Lars Juhl Jensen

发表

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Davide Heller, Damian Szklarczyk, Christian von Mering, 2018, Nucleic Acids Res..

Drug-Induced Regulation of Target Expression

Peer Bork, Lars Juhl Jensen, Michael Kuhn, 2010, PLoS Comput. Biol..

RAIN: RNA–protein Association and Interaction Networks

Christian von Mering, Jan Gorodkin, Lars Juhl Jensen, 2017, Database J. Biol. Databases Curation.

Prediction of human protein function according to Gene Ontology categories

Søren Brunak, Lars Juhl Jensen, Ramneek Gupta, 2003, Bioinform..

Design, implementation, and operation of a rapid, robust named entity recognition web service

Lars Juhl Jensen, Sune Pletscher-Frankild, Sune Pletscher-Frankild, 2019, Journal of Cheminformatics.

TIGA: Target illumination GWAS analytics

Tudor I. Oprea, Lars Juhl Jensen, Anna Waller, 2020, bioRxiv.

Creation and evaluation of a dictionary-based tagger for virus species and proteins

Helen Cook, Lars Juhl Jensen, Rudolfs Berzins, 2017, BioNLP.

A dictionary- and rule-based system for identification of bacteria and habitats in text

Helen Cook, Lars Juhl Jensen, Evangelos Pafilis, 2016, BioNLP.

Tagger: BeCalm API for rapid named entity recognition

Lars Juhl Jensen, 2017 .

EXTRACT 2.0: interactive identification of biological entities mentioned in text to assist database curation and knowledge extraction

Lars Juhl Jensen, Evangelos Pafilis, Christos Arvanitidis, 2017 .

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction

Reinhard Schneider, Georgios A. Pavlopoulos, Lars Juhl Jensen, 2013, 13th IEEE International Conference on BioInformatics and BioEngineering.

miRandola 2017: a curated knowledge base of non-invasive biomarkers

Alfredo Pulvirenti, Søren Brunak, Rosalba Giugno, 2017, Nucleic Acids Res..

ArrayProspector: a web resource of functional associations inferred from microarray expression data

Christian von Mering, Julien Lagarde, Peer Bork, 2004, Nucleic Acids Res..

TISSUES v1 (human, text mining, filtered)

Christian Stolte, Lars Juhl Jensen, Sune Pletscher-Frankild, 2015 .

Ten Simple Rules for Getting Help from Online Scientific Communities

Melanie I. Stefan, Giovanni Marco Dall'Olio, Jaume Bertranpetit, 2011, PLoS Comput. Biol..

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

Lars Juhl Jensen, Jennifer Hammock, Sarah Faulwetter, 2014, bioRxiv.

Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments

Søren Brunak, Lars Juhl Jensen, Nicholas Paul Gauthier, 2007, Nucleic Acids Res..

COMPARTMENTS v1 (worm, text mining)

Christian Stolte, Lars Juhl Jensen, Reinhard Schneider, 2015 .

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

Søren Brunak, Lars Juhl Jensen, Hans Henrik Stærfeldt, 2018, PLoS Comput. Biol..

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision

Lars Juhl Jensen, Alexander Junge, 2020, Bioinform..

STITCH: interaction networks of chemicals and proteins

Christian von Mering, Peer Bork, Lars Juhl Jensen, 2007, Nucleic Acids Res..

DistiLD Database: diseases and traits in linkage disequilibrium blocks

Lars Juhl Jensen, Heiko Horn, Albert Pallejà, 2011, Nucleic Acids Res..

eggNOG v4.0: nested orthology inference across 3686 organisms

Damian Szklarczyk, Christian von Mering, Peer Bork, 2013, Nucleic Acids Res..

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

Lars Juhl Jensen, Marc Legeay, John H Morris, 2020, F1000Research.

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

Søren Brunak, Lars Juhl Jensen, Massimo Andreatta, 2011, PLoS Comput. Biol..

A Comprehensive Approach Characterizing Fusion Proteins and Their Interactions Using Biomedical Literature

Somnath Tagore, Lars Juhl Jensen, Alessandro Gorohovski, 2018, bioRxiv.

SuperTarget and Matador: resources for exploring drug-target relationships

Robert B. Russell, Philip E. Bourne, Reinhard Schneider, 2007, Nucleic Acids Res..

Extraction of regulatory gene/protein networks from Medline

Peer Bork, Lars Juhl Jensen, Jasmin Saric, 2006, Bioinform..

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

Lars Juhl Jensen, Jennifer Hammock, Sarah Faulwetter, 2015, Bioinform..

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

Lars Juhl Jensen, Rasmus Wernersson, Alberto Santos, 2014, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2012, Nucleic Acids Res..

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

Christian von Mering, Peer Bork, Sean D. Hooper, 2004, Nucleic Acids Res..

DoReMi: context-based prioritization of linear motif matches

Lars Juhl Jensen, Heiko Horn, Niall J. Haslam, 2014, PeerJ.

Large-scale Extraction of Protein/Gene Relations for Model Organisms

Peer Bork, Lars Juhl Jensen, Jasmin Saric, 2005 .

Real-time tagging of biomedical entities

Lars Juhl Jensen, E Pafilis, 2016 .

TISSUES v1 (human, text mining, full)

Christian Stolte, Lars Juhl Jensen, Sune Pletscher-Frankild, 2015 .

STRING and STITCH: known and predicted interactions between proteins and chemicals

Christian von Mering, Peer Bork, Lars Juhl Jensen, 2008 .

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

Davide Heller, Damian Szklarczyk, Christian von Mering, 2014, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2010, Nucleic Acids Res..

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision

Lars Juhl Jensen, Alexander Junge, L. Jensen, 2018, bioRxiv.

Phospho.ELM: a database of phosphorylation sites—update 2008

Allegra Via, Lars Juhl Jensen, Toby J. Gibson, 2007, Nucleic Acids Res..

Integrative Systems Biology

Lars Juhl Jensen, K. Tsafou, L. Jensen, 2016 .

NetworKIN: a resource for exploring cellular phosphorylation networks

Tony Pawson, Peer Bork, Lars Juhl Jensen, 2007, Nucleic Acids Res..

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

Brent S. Pedersen, Giovanni Marco Dall'Olio, Lars Juhl Jensen, 2011, PLoS Comput. Biol..

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

Christian von Mering, Andrea Franceschini, Jianyi Lin, 2015, Bioinform..

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

Christian von Mering, Peer Bork, Berend Snel, 2006, Nucleic Acids Res..

Application of text mining for identification of ADRs in clinical notes of electronic patient records-a literature review

Lars Juhl Jensen, Pernille Warrer, Lise Aagaard, 2013 .

COMPARTMENTS: unification and visualization of protein subcellular localization evidence

Christian Stolte, Lars Juhl Jensen, Reinhard Schneider, 2014, Database J. Biol. Databases Curation.

Comprehensive comparison of large-scale tissue expression datasets

Christian Stolte, Lars Juhl Jensen, Sune Pletscher-Frankild, 2015, bioRxiv.

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

Davide Heller, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

Damian Szklarczyk, Jan Gorodkin, Lars Juhl Jensen, 2012, BMC Systems Biology.

LocText: relation extraction of protein localizations to assist database curation

Burkhard Rost, Lars Juhl Jensen, Aleksandar Bojchevski, 2018, BMC Bioinformatics.

Extracting Regulatory Gene Expression Networks From Pubmed

Peer Bork, Lars Juhl Jensen, Jasmin Saric, 2004, ACL.

The SIDER database of drugs and side effects

Peer Bork, Ivica Letunic, Lars Juhl Jensen, 2015, Nucleic Acids Res..

COMPARTMENTS v1 (fly, text mining)

Christian Stolte, Lars Juhl Jensen, Reinhard Schneider, 2015 .

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

Lars Juhl Jensen, Steen Knudsen, L. Jensen, 2000, Bioinform..

Extraction of Transcript Diversity from Scientific Literature

Peer Bork, Lars Juhl Jensen, Parantu K. Shah, 2005, PLoS Comput. Biol..

Large-scale extraction of gene regulation for model organisms in an ontological context

Lars Juhl Jensen, Jasmin Saric, Isabel Rojas, 2004, Silico Biol..

Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease

Søren Brunak, Lars Juhl Jensen, Dhouha Grissa, 2020, European Grid Conference.

Clinical Knowledge Graph Integrates Proteomics Data into Clinical Decision-Making

Lars Juhl Jensen, Philipp E. Geyer, Alberto Santos, 2020, bioRxiv.

Are graph databases ready for bioinformatics?

Lars Juhl Jensen, Christian Theil Have, C. Have, 2013, Bioinform..

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

Damian Szklarczyk, Christian von Mering, Peer Bork, 2009, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, John H. Morris, 2018, Nucleic Acids Res..

Biomedical literature mining (and why we really need Open Access)

Lars Juhl Jensen, L. Jensen, 2007 .

Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text

Robert Eriksson, Søren Brunak, Lars Juhl Jensen, 2013, J. Am. Medical Informatics Assoc..

DISEASES v1 (human, text mining, full)

Lars Juhl Jensen, Sune Pletscher-Frankild, Janos X. Binder, 2015 .

Drug Target Ontology to Classify and Integrate Drug Discovery Data

Rajarshi Guha, Tudor I. Oprea, Cristian G. Bologa, 2017 .

TIN-X: target importance and novelty explorer

Tudor I. Oprea, Cristian G. Bologa, Larry A. Sklar, 2017, Bioinform..

The rise and fall of supervised machine learning techniques

Alex Bateman, Lars Juhl Jensen, L. Jensen, 2011, Bioinform..

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

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2009, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, John H. Morris, 2016, Nucleic Acids Res..

Seqenv: linking sequences to environments through text mining

Lars Juhl Jensen, Anastasis Oulas, Evangelos Pafilis, 2016, PeerJ.

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

Søren Brunak, Lars Juhl Jensen, Nicholas Paul Gauthier, 2009, Nucleic Acids Res..

STITCH 3: zooming in on protein–chemical interactions

Damian Szklarczyk, Christian von Mering, Andrea Franceschini, 2011, Nucleic Acids Res..

ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins

Milana Frenkel-Morgenstern, Lars Juhl Jensen, Somnath Tagore, 2019, PLoS Comput. Biol..

EXTRACT 2.0: text-mining-assisted interactive annotation of biomedical named entities and ontology terms

Lars Juhl Jensen, Evangelos Pafilis, Rūdolfs Bērziņš, 2017, bioRxiv.

Entity mention in articles used for benchmark

Lars Juhl Jensen, David Westergaard, L. Jensen, 2018 .

Reflect: augmented browsing for the life scientist

Michael Kuhn, Lars Juhl Jensen, Evangelos Pafilis, 2009, Nature Biotechnology.

Overview of the interactive task in BioCreative V

Jeyakumar Natarajan, Shruti Rao, Zhiyong Lu, 2015, Database J. Biol. Databases Curation.

TISSUES 2.0: an integrative web resource on mammalian tissue expression

Jan Gorodkin, Christian Stolte, Lars Juhl Jensen, 2018, Database J. Biol. Databases Curation.

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles

Jan Gorodkin, Lars Juhl Jensen, Xiaoyong Pan, 2018, Bioinform..

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

Damian Szklarczyk, Christian von Mering, Peer Bork, 2011, Nucleic Acids Res..

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

Damian Szklarczyk, Christian von Mering, Peer Bork, 2015, Nucleic Acids Res..

Linked annotations: a middle ground for manual curation of biomedical databases and text corpora

Burkhard Rost, Lars Juhl Jensen, Juan Miguel Cejuela, 2015, BMC Proceedings.

eggNOG: automated construction and annotation of orthologous groups of genes

Christian von Mering, Peer Bork, Jean Muller, 2007, Nucleic Acids Res..

Cytoscape stringApp: Network analysis and visualization of proteomics data

John H. Morris, Jan Gorodkin, Lars Juhl Jensen, 2018, bioRxiv.

Protein-protein interaction databases.

Damian Szklarczyk, Lars Juhl Jensen, L. Jensen, 2015, Methods in molecular biology.

Improving peptide-spectrum matching by fragmentation prediction using Hidden Markov Models

Lars Juhl Jensen, Jan C. Refsgaard, Ufuk Kirik, 2018, bioRxiv.

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

Christian von Mering, Peer Bork, Jean Muller, 2008, Nucleic Acids Res..

Protein-driven inference of miRNA–disease associations

Jan Gorodkin, Lars Juhl Jensen, Sune Pletscher-Frankild, 2013, Bioinform..

Microblogging the ISMB: A New Approach to Conference Reporting

Pedro Beltrão, Lars Juhl Jensen, Shirley Wu, 2009, PLoS Comput. Biol..

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

Lars Juhl Jensen, Barbra D. Ferrell, Pier Luigi Buttigieg, 2016, Database J. Biol. Databases Curation.

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

Damian Szklarczyk, Christian von Mering, Thomas Blicher, 2013, Nucleic Acids Res..

Sharing annotations better: RESTful Open Annotation

Sampo Pyysalo, Chen Li, Filip Ginter, 2015, ACL.

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

Peer Bork, Søren Brunak, Lars Juhl Jensen, 2005, Bioinform..

A Guide to Dictionary-Based Text Mining.

Lars Juhl Jensen, Helen V Cook, L. Jensen, 2019, Methods in molecular biology.

One tagger, many uses: Illustrating the power of ontologies in dictionary-based named entity recognition

Lars Juhl Jensen, L. Jensen, L. Jensen, 2016, bioRxiv.

Text mining of 15 million full-text scientific articles

Lars Juhl Jensen, David Westergaard, Hans-Henrik Stærfeldt, 2017, bioRxiv.

Pharos: Collating protein information to shed light on the druggable genome

Rajarshi Guha, Tudor I. Oprea, Larry A. Sklar, 2016, Nucleic Acids Res..

Drug target ontology to classify and integrate drug discovery data

Rajarshi Guha, Tudor I. Oprea, Ubbo Visser, 2017, J. Biomed. Semant..

Linked annotations: a middle ground for manual curation of biomedical databases and text corpora

Burkhard Rost, Lars Juhl Jensen, Juan Miguel Cejuela, 2015 .

COMPARTMENTS v1 (mouse, text mining)

Christian Stolte, Lars Juhl Jensen, Sune Pletscher-Frankild, 2015 .

DISEASES v1 (human, knowledge, filtered)

Lars Juhl Jensen, Sune Pletscher-Frankild, Janos X. Binder, 2015 .

Reflect: A practical approach to web semantics

Michael Kuhn, Lars Juhl Jensen, Venkata P. Satagopam, 2010, J. Web Semant..

TCRD and Pharos 2021: mining the human proteome for disease biology

Anton Simeonov, Tudor I. Oprea, Noel Southall, 2020, Nucleic Acids Res..

TIGA: Target illumination GWAS analytics

Christophe G. Lambert, Tudor I. Oprea, Lars Juhl Jensen, 2020, bioRxiv.

Accurate Quantification of Site-specific Acetylation Stoichiometry Reveals the Impact of Sirtuin Deacetylase CobB on the E. coli Acetylome*

Chunaram Choudhary, Lars Juhl Jensen, L. Jensen, 2017, Molecular & Cellular Proteomics.

Alcoholic liver disease: A registry view on comorbidities and disease prediction

Søren Brunak, Lars Juhl Jensen, Dhouha Grissa, 2020, PLoS Comput. Biol..

Functionality of system components: conservation of protein function in protein feature space.

Søren Brunak, Lars Juhl Jensen, David W Ussery, 2003, Genome research.

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.

Peer Bork, Lokesh P. Tripathi, Lars Juhl Jensen, 2008, Gene.

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome

Lars Juhl Jensen, Thomas Sicheritz-Pontén, Marie Skovgaard, 2003, BMC Genomics.

Transcriptional Regulation Is a Major Controller of Cell Cycle Transition Dynamics

Luca Cardelli, Lars Juhl Jensen, Alessandro Romanel, 2012, PloS one.

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

Milana Frenkel-Morgenstern, Lars Juhl Jensen, Tamar Danon, 2012, Molecular systems biology.

WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA

Jan Gorodkin, Lars Juhl Jensen, Xiaoyong Pan, 2018, Genes.

A Comparison of Protein Kinases Inhibitor Screening Methods Using Both Enzymatic Activity and Binding Affinity Determination

Lars Juhl Jensen, Stefan Knapp, L. Jensen, 2014, PloS one.

Re‐analysis of data and its integration

Lars M Steinmetz, Lars Juhl Jensen, L. Steinmetz, 2005, FEBS letters.

Identification of Novel Type 1 Diabetes Candidate Genes by Integrating Genome-Wide Association Data, Protein-Protein Interactions, and Human Pancreatic Islet Gene Expression

Lars Juhl Jensen, Albert Palleja, L. Jensen, 2012, Diabetes.

Unexplored therapeutic opportunities in the human genome

Anton Simeonov, Christian von Mering, Tudor I. Oprea, 2018, Nature Reviews Drug Discovery.

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

Jan Gorodkin, Lars Juhl Jensen, Anne Wenzel, 2018, PloS one.

Gene–Tissue relationships from the TISSUES database

Daniel Himmelstein, Lars Juhl Jensen, L. Jensen, 2015 .

Unexplored therapeutic opportunities in the human genome

Anton Simeonov, Christian von Mering, Tudor I. Oprea, 2018, Nature Reviews Drug Discovery.

Comprehensive comparison of large-scale tissue expression datasets

Christian Stolte, Lars Juhl Jensen, Sune Pletscher-Frankild, 2015, bioRxiv.

The TISSUES resource for the tissue-specificity of genes

Daniel Himmelstein, Lars Juhl Jensen, L. Jensen, 2015 .

Prediction of novel archaeal enzymes from sequence‐derived features

Søren Brunak, Lars Juhl Jensen, Marie Skovgaard, 2002, Protein science : a publication of the Protein Society.

Not Comparable, But Complementary

Peer Bork, Lars Juhl Jensen, P. Bork, 2008, Science.

Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

Attila Tóth, Lars Juhl Jensen, Attila Csikász-Nagy, 2009, Molecular systems biology.