Eugene Kolker

Eugene Kolker

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Eugene Kolker

Eugene Kolker

Publications by authors named "Eugene Kolker"

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Genic insights from integrated human proteomics in GeneCards.

Database (Oxford) 2016 5;2016. Epub 2016 Apr 5.

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel.

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http://dx.doi.org/10.1093/database/baw030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820835PMC
October 2016

Precision Medicine 2.0: The Rise of Glocal Innovation, Superconnectors, and Design Thinking.

OMICS 2016 09;20(9):493-5

12 Faculty of Communications, Gaziantep University , Gaziantep, Turkey .

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http://dx.doi.org/10.1089/omi.2016.0129DOI Listing
September 2016

How Healthcare Can Refocus on Its Super-Customers (Patients, n =1) and Customers (Doctors and Nurses) by Leveraging Lessons from Amazon, Uber, and Watson.

OMICS 2016 06;20(6):329-33

5 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.

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http://dx.doi.org/10.1089/omi.2016.0077DOI Listing
June 2016

Health Care Transformation: A Strategy Rooted in Data and Analytics.

Acad Med 2016 Feb;91(2):165-7

J. Koster is former CEO, Providence Health & Services, Renton, Washington, board member, Banner Health, Phoenix, Arizona, and board member, Sutter Health, Sacramento, California. E. Stewart is senior scientist, Seattle Children's Research Institute, Seattle, Washington. E. Kolker is chief data officer, Seattle Children's Hospital, and lead, Seattle Children's Data & Analytics Team, Seattle, Washington; affiliate professor, Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington School of Medicine, Seattle, Washington; and adjunct professor, Department of Chemistry and Chemical Biology, Northeastern University College of Science, Boston, Massachusetts.

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http://pdfs.journals.lww.com/academicmedicine/2016/02000/Hea
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http://dx.doi.org/10.1097/ACM.0000000000001047DOI Listing
February 2016

Precision Nutrition 4.0: A Big Data and Ethics Foresight Analysis--Convergence of Agrigenomics, Nutrigenomics, Nutriproteomics, and Nutrimetabolomics.

OMICS 2016 Feb 19;20(2):69-75. Epub 2016 Jan 19.

3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.

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http://dx.doi.org/10.1089/omi.2015.0193DOI Listing
February 2016

Finding Text-Supported Gene-to-Disease Co-appearances with MOPED-Digger.

OMICS 2015 Dec 17;19(12):754-6. Epub 2015 Nov 17.

1 High-Throughput Analysis Core, Seattle Children's Research Institute , Seattle, Washington.

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http://dx.doi.org/10.1089/omi.2015.0151DOI Listing
December 2015

Can "normal" protein expression ranges be estimated with high-throughput proteomics?

J Proteome Res 2015 Jun 27;14(6):2398-407. Epub 2015 Apr 27.

†Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, United States.

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http://dx.doi.org/10.1021/acs.jproteome.5b00176DOI Listing
June 2015

Personalized dentistry meets OMICS and "one health": from Cinderella of healthcare to mainstream?

OMICS 2015 Mar;19(3):145-6

1 Department of Periodontology, Faculty of Dentistry, International Technology and Innovation Policy, Gaziantep University , Gaziantep, Turkey .

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http://dx.doi.org/10.1089/omi.2015.0016DOI Listing
March 2015

Beyond protein expression, MOPED goes multi-omics.

Nucleic Acids Res 2015 Jan 17;43(Database issue):D1145-51. Epub 2014 Nov 17.

Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101 Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington, Seattle, WA, USA 98109 Department of Chemistry and Chemical Biology, College of Science, Northeastern University, Boston, MA 02115

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http://dx.doi.org/10.1093/nar/gku1175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383969PMC
January 2015

Optimizing high performance computing workflow for protein functional annotation.

Concurr Comput 2014 Sep;26(13):2112-2121

Bioinformatics & High-throughput Analysis Laboratory, SCRI, High-throughput Analysis Core, SCRI, Predicitive Analytics, Seattle Children's Hospital, Departments of Pediatrics and Biomedical Informatics & Medical Education, University of Washington, DELSA Global.

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http://dx.doi.org/10.1002/cpe.3264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4194055PMC
September 2014

Designing a post-genomics knowledge ecosystem to translate pharmacogenomics into public health action.

Genome Med 2012 29;4(11):91. Epub 2012 Nov 29.

Research Group on Complex Collaboration, Desautels Faculty of Management, McGill University, 1001 Sherbrooke Street West, Montreal, QC, Canada H3A 1G5 ; Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, 740 Dr. Penfield Avenue, Suite 5200, Montreal, QC, Canada H3A 0G1 ; Data-Enabled Life Sciences Alliance International (DELSA Global), Seattle, WA 98101, USA.

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http://genomemedicine.biomedcentral.com/articles/10.1186/gm3
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http://dx.doi.org/10.1186/gm392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3580424PMC
May 2014

OMICS studies: How about metadata checklist and data publications?

J Proteome Res 2014 Mar 5;13(3):1783-4. Epub 2014 Feb 5.

Seattle Children's Research Insitute , 1900 Ninth Avenue, Seattle, Washington 98101, United States.

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http://dx.doi.org/10.1021/pr4011662DOI Listing
March 2014

Healthcare Analytics: Creating a Prioritized Improvement System with Performance Benchmarking.

Big Data 2014 Mar;2(1):50-4

4 Data-Enabled Life Sciences Alliance (DELSA Global), University of Washington , Seattle, WA, USA .

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http://dx.doi.org/10.1089/big.2014.0004DOI Listing
March 2014

Introducing a Metadata Checklist for Omics Data.

Big Data 2013 Dec;1(4):195

2 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute ; Seattle, Washington.

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http://dx.doi.org/10.1089/big.2013.1515DOI Listing
December 2013

Metadata Checklist for the Integrated Personal Omics Study: Proteomics and Metabolomics Experiments.

Big Data 2013 Dec;1(4):202-6

3 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.

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http://dx.doi.org/10.1089/big.2013.0040DOI Listing
December 2013

Predictive Analytics In Healthcare: Medications as a Predictor of Medical Complexity.

Big Data 2013 Dec 5;1(4):237-44. Epub 2013 Dec 5.

1 Bioinformatics and High-Throughput Data Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.

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http://dx.doi.org/10.1089/big.2013.0024DOI Listing
December 2013

Differential expression analysis for pathways.

PLoS Comput Biol 2013 14;9(3):e1002967. Epub 2013 Mar 14.

Bioinformatics & High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1002967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597535PMC
November 2013

Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile.

Metabolites 2013 Sep 3;3(3):741-60. Epub 2013 Sep 3.

Bioinformatics and High-throughput Analysis Laboratory, and High-throughput Analysis Core, Seattle Children's Research Institute, Seattle, 98101, USA.

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http://dx.doi.org/10.3390/metabo3030741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901289PMC
September 2013

Delsa Workshop IV: Launching the Quantified Human Initiative.

Big Data 2013 Sep;1(3):187-90

1 Bioinformatics and High-throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.

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http://dx.doi.org/10.1089/big.2013.0022DOI Listing
September 2013

Unraveling the Complexities of Life Sciences Data.

Big Data 2013 Mar 7;1(1):42-50. Epub 2012 Nov 7.

1 Bioinformatics and High-throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington.

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http://dx.doi.org/10.1089/big.2012.1505DOI Listing
March 2013

Opportunities and challenges for the life sciences community.

OMICS 2012 Mar;16(3):138-47

Bioinformatics & High-throughput Analysis Lab and High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington 98101, USA.

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http://dx.doi.org/10.1089/omi.2011.0152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3300061PMC
March 2012

MOPED: Model Organism Protein Expression Database.

Nucleic Acids Res 2012 Jan 1;40(Database issue):D1093-9. Epub 2011 Dec 1.

Bioinformatics and High-throughput Analysis Laboratory, High-throughput Analysis Core, Center for Developmental Therapeutics, Seattle Children's Research Institute, Predicitive Analytics, Seattle Children's Hospital, Seattle, WA 98105, USA.

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http://dx.doi.org/10.1093/nar/gkr1177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245040PMC
January 2012

SPIRE: Systematic protein investigative research environment.

J Proteomics 2011 Dec 13;75(1):122-6. Epub 2011 May 13.

Bioinformatics & High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, WA, USA.

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http://dx.doi.org/10.1016/j.jprot.2011.05.009DOI Listing
December 2011

Classifying proteins into functional groups based on all-versus-all BLAST of 10 million proteins.

OMICS 2011 Jul-Aug;15(7-8):513-21

High-Throughput Analysis Core, Seattle Children's Research Institute, Washington, USA.

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http://dx.doi.org/10.1089/omi.2011.0101DOI Listing
November 2011

Design and initial characterization of the SC-200 proteomics standard mixture.

OMICS 2011 Jan-Feb;15(1-2):73-82. Epub 2011 Jan 21.

Seattle Children's Research Institute, Bioinformatics and High-throughput Analysis Laboratory, Seattle Children's Research Institute, High-throughput Analysis Core, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1089/omi.2010.0118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110723PMC
May 2011

Special issue on data-intensive science.

Authors:
Eugene Kolker

OMICS 2011 Apr;15(4):197-8

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http://dx.doi.org/10.1089/omi.2011.02edDOI Listing
April 2011

Communication and data-intensive science in the beginning of the 21st century.

OMICS 2011 Apr;15(4):213-5

Pacific Northwest Diabetes Research Institute , Seattle, Wahsington, USA.

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http://dx.doi.org/10.1089/omi.2011.0008DOI Listing
April 2011

Policy and data-intensive scientific discovery in the beginning of the 21st century.

OMICS 2011 Apr;15(4):221-5

Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada.

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http://dx.doi.org/10.1089/omi.2011.0007DOI Listing
April 2011

The necessity of adjusting tests of protein category enrichment in discovery proteomics.

Bioinformatics 2010 Dec 9;26(24):3007-11. Epub 2010 Nov 9.

Bioinformatics and High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, WA 98101, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995116PMC
December 2010

A vision for 21st century U.S. Policy to support sustainable advancement of scientific discovery and technological innovation.

Authors:
Eugene Kolker

OMICS 2010 Aug;14(4):333-5

Bioinformatics & High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington, USA.

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http://dx.doi.org/10.1089/omi.2010.0068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133827PMC
August 2010

Estimating false discovery rates for peptide and protein identification using randomized databases.

Proteomics 2010 Jun;10(12):2369-76

Bioinformatics & High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, WA 98101, USA.

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http://dx.doi.org/10.1002/pmic.200900619DOI Listing
June 2010

Editorial: global issues.

Authors:
Eugene Kolker

OMICS 2010 Jun;14(3):229

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http://dx.doi.org/10.1089/omi.2010.ed02DOI Listing
June 2010

Meta-analysis for protein identification: a case study on yeast data.

OMICS 2010 Jun;14(3):309-14

Bioinformatics & High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, USA.

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http://dx.doi.org/10.1089/omi.2010.0034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133781PMC
June 2010

Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.

Mol Biosyst 2010 Apr 9;6(4):721-8. Epub 2010 Feb 9.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1039/b908047cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071642PMC
April 2010

Modeling sequence and function similarity between proteins for protein functional annotation.

Proc Int Symp High Perform Distrib Comput 2010 ;2010:499-502

Seattle Children's Research Institute, 1900 Ninth Avenue, Seattle, WA 98101,

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http://dx.doi.org/10.1145/1851476.1851548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120521PMC
January 2010

OMICS: 2009, 2010, and Beyond.

Authors:
Eugene Kolker

OMICS 2009 Dec;13(6):451

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http://dx.doi.org/10.1089/omi.2009.ED03DOI Listing
December 2009

A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions.

PLoS One 2009 Oct 21;4(10):e7546. Epub 2009 Oct 21.

Bioinformatics and High-throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007546PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760442PMC
October 2009

Meeting report: the 2009 Westlake International Conference on Personalized Medicine.

OMICS 2009 Aug;13(4):285-9

Zhejiang-California Nanosystems Institute, Zhejiang University, Hangzhou 310029, People's Republic of China.

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http://dx.doi.org/10.1089/omi.2009.0MReDOI Listing
August 2009

Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.

OMICS 2009 Feb;13(1):1-6

Department of Social and Preventive Medicine, Faculty of Medicine, University of Montréal, Montréal, Québec, Canada.

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http://dx.doi.org/10.1089/omi.2009.0013DOI Listing
February 2009

Staphylococcus aureus elicits marked alterations in the airway proteome during early pneumonia.

Infect Immun 2008 Dec 13;76(12):5862-72. Epub 2008 Oct 13.

Division of Infectious Diseases, Center for Childhood Infections and Prematurity Research, University of Washington School of Medicine, Seattle, Washington, USA.

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http://dx.doi.org/10.1128/IAI.00865-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583584PMC
December 2008

Validating annotations for uncharacterized proteins in Shewanella oneidensis.

OMICS 2008 Sep;12(3):211-5

Department of Medical Education and Biomedical Informatics, Division of Biomedical and Health Informatics, University of Washington, Seattle, Washington 98101-1304, USA.

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http://dx.doi.org/10.1089/omi.2008.0051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189009PMC
September 2008

A note on the false discovery rate and inconsistent comparisons between experiments.

Bioinformatics 2008 May 19;24(10):1225-8. Epub 2008 Apr 19.

Seattle Children's Research Institute, Seattle, WA 98101, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn120DOI Listing
May 2008

Experiment-specific estimation of peptide identification probabilities using a randomized database.

OMICS 2007 ;11(4):351-65

Seattle Children's Hospital and Regional Medical Center, Seattle, WA 98101, USA.

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http://dx.doi.org/10.1089/omi.2007.0040DOI Listing
March 2008

Host airway proteins interact with Staphylococcus aureus during early pneumonia.

Infect Immun 2008 Mar 14;76(3):888-98. Epub 2008 Jan 14.

Division of Infectious Diseases, Center for Childhood Infections and Prematurity Research, Seattle Children's Hospital Research Institute, 1900 9th Ave., Seattle, WA 98101, USA.

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http://dx.doi.org/10.1128/IAI.01301-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258841PMC
March 2008

Experimental standards for high-throughput proteomics.

OMICS 2006 ;10(2):152-7

The BIATECH Institute, Bothell, Washington 98011, USA.

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http://dx.doi.org/10.1089/omi.2006.10.152DOI Listing
November 2007

A predictive model for identifying proteins by a single peptide match.

Bioinformatics 2007 Feb 22;23(3):277-80. Epub 2006 Nov 22.

The BIATECH Institute, Bothell, WA 98011, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl595DOI Listing
February 2007

New metrics for comparative genomics.

Curr Opin Biotechnol 2006 Oct 15;17(5):440-7. Epub 2006 Sep 15.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1016/j.copbio.2006.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764326PMC
October 2006

Protein identification and expression analysis using mass spectrometry.

Trends Microbiol 2006 May 17;14(5):229-35. Epub 2006 Apr 17.

The BIATECH Institute, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA.

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http://dx.doi.org/10.1016/j.tim.2006.03.005DOI Listing
May 2006

Randomized sequence databases for tandem mass spectrometry peptide and protein identification.

OMICS 2005 ;9(4):364-79

The BIATECH Institute, 19310 N. Creek Parkway South, Suite 115, Bothell, WA 98011, USA.

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http://dx.doi.org/10.1089/omi.2005.9.364DOI Listing
March 2006

Charge state estimation for tandem mass spectrometry proteomics.

OMICS 2005 ;9(3):233-50

BIATECH, Bothell, Washington 98011, USA.

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http://dx.doi.org/10.1089/omi.2005.9.233DOI Listing
December 2005

Spectral quality assessment for high-throughput tandem mass spectrometry proteomics.

OMICS 2004 ;8(3):255-65

BIATECH, Bothell, Washington 98011, USA.

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http://dx.doi.org/10.1089/omi.2004.8.255DOI Listing
March 2005

Standard mixtures for proteome studies.

OMICS 2004 ;8(1):79-92

BIATECH, Bothell, Washington 98011, USA.

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http://dx.doi.org/10.1089/153623104773547507DOI Listing
November 2004

Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis.

Bioinformatics 2002 ;18 Suppl 1:S337-44

Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_1.s337DOI Listing
October 2004

Statistical analysis of global gene expression data: some practical considerations.

Curr Opin Biotechnol 2004 Feb;15(1):52-7

BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA.

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http://dx.doi.org/10.1016/j.copbio.2003.12.004DOI Listing
February 2004

A statistical model for identifying proteins by tandem mass spectrometry.

Anal Chem 2003 Sep;75(17):4646-58

Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.

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http://dx.doi.org/10.1021/ac0341261DOI Listing
September 2003

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Anal Chem 2002 Oct;74(20):5383-92

Institute for Systems Biology, Seattle, Washington 98103, USA.

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http://dx.doi.org/10.1021/ac025747hDOI Listing
October 2002

Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays.

Nucleic Acids Res 2002 Sep;30(17):3732-8

Department of Computer Science, University of Washington, Seattle, WA 98195, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137427PMC
http://dx.doi.org/10.1093/nar/gkf505DOI Listing
September 2002