, : 15(4)203-7
  • Smith A, Balazinska M, Baru C, Gomelsky M, McLennan M, Rose L, Smith B, Stewart E, Kolker E
    Biology and data-intensive scientific discovery in the beginning of the 21st century.
    21476842 Omics : a journal of integrative biology , 2011 Apr, : 15(4)209-12
  • Faris J, Kolker E, Szalay A, Bradlow L, Deelman E, Feng W, Qiu J, Russell D, Stewart E, Kolker E
    Communication and data-intensive science in the beginning of the 21st century.
    21476843 Omics : a journal of integrative biology , 2011 Apr, : 15(4)213-5
  • Wolf F, Hobby R, Lowry S, Bauman A, Franza BR, Lin B, Rapson S, Stewart E, Kolker E
    Education and data-intensive science in the beginning of the 21st century.
    21476844 Omics : a journal of integrative biology , 2011 Apr, : 15(4)217-9
  • Ozdemir V, Smith C, Bongiovanni K, Cullen D, Knoppers BM, Lowe A, Peters M, Robbins R, Stewart E, Yee G, Yu YK, Kolker E
    Policy and data-intensive scientific discovery in the beginning of the 21st century.
    21476845 Omics : a journal of integrative biology , 2011 Apr, : 15(4)221-5
  • Bauman A, Higdon R, Rapson S, Loiue B, Hogan J, Stacy R, Napuli A, Guo W, van Voorhis W, Roach J, Lu V, Landorf E, Stewart E, Kolker N, Collart F, Myler P, van Belle G, Kolker E
    Design and initial characterization of the SC-200 proteomics standard mixture.
    21250827 Omics : a journal of integrative biology , 2011 Jan. : 15(1-2)73-82 PMCID: PMC3110723
  • Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R
    Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project.
    21304727 Standards in genomic sciences , 2010 Dec. 25 : 3(3)243-8 PMCID: PMC3035311
  • Louie B, Higdon R, Kolker E
    The necessity of adjusting tests of protein category enrichment in discovery proteomics.
    21068002 Bioinformatics (Oxford, England) , 2010 Dec. 15 : 26(24)3007-11 PMCID: PMC2995116
  • Davidsen T, Madupu R, Sterk P, Field D, Garrity G, Gilbert J, Glöckner FO, Hirschman L, Kolker E, Kottmann R, Kyrpides N, Meyer F, Morrison N, Schriml L, Tatusova T, Wooley J
    Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9.
    21304722 Standards in genomic sciences , 2010 Dec. 4 : 3(3)216-24 PMCID: PMC3035308
  • Hather GJ, Haynes W, Higdon R, Kolker N, Stewart EA, Arzberger P, Chain P, Field D, Franza BR, Lin B, Meyer F, Ozdemir V, Smith CV, van Belle G, Wooley J, Kolker E
    The United States of America and scientific research.
    20808949 PloS one , 2010 Aug. 16 : 5(8)e12203 PMCID: PMC2922381
  • Kolker E
    A vision for 21st century U.S. Policy to support sustainable advancement of scientific discovery and technological innovation.
    20673064 Omics : a journal of integrative biology , 2010 Aug. : 14(4)333-5 PMCID: PMC3133827
  • Hirschman L, Sterk P, Field D, Wooley J, Cochrane G, Gilbert J, Kolker E, Kyrpides N, Meyer F, Mizrachi I, Nakamura Y, Sansone SA, Schriml L, Tatusova T, White O, Yilmaz P
    Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
    21304719 Standards in genomic sciences , 2010 June 15 : 2(3)357-60 PMCID: PMC3035291
  • Hather G, Higdon R, Bauman A, von Haller PD, Kolker E
    Estimating false discovery rates for peptide and protein identification using randomized databases.
    20391536 Proteomics , 2010 June : 10(12)2369-76
  • Kolker E
    Editorial: global issues.
    20569182 Omics : a journal of integrative biology , 2010 June : 14(3)229
  • Higdon R, Haynes W, Kolker E
    Meta-analysis for protein identification: a case study on yeast data.
    20569183 Omics : a journal of integrative biology , 2010 June : 14(3)309-14 PMCID: PMC3133781
  • Galperin MY, Higdon R, Kolker E
    Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.
    20237650 Molecular bioSystems , 2010 Apr, : 6(4)721-8 PMCID: PMC3071642
  • Louie B, Bergen S, Higdon R, Kolker E
    Quantifying protein function specificity in the gene ontology.
    21304708 Standards in genomic sciences , 2010 Mar. 30 : 2(2)238-44 PMCID: PMC3035283
  • Kolker E
    OMICS: 2009, 2010, and Beyond.
    20001859 Omics : a journal of integrative biology , 2009 Dec. : 13(6)451
  • Louie B, Higdon R, Kolker E
    A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions.
    19844580 PloS one , 2009 Oct. 21 : 4(10)e7546 PMCID: PMC2760442
  • Field D, Sansone SA, Collis A, Booth T, Dukes P, Gregurick SK, Kennedy K, Kolar P, Kolker E, Maxon M, Millard S, Mugabushaka AM, Perrin N, Remacle JE, Remington K, Rocca-Serra P, Taylor CF, Thorley M, Tiwari B, Wilbanks J
    Megascience. 'Omics data sharing.
    19815759 Science (New York, N.Y.) , 2009 Oct. 9 : 326(5950)234-6 PMCID: PMC2770171
  • Lin B, Strickland SJ, Wang J, Qi L, Kolker E, Nam HG, Li L, Gu J
    Meeting report: the 2009 Westlake International Conference on Personalized Medicine.
    19691437 Omics : a journal of integrative biology , 2009 Aug. : 13(4)285-9
  • Ozdemir V, Motulsky AG, Kolker E, Godard B
    Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.
    19290807 Omics : a journal of integrative biology , 2009 Feb. : 13(1)1-6
  • Ozdemir V, Suarez-Kurtz G, Stenne R, Somogyi AA, Someya T, Kayaalp SO, Kolker E
    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.
    19290811 Omics : a journal of integrative biology , 2009 Feb. : 13(1)43-61 PMCID: PMC2727354
  • Eugene Kolker, PhD
    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
  • Ventura CL, Higdon R, Hohmann L, Martin D, Kolker E, Liggitt HD, Skerrett SJ, Rubens CE
    Staphylococcus aureus elicits marked alterations in the airway proteome during early pneumonia.
    18852243 Infection and immunity , 2008 Dec. : 76(12)5862-72 PMCID: PMC2583584
  • Louie B, Tarczy-Hornoch P, Higdon R, Kolker E
    Validating annotations for uncharacterized proteins in Shewanella oneidensis.
    18687039 Omics : a journal of integrative biology , 2008 Sept. : 12(3)211-5 PMCID: PMC3189009
  • Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S
    Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
    18688244 Nature biotechnology , 2008 Aug. : 26(8)889-96 PMCID: PMC2771753
  • Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T
    Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.
    18564914 Omics : a journal of integrative biology , 2008 June : 12(2)101-8
  • Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O
    Toward a standards-compliant genomic and metagenomic publication record.
    18564916 Omics : a journal of integrative biology , 2008 June : 12(2)157-60
  • Higdon R, van Belle G, Kolker E
    A note on the false discovery rate and inconsistent comparisons between experiments.
    18424815 Bioinformatics (Oxford, England) , 2008 May 15 : 24(10)1225-8
  • Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
    The minimum information about a genome sequence (MIGS) specification.
    18464787 Nature biotechnology , 2008 May : 26(5)541-7 PMCID: PMC2409278
  • Ventura CL, Higdon R, Kolker E, Skerrett SJ, Rubens CE
    Host airway proteins interact with Staphylococcus aureus during early pneumonia.
    18195024 Infection and immunity , 2008 Mar. : 76(3)888-98 PMCID: PMC2258841
  • Kolker E, Hogan JM, Higdon R, Kolker N, Landorf E, Yakunin AF, Collart FR, van Belle G
    Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression.
    17890649 Proteomics , 2007 Oct. : 7(20)3693-8
  • Higdon R, Kolker E
    A predictive model for identifying proteins by a single peptide match.
    17121779 Bioinformatics (Oxford, England) , 2007 Feb. 1 : 23(3)277-80
  • Higdon R, Hogan JM, Kolker N, van Belle G, Kolker E
    Experiment-specific estimation of peptide identification probabilities using a randomized database.
    18092908 Omics : a journal of integrative biology , 2007 : 11(4)351-65
  • Galperin MY, Kolker E
    New metrics for comparative genomics.
    16978854 Current opinion in biotechnology , 2006 Oct. : 17(5)440-7 PMCID: PMC1764326
  • Kolker E, Higdon R, Hogan JM
    Protein identification and expression analysis using mass spectrometry.
    16603360 Trends in microbiology , 2006 May : 14(5)229-35
  • Hogan JM, Higdon R, Kolker E
    Experimental standards for high-throughput proteomics.
    16901220 Omics : a journal of integrative biology , 2006 : 10(2)152-7
  • Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM
    Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.
    15684069 Proceedings of the National Academy of Sciences of the United States of America , 2005 Feb. 8 : 102(6)2099-104 PMCID: PMC548307
  • Higdon R, Hogan JM, Van Belle G, Kolker E
    Randomized sequence databases for tandem mass spectrometry peptide and protein identification.
    16402894 Omics : a journal of integrative biology , 2005 : 9(4)364-79
  • Hogan JM, Higdon R, Kolker N, Kolker E
    Charge state estimation for tandem mass spectrometry proteomics.
    16209638 Omics : a journal of integrative biology , 2005 : 9(3)233-50
  • Eugene Kolker, PhD
    Integration of data for gene annotation using the BioMediator system
    AMIA Annual Symposium Proceedings , 2005 : 1036
  • Holzman T, Kolker E
    Statistical analysis of global gene expression data: some practical considerations.
    15102467 Current opinion in biotechnology , 2004 Feb. : 15(1)52-7
  • Higdon R, Kolker N, Picone A, van Belle G, Kolker E
    LIP index for peptide classification using MS/MS and SEQUEST search via logistic regression.
    15703482 Omics : a journal of integrative biology , 2004 : 8(4)357-69
  • Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R Jr, Tyler RE, Akerley BJ, Smith AL, Palsson BO, Kolker E
    In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
    15107235 Omics : a journal of integrative biology , 2004 : 8(1)25-41
  • Purvine S, Picone AF, Kolker E
    Standard mixtures for proteome studies.
    15107238 Omics : a journal of integrative biology , 2004 : 8(1)79-92
  • Kolker E, Makarova KS, Shabalina S, Picone AF, Purvine S, Holzman T, Cherny T, Armbruster D, Munson RS Jr, Kolesov G, Frishman D, Galperin MY
    Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae.
    15121896 Nucleic acids research , 2004 : 32(8)2353-61 PMCID: PMC419445
  • Purvine S, Kolker N, Kolker E
    Spectral quality assessment for high-throughput tandem mass spectrometry proteomics.
    15669717 Omics : a journal of integrative biology , 2004 : 8(3)255-65
  • Eugene Kolker, PhD
    Statistical analysis of global gene expression data: Some practical considerations
    Current Opinion in Biotechnology , 2003 : 15(1)52-57
  • Eugene Kolker, PhD
    Annotating and re-annotating genomes
    OMICS , 2003 : 7(2)141
  • Eugene Kolker, PhD
    Initial proteome analysis of model microorganism Haemophilus influenzae Rd KW20
    Journal of Bacteriology , 2003 : 185(15)
  • Eugene Kolker, PhD
    Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    Analytical Chemistry , 2002 : 74(20)5383-5392
  • Eugene Kolker, PhD
    H. influenzae consortium: Integrative study of H. influenzae-Human interactions
    OMICS , 2002 : 6(4)341-348
  • Eugene Kolker, PhD
    Integrative Microbiology
    OMICS , 2002 : 6(4)285
  • Eugene Kolker, PhD
    Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
    Bioinformatics , 2002 : 18(S1)337-344
  • Eugene Kolker, PhD
    Experimental protein mixture for validating tandem mass spectrometry analysis
    OMICS , 2002 : 6(2)207-212
  • Eugene Kolker, PhD
    Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
    Nucleic Acids Research , 2002 : 30(17)3737-3738
  • Eugene Kolker, PhD
    Spectral analysis of distributions: finding periodic component in eukaryotic enzyme length data
    OMICS , 2002 : 6(1)123-130
  • Eugene Kolker, PhD
    Differential isotopic labeling of peptides for quantitation and de novo sequence derivation
    Rapid Communications in Mass Spectrometry , 2001 : 15(14)1214-1221
  • Eugene Kolker, PhD
    Segments, folds and overall protein structure
    Biological Structure and Dynamics , 1996 : 257-265
  • Eugene Kolker, PhD
    Sequence sizes of eukaryotic enzymes
    Pacific Symposium on Biocomputing '96 , 1996 : 351-361
  • Eugene Kolker, PhD
    Sequence markers of segmented protein structure
    Modeling of Biomolecular Structures and Mechanisms , 1995 : 461-471
  • Eugene Kolker, PhD
    Periodic recurrence of methionines: Fossil of gene fusion?
    Proceedings of the National Academy of Sciences of USA , 1995 : 92(2)557-560
  • Berman AL, Kolker E, Trifonov EN
    Underlying order in protein sequence organization
    Proceedings of the National Academy of Sciences of USA , 1994 : 91(9)4044-4047
  • Eugene Kolker, PhD
    MOPED: Model Organism Protein Expression Database
  • Eugene Kolker, PhD
    SPIRE: Systematic Protein Investigative Research Environment
  • Eugene Kolker, PhD
    Peptide_Prophet, Protein_Prophet and Proteomics Standards

Research Funding

Grant Title Grantor Amount Award Date
Investigation of Childhood Cancer SCRI/NEU
Analysis of best practices for Childrens and Adult Hospitals SCRI-NEU
PASS: Transformative Collaborative Project NIDDK, NIH, Co-PI, PI: Hebrok
Community Driven Proteomics Analysis Environment NSF, PI $
Mechanical support of children with end-stage cardiac failure. McMillen Foundation, PI $
Metabolism during Mechanical Circulatory Support in the Developing Heart. NHLBI, NIH, Co-PI, PI: Portman