Lars Juhl Jensen

91 papers A* 1C 1Journal 84Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations.
Database J. Biol. Databases Curation
Esmaeil Nourani, Evangelia-Mantelena Makri, Xiqing Mao, Sampo Pyysalo, Søren Brunak, Katerina C. Nastou, Lars Juhl Jensen
2025 J jnl
SPACE: STRING proteins as complementary embeddings.
Bioinform.
Dewei Hu, Damian Szklarczyk, Christian von Mering, Lars Juhl Jensen
2024 J jnl
ECCB2024: The 23rd European Conference on Computational Biology.
Bioinform.
Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F. Heil, Merja Heinäniemi, Lars Juhl Jensen, Sini Junttila, Lukas Käll, Asta Laiho, Peter Maccallum, Matti Nykter, Bengt Persson, Tomi Suomi, Tim Van Den Bossche, Tommi H. Nyrönen, Laura L. Elo
2024 J jnl
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.
Bioinform.
Mikaela Koutrouli, Katerina C. Nastou, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen
2024 J jnl
Graph databases in systems biology: a systematic review.
Briefings Bioinform.
Ilya Mazein, Adrien Rougny, Alexander Mazein, Ron Henkel, Lea Gütebier, Lea Michaelis, Marek Ostaszewski, Reinhard Schneider, Venkata P. Satagopam, Lars Juhl Jensen, Dagmar Waltemath, Judith A. H. Wodke, Irina Balaur
2024 J jnl
Improving dictionary-based named entity recognition with deep learning.
Bioinform.
Katerina C. Nastou, Mikaela Koutrouli, Sampo Pyysalo, Lars Juhl Jensen
2024 J jnl
Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition.
Bioinform.
Esmaeil Nourani, Mikaela Koutrouli, Yijia Xie, Danai Vagiaki, Sampo Pyysalo, Katerina C. Nastou, Søren Brunak, Lars Juhl Jensen
2024 J jnl
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature.
Database J. Biol. Databases Curation
Katerina C. Nastou, Farrokh Mehryary, Tomoko Ohta, Jouni Luoma, Sampo Pyysalo, Lars Juhl Jensen
2024 J jnl
STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature.
Bioinform.
Farrokh Mehryary, Katerina C. Nastou, Tomoko Ohta, Lars Juhl Jensen, Sampo Pyysalo
2023 J jnl
Pharos 2023: an integrated resource for the understudied human proteome.
Nucleic Acids Res.
Keith J. Kelleher, Timothy Sheils, Stephen L. Mathias, Jeremy J. Yang, Vincent T. Metzger, Vishal B. Siramshetty, Dac-Trung Nguyen, Lars Juhl Jensen, Dusica Vidovic, Stephan C. Schürer, Jayme Holmes, Karlie R. Sharma, Ajay Pillai, Cristian Bologa, Jeremy S. Edwards, Ewy A. Mathé, Tudor I. Oprea
2023 J jnl
S1000: a better taxonomic name corpus for biomedical information extraction.
Bioinform.
Jouni Luoma, Katerina C. Nastou, Tomoko Ohta, Harttu Toivonen, Evangelos Pafilis, Lars Juhl Jensen, Sampo Pyysalo
2023 J jnl
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Nucleic Acids Res.
Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina C. Nastou, Farrokh Mehryary, Radja Hachilif, Annika L. Gable, Tao Fang, Nadezhda T. Doncheva, Sampo Pyysalo, Peer Bork, Lars Juhl Jensen, Christian von Mering
2023 J jnl
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Nucleic Acids Res.
Ana Hernández-Plaza, Damian Szklarczyk, Jorge Botas, Carlos P. Cantalapiedra, Joaquín Giner-Lamia, Daniel R. Mende, Rebecca Kirsch, Thomas Rattei, Ivica Letunic, Lars Juhl Jensen, Peer Bork, Christian von Mering, Jaime Huerta-Cepas
2022 J jnl
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research.
J. Chem. Inf. Model.
Gergely Zahoránszky-Köhalmi, Vishal B. Siramshetty, Praveen Kumar, Manideep Gurumurthy, Busola Grillo, Biju Mathew, Dimitrios Metaxatos, Mark Backus, Tim Mierzwa, Reid Simon, Ivan Grishagin, Laura Brovold, Ewy A. Mathé, Matthew D. Hall, Samuel G. Michael, Alexander G. Godfrey, Jordi Mestres, Lars Juhl Jensen, Tudor I. Oprea
2022 J jnl
Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration.
Database J. Biol. Databases Curation
Dhouha Grissa, Alexander Junge, Tudor I. Oprea, Lars Juhl Jensen
2022 J jnl
Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies.
PLoS Comput. Biol.
Marie Locard-Paulet, Oana Palasca, Lars Juhl Jensen
2021 J jnl
TCRD and Pharos 2021: mining the human proteome for disease biology.
Nucleic Acids Res.
Timothy Sheils, Stephen L. Mathias, Keith J. Kelleher, Vishal B. Siramshetty, Dac-Trung Nguyen, Cristian Bologa, Lars Juhl Jensen, Dusica Vidovic, Amar Koleti, Stephan C. Schürer, Anna Waller, Jeremy J. Yang, Jayme Holmes, Giovanni Bocci, Noel Southall, Poorva Dharkar, Ewy A. Mathé, Anton Simeonov, Tudor I. Oprea
2021 J jnl
TIGA: target illumination GWAS analytics.
Bioinform.
Jeremy J. Yang, Dhouha Grissa, Christophe G. Lambert, Cristian Bologa, Stephen L. Mathias, Anna Waller, David J. Wild, Lars Juhl Jensen, Tudor I. Oprea
2021 J jnl
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Nucleic Acids Res.
Damian Szklarczyk, Annika L. Gable, Katerina C. Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T. Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars Juhl Jensen, Christian von Mering
2020 J jnl
Alcoholic liver disease: A registry view on comorbidities and disease prediction.
PLoS Comput. Biol.
Dhouha Grissa, Ditlev Nytoft Rasmussen, Aleksander Krag, Søren Brunak, Lars Juhl Jensen
2020 J jnl
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision.
Bioinform.
Alexander Junge, Lars Juhl Jensen
2020 — conf
Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease.
EGC
Dhouha Grissa, Ditlev Nytoft Rasmussen, Aleksander Krag, Søren Brunak, Lars Juhl Jensen
2020 J jnl
Visualize omics data on networks with Omics Visualizer, a Cytoscape App.
F1000Research
Marc Legeay, Nadezhda T. Doncheva, John H. Morris, Lars Juhl Jensen
2019 J jnl
Design, implementation, and operation of a rapid, robust named entity recognition web service.
J. Cheminformatics
Sune Pletscher-Frankild, Lars Juhl Jensen
2019 J jnl
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.
Bioinform.
Xiaoyong Pan, Lars Juhl Jensen, Jan Gorodkin
2019 J jnl
ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.
PLoS Comput. Biol.
Somnath Tagore, Alessandro Gorohovski, Lars Juhl Jensen, Milana Frenkel-Morgenstern
2019 J jnl
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Nucleic Acids Res.
Damian Szklarczyk, Annika L. Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T. Doncheva, John H. Morris, Peer Bork, Lars Juhl Jensen, Christian von Mering
2019 J jnl
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Nucleic Acids Res.
Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K. Forslund, Helen Cook, Daniel R. Mende, Ivica Letunic, Thomas Rattei, Lars Juhl Jensen, Christian von Mering, Peer Bork
2018 J jnl
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.
PLoS Comput. Biol.
David Westergaard, Hans Henrik Stærfeldt, Christian Tønsberg, Lars Juhl Jensen, Søren Brunak
2018 J jnl
LocText: relation extraction of protein localizations to assist database curation.
BMC Bioinform.
Juan Miguel Cejuela, Shrikant Vinchurkar, Tatyana Goldberg, Madhukar Sollepura Prabhu Shankar, Ashish Baghudana, Aleksandar Bojchevski, Carsten Uhlig, André Ofner, Pandu Raharja-Liu, Lars Juhl Jensen, Burkhard Rost
2018 J jnl
TISSUES 2.0: an integrative web resource on mammalian tissue expression.
Database J. Biol. Databases Curation
Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
2018 J jnl
TISSUES 2.0: an integrative web resource on mammalian tissue expression.
Database J. Biol. Databases Curation
Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
2018 J jnl
miRandola 2017: a curated knowledge base of non-invasive biomarkers.
Nucleic Acids Res.
Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Laganà, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars Juhl Jensen, Søren Brunak, Marco Pellegrini, Alfredo Ferro
2017 — conf
Creation and evaluation of a dictionary-based tagger for virus species and proteins.
BioNLP
Helen Cook, Rudolfs Berzins, Cristina Leal Rodriguez, Juan Miguel Cejuela, Lars Juhl Jensen
2017 J jnl
Drug target ontology to classify and integrate drug discovery data.
J. Biomed. Semant.
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J. Yang, Cristian Bologa, Tudor I. Oprea, Stephan C. Schürer
2017 J jnl
Pharos: Collating protein information to shed light on the druggable genome.
Nucleic Acids Res.
Dac-Trung Nguyen, Stephen L. Mathias, Cristian Bologa, Søren Brunak, Nicolas F. Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha
2017 J jnl
RAIN: RNA-protein Association and Interaction Networks.
Database J. Biol. Databases Curation
Alexander Junge, Jan C. Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T. Workman, Lars Juhl Jensen, Jan Gorodkin
2017 J jnl
TIN-X: target importance and novelty explorer.
Bioinform.
Daniel Cannon, Jeremy J. Yang, Stephen L. Mathias, Oleg Ursu, Subramani Mani, Anna Waller, Stephan C. Schürer, Lars Juhl Jensen, Larry A. Sklar, Cristian Bologa, Tudor I. Oprea
2017 J jnl
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Nucleic Acids Res.
Damian Szklarczyk, John H. Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T. Doncheva, Alexander Roth, Peer Bork, Lars Juhl Jensen, Christian von Mering
2016 — conf
A dictionary- and rule-based system for identification of bacteria and habitats in text.
BioNLP (Shared Task)
Helen Cook, Evangelos Pafilis, Lars Juhl Jensen
2016 J jnl
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.
Database J. Biol. Databases Curation
Evangelos Pafilis, Pier Luigi Buttigieg, Barbra Ferrell, Emiliano Pereira, Julia Schnetzer, Christos Arvanitidis, Lars Juhl Jensen
2016 — conf
One Tagger, Many Uses: Illustrating the Power of Ontologies in Dictionary-based Named Entity Recognition.
ICBO/BioCreative
Lars Juhl Jensen
2016 J jnl
Overview of the interactive task in BioCreative V.
Database J. Biol. Databases Curation
Qinghua Wang, Shabbir Syed-Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios V. Gkoutos, Afroza Khanam Irin, Lars Juhl Jensen, Silvia Jimenez, Toni Rose Jue, Ingrid M. Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew E. Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel M. Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole A. Vasilevsky, Xiaodong Wang, Andrew Chatr-aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna R. McEntyre, Sandra E. Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary L. Schaeffer, Cathy H. Wu, Lynette Hirschman, Cecilia N. Arighi
2016 J jnl
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Nucleic Acids Res.
Damian Szklarczyk, Alberto Santos, Christian von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn
2016 J jnl
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.
Bioinform.
Andrea Franceschini, Jianyi Lin, Christian von Mering, Lars Juhl Jensen
2016 J jnl
The SIDER database of drugs and side effects.
Nucleic Acids Res.
Michael Kuhn, Ivica Letunic, Lars Juhl Jensen, Peer Bork
2016 J jnl
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Nucleic Acids Res.
Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, Mathias C. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork
2015 J jnl
Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes.
Nucleic Acids Res.
Alberto Santos, Rasmus Wernersson, Lars Juhl Jensen
2015 J jnl
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.
Bioinform.
Evangelos Pafilis, Sune Pletscher-Frankild, Julia Schnetzer, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Katerina Vasileiadou, Patrick Leary, Jennifer Hammock, Katja Schulz, Cynthia Sims Parr, Christos Arvanitidis, Lars Juhl Jensen
2015 J jnl
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Nucleic Acids Res.
Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos, Kalliopi Tsafou, Michael Kuhn, Peer Bork, Lars Juhl Jensen, Christian von Mering
2015 — conf
Sharing annotations better: RESTful Open Annotation.
ACL (System Demonstrations)
Sampo Pyysalo, Jorge Campos, Juan Miguel Cejuela, Filip Ginter, Kai Hakala, Chen Li, Pontus Stenetorp, Lars Juhl Jensen
2014 J jnl
COMPARTMENTS: unification and visualization of protein subcellular localization evidence.
Database J. Biol. Databases Curation
Janos X. Binder, Sune Pletscher-Frankild, Kalliopi Tsafou, Christian Stolte, Seán I. O'Donoghue, Reinhard Schneider, Lars Juhl Jensen
2014 J jnl
Protein-driven inference of miRNA-disease associations.
Bioinform.
Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen
2014 J jnl
STITCH 4: integration of protein-chemical interactions with user data.
Nucleic Acids Res.
Michael Kuhn, Damian Szklarczyk, Sune Pletscher-Frankild, Thomas H. Blicher, Christian von Mering, Lars Juhl Jensen, Peer Bork
2014 J jnl
eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res.
Sean Powell, Kristoffer Forslund, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Jaime Huerta-Cepas, Toni Gabaldón, Thomas Rattei, Christopher J. Creevey, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork
2013 J jnl
Are graph databases ready for bioinformatics?
Bioinform.
Christian Theil Have, Lars Juhl Jensen
2013 J jnl
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text.
J. Am. Medical Informatics Assoc.
Robert Eriksson, Peter Bjødstrup Jensen, Sune Frankild, Lars Juhl Jensen, Søren Brunak
2013 C conf
OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction.
BIBE
Evangelos Pafilis, Georgios A. Pavlopoulos, Venkata P. Satagopam, Nikolas Papanikolaou, Heiko Horn, Christos Arvanitidis, Lars Juhl Jensen, Reinhard Schneider, Ioannis Iliopoulos
2013 J jnl
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Nucleic Acids Res.
Andrea Franceschini, Damian Szklarczyk, Sune Frankild, Michael Kuhn, Milan Simonovic, Alexander Roth, Jianyi Lin, Pablo Minguez, Peer Bork, Christian von Mering, Lars Juhl Jensen
2012 J jnl
DistiLD Database: diseases and traits in linkage disequilibrium blocks.
Nucleic Acids Res.
Albert Pallejà, Heiko Horn, Sabrina Eliasson, Lars Juhl Jensen
2012 J jnl
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs.
BMC Syst. Biol.
Larry Croft, Damian Szklarczyk, Lars Juhl Jensen, Jan Gorodkin
2012 J jnl
STITCH 3: zooming in on protein-chemical interactions.
Nucleic Acids Res.
Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Christian von Mering, Lars Juhl Jensen, Peer Bork
2012 J jnl
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res.
Sean Powell, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Michael Kuhn, Jean Muller, Roland Arnold, Thomas Rattei, Ivica Letunic, Tobias Doerks, Lars Juhl Jensen, Christian von Mering, Peer Bork
2011 J jnl
BioStar: An Online Question & Answer Resource for the Bioinformatics Community.
PLoS Comput. Biol.
Laurence D. Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall'Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S. Pedersen, Mary E. Mangan, Christopher A. Miller, István Albert
2011 J jnl
Phospho.ELM: a database of phosphorylation sites - update 2011.
Nucleic Acids Res.
Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars Juhl Jensen, Toby J. Gibson, Francesca Diella
2011 J jnl
Ten Simple Rules for Getting Help from Online Scientific Communities.
PLoS Comput. Biol.
Giovanni Marco Dall'Olio, Jacopo Marino, Michael Schubert, Kevin L. Keys, Melanie I. Stefan, Colin S. Gillespie, Pierre Poulain, Khader Shameer, Robert Sugar, Brandon M. Invergo, Lars Juhl Jensen, Jaume Bertranpetit, Hafid Laayouni
2011 J jnl
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Nucleic Acids Res.
Damian Szklarczyk, Andrea Franceschini, Michael Kuhn, Milan Simonovic, Alexander Roth, Pablo Minguez, Tobias Doerks, Manuel Stark, Jean Muller, Peer Bork, Lars Juhl Jensen, Christian von Mering
2011 J jnl
The rise and fall of supervised machine learning techniques.
Bioinform.
Lars Juhl Jensen, Alex Bateman
2011 J jnl
Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts.
PLoS Comput. Biol.
Francisco S. Roque, Peter Bjødstrup Jensen, Henriette Schmock, Marlene Dalgaard, Massimo Andreatta, Thomas Folkmann Hansen, Karen Søeby, Søren Bredkjær, Anders Juul, Thomas Werge, Lars Juhl Jensen, Søren Brunak
2010 J jnl
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results.
Nucleic Acids Res.
Nicholas Paul Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, Thomas Skøt Jensen
2010 J jnl
Drug-Induced Regulation of Target Expression.
PLoS Comput. Biol.
Murat Iskar, Monica Campillos, Michael Kuhn, Lars Juhl Jensen, Vera van Noort, Peer Bork
2010 J jnl
Reflect: A practical approach to web semantics.
J. Web Semant.
Seán I. O'Donoghue, Heiko Horn, Evangelos Pafilis, Sven Haag, Michael Kuhn, Venkata P. Satagopam, Reinhard Schneider, Lars Juhl Jensen
2010 J jnl
STITCH 2: an interaction network database for small molecules and proteins.
Nucleic Acids Res.
Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer, Peer Bork
2010 J jnl
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Nucleic Acids Res.
Jean Muller, Damian Szklarczyk, Philippe Julien, Ivica Letunic, Alexander Roth, Michael Kuhn, Sean Powell, Christian von Mering, Tobias Doerks, Lars Juhl Jensen, Peer Bork
2009 J jnl
Microblogging the ISMB: A New Approach to Conference Reporting.
PLoS Comput. Biol.
Neil F. W. Saunders, Pedro Beltrão, Lars Juhl Jensen, Daniel Jurczak, Roland Krause, Michael Kuhn, Shirley Wu
2009 J jnl
STRING 8 - a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Res.
Lars Juhl Jensen, Michael Kuhn, Manuel Stark, Samuel Chaffron, Christopher J. Creevey, Jean Muller, Tobias Doerks, Philippe Julien, Alexander Roth, Milan Simonovic, Peer Bork, Christian von Mering
2008 J jnl
Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments.
Nucleic Acids Res.
Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, Thomas Skøt Jensen
2008 J jnl
NetworKIN: a resource for exploring cellular phosphorylation networks.
Nucleic Acids Res.
Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, Tony Pawson
2008 J jnl
STITCH: interaction networks of chemicals and proteins.
Nucleic Acids Res.
Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, Peer Bork
2008 J jnl
SuperTarget and Matador: resources for exploring drug-target relationships.
Nucleic Acids Res.
Stefan Günther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen, Reinhard Schneider, Roman Skoblo, Robert B. Russell, Philip E. Bourne, Peer Bork, Robert Preissner
2008 J jnl
eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic Acids Res.
Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, Peer Bork
2007 J jnl
STRING 7 - recent developments in the integration and prediction of protein interactions.
Nucleic Acids Res.
Christian von Mering, Lars Juhl Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, Peer Bork
2006 J jnl
Extraction of regulatory gene/protein networks from Medline.
Bioinform.
Jasmin Saric, Lars Juhl Jensen, Rossitza Ouzounova, Isabel Rojas, Peer Bork
2005 J jnl
Comparison of computational methods for the identification of cell cycle-regulated genes.
Bioinform.
Ulrik de Lichtenberg, Lars Juhl Jensen, Anders Fausbøll, Thomas Skøt Jensen, Peer Bork, Søren Brunak
2005 J jnl
Extraction of Transcript Diversity from Scientific Literature.
PLoS Comput. Biol.
Parantu K. Shah, Lars Juhl Jensen, Stéphanie Boué, Peer Bork
2005 J jnl
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res.
Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork
2004 J jnl
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Nucleic Acids Res.
Lars Juhl Jensen, Julien Lagarde, Christian von Mering, Peer Bork
2004 A* conf
Extracting Regulatory Gene Expression Networks From Pubmed.
ACL
Jasmin Saric, Lars Juhl Jensen, Peer Bork, Rossitza Ouzounova, Isabel Rojas
2004 J jnl
Large-scale extraction of gene regulation for model organisms in an ontological context.
Silico Biol.
Jasmin Saric, Lars Juhl Jensen, Isabel Rojas
2003 J jnl
Prediction of human protein function according to Gene Ontology categories.
Bioinform.
Lars Juhl Jensen, Ramneek Gupta, Hans Henrik Stærfeldt, Søren Brunak
2000 J jnl
Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation.
Bioinform.
Lars Juhl Jensen, Steen Knudsen