List of works - Lars Juhl Jensen

STRING v10: protein-protein interaction networks, integrated over the tree of life

scientific article (publication date: 2015)

Proteome survey reveals modularity of the yeast cell machinery

scientific article

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

scientific article (publication date: 2013)

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

scientific article

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

scientific article published on 18 October 2016

STRING 8--a global view on proteins and their functional interactions in 630 organisms

scientific article

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

scientific article

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

scientific article published on 22 November 2018

Drug target identification using side-effect similarity

scientific article (publication date: 11 July 2008)

Protein disorder prediction: implications for structural proteomics

scientific article (publication date: November 2003)

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

scientific article

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

scientific article (publication date: 17 November 2015)

Feature-based prediction of non-classical and leaderless protein secretion

scientific article

Systematic Discovery of In Vivo Phosphorylation Networks

scientific article (publication date: June 2007)

A side effect resource to capture phenotypic effects of drugs

scientific article (publication date: 19 January 2010)

STITCH: interaction networks of chemicals and proteins

scientific article

STRING 7--recent developments in the integration and prediction of protein interactions

scientific article

Mining electronic health records: towards better research applications and clinical care

scientific article (publication date: 2 May 2012)

SuperTarget and Matador: resources for exploring drug-target relationships

scientific article

A new non-linear normalization method for reducing variability in DNA microarray experiments

scientific article

Literature mining for the biologist: from information retrieval to biological discovery

scientific article (publication date: February 2006)

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

scientific article

Phospho.ELM: a database of phosphorylation sites--update 2011

scientific article

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

scientific article published on 29 April 2017

STITCH 4: integration of protein-chemical interactions with user data

scientific article

eggNOG: automated construction and annotation of orthologous groups of genes

scientific article (publication date: 23 December 2007)

STITCH 2: an interaction network database for small molecules and proteins

scientific article (publication date: 2010)

The SIDER database of drugs and side effects

scientific article (publication date: 19 October 2015)

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

scientific article (publication date: 23 February 2007)

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

scientific article (publication date: 20 November 2015)

A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

scientific article (publication date: June 2006)

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

scientific article

STITCH 3: zooming in on protein-chemical interactions

scientific article (publication date: 9 November 2011)

DISEASES: Text mining and data integration of disease–gene associations

scientific article (publication date: March 2015)

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

scientific article (publication date: 9 January 2015)

A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

scientific article (publication date: September 2013)

Protein interaction networks from yeast to human

scientific article (publication date: June 2004)

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

scientific article (publication date: June 2002)

A DNA structural atlas for Escherichia coli

scientific article (publication date: June 2000)

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

scientific article (publication date: 25 February 2014)

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

scientific article (publication date: 25 August 2011)

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

scientific article (publication date: July 2004)

Comparison of computational methods for the identification of cell cycle-regulated genes

scientific article (publication date: 28 October 2004)

On the total number of genes and their length distribution in complete microbial genomes

scientific article published in August 2001

Co-evolution of transcriptional and post-translational cell-cycle regulation

scientific article (publication date: 27 September 2006)

KinomeXplorer: an integrated platform for kinome biology studies

scientific article

Prediction of human protein function according to Gene Ontology categories

scientific article (publication date: 22 March 2003)

Acetylation site specificities of lysine deacetylase inhibitors in human cells

scientific article (publication date: 9 March 2015)

List of works by Lars Juhl Jensen

STRING v10: protein-protein interaction networks, integrated over the tree of life

Proteome survey reveals modularity of the yeast cell machinery

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

STRING 8--a global view on proteins and their functional interactions in 630 organisms

Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Drug target identification using side-effect similarity

Protein disorder prediction: implications for structural proteomics

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Feature-based prediction of non-classical and leaderless protein secretion

Systematic Discovery of In Vivo Phosphorylation Networks

A side effect resource to capture phenotypic effects of drugs

STITCH: interaction networks of chemicals and proteins

STRING 7--recent developments in the integration and prediction of protein interactions

Mining electronic health records: towards better research applications and clinical care

SuperTarget and Matador: resources for exploring drug-target relationships

A new non-linear normalization method for reducing variability in DNA microarray experiments

Literature mining for the biologist: from information retrieval to biological discovery

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Phospho.ELM: a database of phosphorylation sites--update 2011

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

eggNOG v4.0: nested orthology inference across 3686 organisms

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

STITCH 4: integration of protein-chemical interactions with user data

eggNOG: automated construction and annotation of orthologous groups of genes

STITCH 2: an interaction network database for small molecules and proteins

The SIDER database of drugs and side effects

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

STITCH 3: zooming in on protein-chemical interactions

DISEASES: Text mining and data integration of disease–gene associations

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

Protein interaction networks from yeast to human

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

A DNA structural atlas for Escherichia coli

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

Comparison of computational methods for the identification of cell cycle-regulated genes

On the total number of genes and their length distribution in complete microbial genomes

Co-evolution of transcriptional and post-translational cell-cycle regulation

KinomeXplorer: an integrated platform for kinome biology studies

Prediction of human protein function according to Gene Ontology categories

Acetylation site specificities of lysine deacetylase inhibitors in human cells