List of works - Eugene Kolker

'Omics data sharing

scientific article

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

scientific article published on March 2016

A Vision for 21st Century U.S. Policy to Support Sustainable Advancement of Scientific Discovery and Technological Innovation ⬇️

scientific article published on August 1, 2010

A statistical model for identifying proteins by tandem mass spectrometry

scientific article (publication date: September 2003)

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

scientific article published on 21 October 2009

An Appeal to the Global Health Community for a Tripartite Innovation: An "Essential Diagnostics List," "Health in All Policies," and "See-Through 21(st) Century Science and Ethics".

scientific article

Bernard Lerer: recipient of the 2014 inaugural Werner Kalow Responsible Innovation Prize in Global Omics and Personalized Medicine (Pacific Rim Association for Clinical Pharmacogenetics).

scientific article published on 20 March 2014

Beyond protein expression, MOPED goes multi-omics

scientific article

Big data and ethics review for health systems research in LMICs: understanding risk, uncertainty and ignorance -- and catching the black swans?

scientific article

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

scientific article

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

scientific article

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

scientific article

Charge state estimation for tandem mass spectrometry proteomics

scientific article published in January 2005

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

scientific article

Delsa Workshop IV: Launching the Quantified Human Initiative

scientific article published on September 2013

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

scientific article

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

scientific article (publication date: 2012)

Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression

scientific article published on October 2007

Differential expression analysis for pathways

scientific article

Dynamic Proteomic Analysis of Pancreatic Mesenchyme Reveals Novel Factors That Enhance Human Embryonic Stem Cell to Pancreatic Cell Differentiation

scientific article

Education and Data-Intensive Science in the Beginning of the 21st Century ⬇️

scientific article published on April 1, 2011

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

scientific article (publication date: 15 October 2002)

Experimental standards for high-throughput proteomics

scientific article published on January 2006

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

scientific article published on 17 November 2015

Genic insights from integrated human proteomics in GeneCards

scientific article published on 5 April 2016

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

scientific article published on February 2009

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

scientific article

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

scientific article published on January 2002

Health Care Transformation: A Strategy Rooted in Data and Analytics

scientific article

Healthcare Analytics: Creating a Prioritized Improvement System with Performance Benchmarking

scientific article published on March 2014

Host airway proteins interact with Staphylococcus aureus during early pneumonia

scientific article

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

scientific article published on June 2016

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

scientific article

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

scientific article published in January 2004

In-silico human genomics with GeneCards

scientific article

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

scientific article

Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes

scientific article published on 03 February 2017

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

scientific article

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

scientific article

Introducing a Metadata Checklist for Omics Data

scientific article

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

scientific article (publication date: June 2014)

MOPED enables discoveries through consistently processed proteomics data

scientific article

MOPED: Model Organism Protein Expression Database

scientific article

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

scientific article (publication date: 4 December 2010)

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

scientific article

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

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

scientific article

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

scientific article published on December 2013

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

scientific article (publication date: 2014)

New metrics for comparative genomics

scientific article (publication date: October 2006)

OMICS studies: How about metadata checklist and data publications?

scientific article published on 5 February 2014

Opportunities and Challenges for the Life Sciences Community ⬇️

scientific article (publication date: March 2012)

Optimizing high performance computing workflow for protein functional annotation

scientific article

Policy and Data-Intensive Scientific Discovery in the Beginning of the 21st Century ⬇️

scientific article published on April 1, 2011

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

scientific article published in September 2016

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

scientific article

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

scientific article published on 5 December 2013

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

scientific article (publication date: August 2008)

Protein identification and expression analysis using mass spectrometry

scientific article

Quantifying Protein Function Specificity in the Gene Ontology ⬇️

scientific article published on March 30, 2010

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

scientific article published in January 2014

Reproducibility: In praise of open research measures

scientific article published in June 2013

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

scientific article

SPIRE: Systematic protein investigative research environment ⬇️

scientific article published on May 13, 2011

Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data

scientific article

Spectral quality assessment for high-throughput tandem mass spectrometry proteomics

scientific article

Standard mixtures for proteome studies

scientific article published on January 2004

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

scientific article

Statistical analysis of global gene expression data: some practical considerations

scientific article published in February 2004

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

scientific article

The United States of America and scientific research

scientific article

The minimum information about a genome sequence (MIGS) specification

scientific article

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

scientific article published on November 9, 2010

The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders

scientific article

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

scientific article

Toward a standards-compliant genomic and metagenomic publication record

scientific article

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

scientific article (publication date: 2014)

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

scientific article (publication date: December 2011)

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

scientific article

Unraveling the Complexities of Life Sciences Data

scientific article

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

scientific article published on 17 August 2011

Validating annotations for uncharacterized proteins in Shewanella oneidensis

scientific article

List of works by Eugene Kolker

'Omics data sharing

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

A Vision for 21st Century U.S. Policy to Support Sustainable Advancement of Scientific Discovery and Technological Innovation ⬇️

A statistical model for identifying proteins by tandem mass spectrometry

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

An Appeal to the Global Health Community for a Tripartite Innovation: An "Essential Diagnostics List," "Health in All Policies," and "See-Through 21(st) Century Science and Ethics".

Bernard Lerer: recipient of the 2014 inaugural Werner Kalow Responsible Innovation Prize in Global Omics and Personalized Medicine (Pacific Rim Association for Clinical Pharmacogenetics).

Beyond protein expression, MOPED goes multi-omics

Big data and ethics review for health systems research in LMICs: understanding risk, uncertainty and ignorance -- and catching the black swans?

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

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

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

Charge state estimation for tandem mass spectrometry proteomics

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

Delsa Workshop IV: Launching the Quantified Human Initiative

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

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

Development of BIATECH-54 standard mixtures for assessment of protein identification and relative expression

Differential expression analysis for pathways

Dynamic Proteomic Analysis of Pancreatic Mesenchyme Reveals Novel Factors That Enhance Human Embryonic Stem Cell to Pancreatic Cell Differentiation

Education and Data-Intensive Science in the Beginning of the 21st Century ⬇️

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

Experimental standards for high-throughput proteomics

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

Genic insights from integrated human proteomics in GeneCards

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

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

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

Health Care Transformation: A Strategy Rooted in Data and Analytics

Healthcare Analytics: Creating a Prioritized Improvement System with Performance Benchmarking

Host airway proteins interact with Staphylococcus aureus during early pneumonia

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

Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae

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

In-silico human genomics with GeneCards

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes

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

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

Introducing a Metadata Checklist for Omics Data

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

MOPED enables discoveries through consistently processed proteomics data

MOPED: Model Organism Protein Expression Database

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

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

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

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

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

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

New metrics for comparative genomics

OMICS studies: How about metadata checklist and data publications?

Opportunities and Challenges for the Life Sciences Community ⬇️

Optimizing high performance computing workflow for protein functional annotation

Policy and Data-Intensive Scientific Discovery in the Beginning of the 21st Century ⬇️

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

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

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

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

Protein identification and expression analysis using mass spectrometry

Quantifying Protein Function Specificity in the Gene Ontology ⬇️

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

Reproducibility: In praise of open research measures

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

SPIRE: Systematic protein investigative research environment ⬇️

Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data

Spectral quality assessment for high-throughput tandem mass spectrometry proteomics

Standard mixtures for proteome studies

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

Statistical analysis of global gene expression data: some practical considerations

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

The United States of America and scientific research

The minimum information about a genome sequence (MIGS) specification

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

The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders

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

Toward a standards-compliant genomic and metagenomic publication record

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

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

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