Eugene Kolker

发表

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

Alexey I Nesvizhskii, Ruedi Aebersold, Andrew Keller, 2002, Analytical chemistry.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Nigel W. Hardy, Chris F. Taylor, John M. Hancock, 2008, Nature Biotechnology.

Toward a standards-compliant genomic and metagenomic publication record.

Frank Oliver Glöckner, Nikos Kyrpides, Owen White, 2008, Omics : a journal of integrative biology.

Unraveling the Complexities of Life Sciences Data

Winston Haynes, Eugene Kolker, Roger Higdon, 2013, Big Data.

Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.

Renzo Kottmann, Victor Markowitz, Frank Oliver Glöckner, 2008, Omics : a journal of integrative biology.

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

Peter Myler, Eugene Kolker, Elizabeth Stewart, 2011, Omics : a journal of integrative biology.

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

Dinesh Manocha, Eugene Kolker, Elizabeth Stewart, 2011, Omics : a journal of integrative biology.

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

David R. Haynor, Eugene Kolker, Brian Tjaden, 2002, ISMB.

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

Eugene Kolker, Michael Snyder, George Mias, 2013, Big Data.

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

Eugene Kolker, Vural Özdemir, E. Kolker, 2016, Omics : a journal of integrative biology.

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

Eugene Kolker, Roger Higdon, Natali Kolker, 2007, Omics : a journal of integrative biology.

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

Winston Haynes, Eugene Kolker, Roger Higdon, 2011, Omics : a journal of integrative biology.

OMICS studies: How about metadata checklist and data publications?

Eugene Kolker, Elizabeth Stewart, E. Kolker, 2014, Journal of proteome research.

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

Eugene Kolker, Roger Higdon, Brenton Louie, 2010, Bioinform..

MOPED: Model Organism Protein Expression Database

Doron Lancet, Winston Haynes, Eugene Kolker, 2011, Nucleic Acids Res..

Modeling sequence and function similarity between proteins for protein functional annotation

Eugene Kolker, Roger Higdon, Brenton Louie, 2010, HPDC '10.

Visualizing the Protein Sequence Universe

Geoffrey C. Fox, Judy Qiu, Yang Ruan, 2012, ECMLS '12.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Lennart Martens, Stefano Toppo, Geoffrey C. Fox, 2013, Big Data.

Integration of Data for Gene Annotation Using the BioMediator System

Peter Mork, Peter Tarczy-Hornoch, Eugene Kolker, 2005, AMIA.

A Case Study: Analyzing City Vitality with Four Pillars of Activity - Live, Work, Shop, and Play

Winston Haynes, Eugene Kolker, Roger Higdon, 2016, Big Data.

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

Eugene Kolker, Gerald van Belle, Roger Higdon, 2008, Bioinform..

A predictive model for identifying proteins by a single peptide match

Eugene Kolker, Roger Higdon, E. Kolker, 2007, Bioinform..

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

Eugene Kolker, Roger Higdon, Jason M Hogan, 2005, Omics : a journal of integrative biology.

IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics.

Winston Haynes, Ruedi Aebersold, Eugene Kolker, 2011, Journal of proteomics.

TOWARD MORE TRANSPARENT AND REPRODUCIBLE

Robert L. Grossman, Lennart Martens, Doron Lancet, 2013 .

Differential Expression Analysis for Pathways

Winston Haynes, Eugene Kolker, Roger Higdon, 2013, PLoS Comput. Biol..

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

Winston Haynes, Christian Roth, Eugene Kolker, 2011, Omics : a journal of integrative biology.

MIENS Minimum Information about an ENvironmental Sequence and The GSC's Not-for-Profit (GSC8 Meeting)

Pelin Yilmaz, Eugene Kolker, 2009 .

Genic insights from integrated human proteomics in GeneCards

Tsviya Olender, Doron Lancet, Marilyn Safran, 2016, Database J. Biol. Databases Curation.

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

Winston Haynes, Eugene Kolker, Roger Higdon, 2010, Omics : a journal of integrative biology.

DELSA Global for “Big Data” and the Bioeconomy: Catalyzing Collective Innovation

Eugene Kolker, Vural Ozdemir, Elizabeth Stewart, 2012 .

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

Magdalena Balazinska, Michael McLennan, Burton J. Smith, 2011, Omics : a journal of integrative biology.

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

Judy Qiu, Ewa Deelman, Eugene Kolker, 2011, Omics : a journal of integrative biology.

MOPED enables discoveries through consistently processed proteomics data.

Doron Lancet, Winston Haynes, Eugene Kolker, 2014, Journal of proteome research.

Beyond protein expression, MOPED goes multi-omics

Eugene Kolker, Roger Higdon, Elizabeth Stewart, 2014, Nucleic Acids Res..

Visualizing the Protein Sequence Universe

Geoffrey C. Fox, Judy Qiu, Eugene Kolker, 2014, Concurr. Comput. Pract. Exp..

Optimizing high performance computing workflow for protein functional annotation

Yuan Liu, Eugene Kolker, Roger Higdon, 2014, Concurr. Comput. Pract. Exp..

Opportunities and challenges for the life sciences community.

Eugene Kolker, Vural Ozdemir, Elizabeth Stewart, 2012, Omics : a journal of integrative biology.

MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data.

Eugene Kolker, Roger Higdon, Elizabeth Stewart, 2014, Omics : a journal of integrative biology.

Introducing a Metadata Checklist for Omics Data

Edd Dumbill, Eugene Kolker, 2013, Big Data.

Healthcare Analytics: Creating a Prioritized Improvement System with Performance Benchmarking

Eugene Kolker, Evelyne Kolker, 2014, Big Data.

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

Eugene Kolker, Roger Higdon, Elizabeth Stewart, 2015, Omics : a journal of integrative biology.

Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20

Alexey I Nesvizhskii, Michael Y. Galperin, Andrew Keller, 2003, Journal of bacteriology.

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.

Eugene Kolker, Vural Ozdemir, Toshiyuki Someya, 2009, Omics : a journal of integrative biology.

Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010

Pelin Yilmaz, Folker Meyer, Lynette Hirschman, 2010, Standards in genomic sciences.

Big Data and Ethics Review for Health Systems Research in LMICs: Understanding Risk, Uncertainty and Ignorance—And Catching the Black Swans?

Türkay Dereli, Eugene Kolker, Vural Özdemir, 2014, The American journal of bioethics : AJOB.

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

Eugene Kolker, Vural Ozdemir, Béatrice Godard, 2009, Omics : a journal of integrative biology.

Special issue on data-intensive science.

Eugene Kolker, E. Kolker, 2011, Omics : a journal of integrative biology.

Experimental standards for high-throughput proteomics.

Eugene Kolker, Roger Higdon, E. Kolker, 2006, Omics : a journal of integrative biology.

H. influenzae Consortium: integrative study of H. influenzae-human interactions.

Eugene Kolker, Bernhard O Palsson, Samuel Purvine, 2002, Omics : a journal of integrative biology.

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

Eugene Kolker, Elizabeth Stewart, E. Kolker, 2016, Academic medicine : journal of the Association of American Medical Colleges.

Quantifying Protein Function Specificity in the Gene Ontology

Eugene Kolker, Roger Higdon, Brenton Louie, 2010, Standards in genomic sciences.

New metrics for comparative genomics.

Michael Y. Galperin, Eugene Kolker, Michael Y Galperin, 2006, Current opinion in biotechnology.

Metadata checklist for the integrated personal OMICS study: proteomics and metabolomics experiments.

Eugene Kolker, Michael Snyder, George Mias, 2014, Omics : a journal of integrative biology.

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9

Renzo Kottmann, Folker Meyer, Frank Oliver Glöckner, 2010, Standards in genomic sciences.

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

Eugene Kolker, Roger Higdon, Andrew Bauman, 2010, Proteomics.

In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.

Michael Y. Galperin, Eugene Kolker, Bernhard O Palsson, 2004, Omics : a journal of integrative biology.

Integrative Microbiology, 2003

Eugene Kolker, 2002 .

Validating annotations for uncharacterized proteins in Shewanella oneidensis.

Peter Tarczy-Hornoch, Eugene Kolker, Roger Higdon, 2008, Omics : a journal of integrative biology.

OMICS: 2009, 2010, and Beyond.

Eugene Kolker, 2009, Omics : a journal of integrative biology.

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

Michael Y. Galperin, Eugene Kolker, Roger Higdon, 2010, Molecular bioSystems.

SPIRE: Systematic protein investigative research environment.

Winston Haynes, Eugene Kolker, Roger Higdon, 2011, Journal of proteomics.

Towards richer descriptions of our collection of genomes andmetagenomes

Robert Stevens, Victor Markowitz, James R. Cole, 2006 .

The United States of America and Scientific Research

Folker Meyer, Peter Arzberger, Winston Haynes, 2010, PloS one.

Corrigendum to “SPIRE: Systematic Protein Investigative Research Environment” [J. Proteomics 75 (1) (2011) 122–126]

Winston Haynes, Eugene Kolker, Roger Higdon, 2012 .

Early Pneumonia Alterations in the Airway Proteome during Elicits Marked Staphylococcus Aureus Supplemental Material

Eugene Kolker, Roger Higdon, Laura Hohmann, 2008 .

Ready to put metadata on the post-2015 development agenda? Linking data publications to responsible innovation and science diplomacy.

Türkay Dereli, Sophie Mohin, Eugene Kolker, 2014, Omics : a journal of integrative biology.

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

Eugene Kolker, Ted Holzman, E. Kolker, 2004, Current opinion in biotechnology.

Charge state estimation for tandem mass spectrometry proteomics.

Eugene Kolker, Roger Higdon, Natali Kolker, 2005, Omics : a journal of integrative biology.

Towards an Ecology of Collective Innovation: Human Variome Project (HVP), Rare Disease Consortium for Autosomal Loci (RaDiCAL) and Data-Enabled Life Sciences Alliance (DELSA).

Yann Joly, Eugene Kolker, Emmanuelle Vaast, 2011, Current pharmacogenomics and personalized medicine.

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

Eugene Kolker, Andrew Bauman, Sean Rapson, 2011, Omics : a journal of integrative biology.

Metagenome Analysis of Contaminated Sediments at the DOE Hanford Site

Lee Ann McCue, Eugene Kolker, Yunfeng Yang, 2005 .

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

Eugene Kolker, 2010, Omics : a journal of integrative biology.

Vaccines of the 21st century and vaccinomics: data-enabled science meets global health to spark collective action for vaccine innovation.

Eugene Kolker, Vural Ozdemir, Bartha M. Knoppers, 2011, Omics : a journal of integrative biology.

Collective theranostics and postgenomics entrepreneurship: rethinking innovations as knowledge ecosystems built by complex collaboration

Eugene Kolker, Vural Özdemir, E. Kolker, 2012, Expert review of molecular diagnostics.

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

Eugene Kolker, Edward S Dove, Vural Özdemir, 2012, Genome Medicine.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Gordon A Anderson, John R Yates, Monica Riley, 2005, Proceedings of the National Academy of Sciences of the United States of America.

'Omics Data Sharing

John Wilbanks, Chris F. Taylor, Susanna-Assunta Sansone, 2009, Science.

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

Eugene Kolker, Bartha M Knoppers, Vural Ozdemir, 2011, Omics : a journal of integrative biology.

Integrative Analysis of Longitudinal Metabolomics Data from a Personal Multi-Omics Profile

Winston Haynes, George I. Mias, Eugene Kolker, 2013, Metabolites.

Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010.

Fredrik Levander, Jürgen Cox, Eugene Kolker, 2011, Journal of proteomics.

Host Airway Proteins Interact with Staphylococcus aureus during Early Pneumonia

Eugene Kolker, Roger Higdon, E. Kolker, 2008, Infection and Immunity.

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

Eugene Kolker, Jun Wang, Biaoyang Lin, 2009, Omics : a journal of integrative biology.

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

Eugene Kolker, Vural Özdemir, Evelyne Kolker, 2016, Omics : a journal of integrative biology.