Lars Juhl Jensen

Orcid: 0000-0001-7885-715X

According to our database1, Lars Juhl Jensen authored at least 81 papers between 2000 and 2024.

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PhD thesis 


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FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.
Bioinform., February, 2024

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Nucleic Acids Res., January, 2023

Pharos 2023: an integrated resource for the understudied human proteome.
Nucleic Acids Res., January, 2023

eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Nucleic Acids Res., January, 2023

Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies.
PLoS Comput. Biol., October, 2022

A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research.
J. Chem. Inf. Model., 2022

Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration.
Database J. Biol. Databases Curation, 2022

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Nucleic Acids Res., 2021

TCRD and Pharos 2021: mining the human proteome for disease biology.
Nucleic Acids Res., 2021

TIGA: target illumination GWAS analytics.
Bioinform., 2021

Alcoholic liver disease: A registry view on comorbidities and disease prediction.
PLoS Comput. Biol., 2020

Visualize omics data on networks with Omics Visualizer, a Cytoscape App.
F1000Research, 2020

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision.
Bioinform., 2020

Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease.
Proceedings of the Extraction et Gestion des Connaissances, 2020

ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.
PLoS Comput. Biol., 2019

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Nucleic Acids Res., 2019

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Nucleic Acids Res., 2019

Design, implementation, and operation of a rapid, robust named entity recognition web service.
J. Cheminformatics, 2019

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.
Bioinform., 2019

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.
PLoS Comput. Biol., 2018

miRandola 2017: a curated knowledge base of non-invasive biomarkers.
Nucleic Acids Res., 2018

LocText: relation extraction of protein localizations to assist database curation.
BMC Bioinform., 2018

TISSUES 2.0: an integrative web resource on mammalian tissue expression.
Database J. Biol. Databases Curation, 2018

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

Pharos: Collating protein information to shed light on the druggable genome.
Nucleic Acids Res., 2017

Drug target ontology to classify and integrate drug discovery data.
J. Biomed. Semant., 2017

TIN-X: target importance and novelty explorer.
Bioinform., 2017

RAIN: RNA-protein Association and Interaction Networks.
Database J. Biol. Databases Curation, 2017

Creation and evaluation of a dictionary-based tagger for virus species and proteins.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Nucleic Acids Res., 2016

The SIDER database of drugs and side effects.
Nucleic Acids Res., 2016

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Nucleic Acids Res., 2016

SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.
Bioinform., 2016

Overview of the interactive task in BioCreative V.
Database J. Biol. Databases Curation, 2016

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.
Database J. Biol. Databases Curation, 2016

One Tagger, Many Uses: Illustrating the Power of Ontologies in Dictionary-based Named Entity Recognition.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

A dictionary- and rule-based system for identification of bacteria and habitats in text.
Proceedings of the 4th BioNLP Shared Task Workshop, BioNLP 2016, 2016

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Nucleic Acids Res., 2015

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes.
Nucleic Acids Res., 2015

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.
Bioinform., 2015

Sharing annotations better: RESTful Open Annotation.
Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing of the Asian Federation of Natural Language Processing, 2015

eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res., 2014

STITCH 4: integration of protein-chemical interactions with user data.
Nucleic Acids Res., 2014

Protein-driven inference of miRNA-disease associations.
Bioinform., 2014

COMPARTMENTS: unification and visualization of protein subcellular localization evidence.
Database J. Biol. Databases Curation, 2014

STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Nucleic Acids Res., 2013

Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text.
J. Am. Medical Informatics Assoc., 2013

Are graph databases ready for bioinformatics?
Bioinform., 2013

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction.
Proceedings of the 13th IEEE International Conference on BioInformatics and BioEngineering, 2013

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res., 2012

DistiLD Database: diseases and traits in linkage disequilibrium blocks.
Nucleic Acids Res., 2012

STITCH 3: zooming in on protein-chemical interactions.
Nucleic Acids Res., 2012

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs.
BMC Syst. Biol., 2012

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts.
PLoS Comput. Biol., 2011

BioStar: An Online Question & Answer Resource for the Bioinformatics Community.
PLoS Comput. Biol., 2011

Ten Simple Rules for Getting Help from Online Scientific Communities.
PLoS Comput. Biol., 2011

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

Phospho.ELM: a database of phosphorylation sites - update 2011.
Nucleic Acids Res., 2011

The rise and fall of supervised machine learning techniques.
Bioinform., 2011

Reflect: A practical approach to web semantics.
J. Web Semant., 2010

Drug-Induced Regulation of Target Expression.
PLoS Comput. Biol., 2010

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Nucleic Acids Res., 2010

STITCH 2: an interaction network database for small molecules and proteins.
Nucleic Acids Res., 2010 version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results.
Nucleic Acids Res., 2010

Microblogging the ISMB: A New Approach to Conference Reporting.
PLoS Comput. Biol., 2009

STRING 8 - a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Res., 2009

NetworKIN: a resource for exploring cellular phosphorylation networks.
Nucleic Acids Res., 2008

STITCH: interaction networks of chemicals and proteins.
Nucleic Acids Res., 2008

eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic Acids Res., 2008

SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic Acids Res., 2008 - a comprehensive multi-organism online database of cell-cycle experiments.
Nucleic Acids Res., 2008

STRING 7 - recent developments in the integration and prediction of protein interactions.
Nucleic Acids Res., 2007

Extraction of regulatory gene/protein networks from Medline.
Bioinform., 2006

Extraction of Transcript Diversity from Scientific Literature.
PLoS Comput. Biol., 2005

STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res., 2005

Comparison of computational methods for the identification of cell cycle-regulated genes.
Bioinform., 2005

ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Nucleic Acids Res., 2004

Large-scale extraction of gene regulation for model organisms in an ontological context.
Silico Biol., 2004

Extracting Regulatory Gene Expression Networks From Pubmed.
Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics, 2004

Prediction of human protein function according to Gene Ontology categories.
Bioinform., 2003

Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation.
Bioinform., 2000