Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. - Lars Juhl Jensen; Steen Knudsen (Bioinform., 2000)

Prediction of human protein function according to Gene Ontology categories. - Lars Juhl Jensen; Ramneek Gupta; Hans Henrik Stærfeldt; Søren Brunak (Bioinform., 2003)

Extracting Regulatory Gene Expression Networks From Pubmed. - Jasmin Saric; Lars Juhl Jensen; Peer Bork; Rossitza Ouzounova; Isabel Rojas (ACL, 2004)

Large-scale extraction of gene regulation for model organisms in an ontological context. - Jasmin Saric; Lars Juhl Jensen; Isabel Rojas (Silico Biol., 2004)

ArrayProspector: a web resource of functional associations inferred from microarray expression data. - Lars Juhl Jensen; Julien Lagarde; Christian von Mering; Peer Bork (Nucleic Acids Res., 2004)

Comparison of computational methods for the identification of cell cycle-regulated genes. - Ulrik de Lichtenberg; Lars Juhl Jensen; Anders Fausbøll; Thomas Skøt Jensen; Peer Bork; Søren Brunak (Bioinform., 2005)

STRING: known and predicted protein-protein associations, integrated and transferred across organisms. - Christian von Mering; Lars Juhl Jensen; Berend Snel; Sean D. Hooper; Markus Krupp; Mathilde Foglierini; Nelly Jouffre; Martijn A. Huynen; Peer Bork (Nucleic Acids Res., 2005)

Extraction of Transcript Diversity from Scientific Literature. - Parantu K. Shah; Lars Juhl Jensen; Stéphanie Boué; Peer Bork (PLoS Comput. Biol., 2005)

Extraction of regulatory gene/protein networks from Medline. - Jasmin Saric; Lars Juhl Jensen; Rossitza Ouzounova; Isabel Rojas; Peer Bork (Bioinform., 2006)

STRING 7 - recent developments in the integration and prediction of protein interactions. - Christian von Mering; Lars Juhl Jensen; Michael Kuhn 004; Samuel Chaffron; Tobias Doerks; Beate Krüger; Berend Snel; Peer Bork (Nucleic Acids Res., 2007)

Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments. - Nicholas Paul Gauthier; Malene Erup Larsen; Rasmus Wernersson; Ulrik de Lichtenberg; Lars Juhl Jensen; Søren Brunak; Thomas Skøt Jensen (Nucleic Acids Res., 2008)

SuperTarget and Matador: resources for exploring drug-target relationships. - Stefan Günther; Michael Kuhn 004; Mathias Dunkel; Monica Campillos; Christian Senger; Evangelia Petsalaki; Jessica Ahmed; Eduardo Garcia Urdiales; Andreas Gewiess; Lars Juhl Jensen; Reinhard Schneider 002; Roman Skoblo; et al. (Nucleic Acids Res., 2008)

eggNOG: automated construction and annotation of orthologous groups of genes. - Lars Juhl Jensen; Philippe Julien; Michael Kuhn 004; Christian von Mering; Jean Muller; Tobias Doerks; Peer Bork (Nucleic Acids Res., 2008)

STITCH: interaction networks of chemicals and proteins. - Michael Kuhn 004; Christian von Mering; Monica Campillos; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2008)

NetworKIN: a resource for exploring cellular phosphorylation networks. - Rune Linding; Lars Juhl Jensen; Adrian Pasculescu; Marina Olhovsky; Karen Colwill; Peer Bork; Michael B. Yaffe; Tony Pawson (Nucleic Acids Res., 2008)

STRING 8 - a global view on proteins and their functional interactions in 630 organisms. - Lars Juhl Jensen; Michael Kuhn 004; Manuel Stark; Samuel Chaffron; Christopher J. Creevey; Jean Muller; Tobias Doerks; Philippe Julien; Alexander Roth 001; Milan Simonovic; Peer Bork; Christian von Mering (Nucleic Acids Res., 2009)

Microblogging the ISMB: A New Approach to Conference Reporting. - Neil F. W. Saunders; Pedro Beltrão; Lars Juhl Jensen; Daniel Jurczak; Roland Krause; Michael Kuhn 004; Shirley Wu (PLoS Comput. Biol., 2009)

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. - Nicholas Paul Gauthier; Lars Juhl Jensen; Rasmus Wernersson; Søren Brunak; Thomas Skøt Jensen (Nucleic Acids Res., 2010)

STITCH 2: an interaction network database for small molecules and proteins. - Michael Kuhn 004; Damian Szklarczyk; Andrea Franceschini; Monica Campillos; Christian von Mering; Lars Juhl Jensen; Andreas Beyer; Peer Bork (Nucleic Acids Res., 2010)

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. - Jean Muller; Damian Szklarczyk; Philippe Julien; Ivica Letunic; Alexander Roth 001; Michael Kuhn 004; Sean Powell; Christian von Mering; Tobias Doerks; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2010)

Drug-Induced Regulation of Target Expression. - Murat Iskar; Monica Campillos; Michael Kuhn 004; Lars Juhl Jensen; Vera van Noort; Peer Bork (PLoS Comput. Biol., 2010)

Reflect: A practical approach to web semantics. - Seán I. O'Donoghue; Heiko Horn; Evangelos Pafilis; Sven Haag; Michael Kuhn 004; Venkata P. Satagopam; Reinhard Schneider 002; Lars Juhl Jensen (J. Web Semant., 2010)

The rise and fall of supervised machine learning techniques. - Lars Juhl Jensen; Alex Bateman (Bioinform., 2011)

Phospho.ELM: a database of phosphorylation sites - update 2011. - Holger Dinkel; Claudia Chica; Allegra Via; Cathryn M. Gould; Lars Juhl Jensen; Toby J. Gibson; Francesca Diella (Nucleic Acids Res., 2011)

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. - Damian Szklarczyk; Andrea Franceschini; Michael Kuhn 004; Milan Simonovic; Alexander Roth 001; Pablo Minguez; Tobias Doerks; Manuel Stark; Jean Muller; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2011)

Ten Simple Rules for Getting Help from Online Scientific Communities. - 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; et al. (PLoS Comput. Biol., 2011)

BioStar: An Online Question & Answer Resource for the Bioinformatics Community. - 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 002; István Albert (PLoS Comput. Biol., 2011)

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

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. - Larry Croft; Damian Szklarczyk; Lars Juhl Jensen; Jan Gorodkin (BMC Syst. Biol., 2012)

STITCH 3: zooming in on protein-chemical interactions. - Michael Kuhn 004; Damian Szklarczyk; Andrea Franceschini; Christian von Mering; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2012)

DistiLD Database: diseases and traits in linkage disequilibrium blocks. - Albert Pallejà; Heiko Horn; Sabrina Eliasson; Lars Juhl Jensen (Nucleic Acids Res., 2012)

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. - Sean Powell; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth 001; Michael Kuhn 004; Jean Muller; Roland Arnold; Thomas Rattei; Ivica Letunic; Tobias Doerks; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2012)

OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction. - Evangelos Pafilis; Georgios A. Pavlopoulos; Venkata P. Satagopam; Nikolas Papanikolaou; Heiko Horn; Christos Arvanitidis; Lars Juhl Jensen; Reinhard Schneider 002; Ioannis Iliopoulos (BIBE, 2013)

Are graph databases ready for bioinformatics? - Christian Theil Have; Lars Juhl Jensen (Bioinform., 2013)

Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. - Robert Eriksson; Peter Bjødstrup Jensen; Sune Frankild; Lars Juhl Jensen; Søren Brunak (J. Am. Medical Informatics Assoc., 2013)

STRING v9.1: protein-protein interaction networks, with increased coverage and integration. - Andrea Franceschini; Damian Szklarczyk; Sune Frankild; Michael Kuhn 004; Milan Simonovic; Alexander Roth 001; Jianyi Lin; Pablo Minguez; Peer Bork; Christian von Mering; Lars Juhl Jensen (Nucleic Acids Res., 2013)

COMPARTMENTS: unification and visualization of protein subcellular localization evidence. - Janos X. Binder; Sune Pletscher-Frankild; Kalliopi Tsafou; Christian Stolte; Seán I. O'Donoghue; Reinhard Schneider 002; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2014)

Protein-driven inference of miRNA-disease associations. - Søren Mørk; Sune Pletscher-Frankild; Albert Pallejà Caro; Jan Gorodkin; Lars Juhl Jensen (Bioinform., 2014)

STITCH 4: integration of protein-chemical interactions with user data. - Michael Kuhn 004; Damian Szklarczyk; Sune Pletscher-Frankild; Thomas H. Blicher; Christian von Mering; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2014)

eggNOG v4.0: nested orthology inference across 3686 organisms. - Sean Powell; Kristoffer Forslund; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth 001; Jaime Huerta-Cepas; Toni Gabaldón; Thomas Rattei; Christopher J. Creevey; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2014)

Sharing annotations better: RESTful Open Annotation. - Sampo Pyysalo; Jorge Campos; Juan Miguel Cejuela; Filip Ginter; Kai Hakala; Chen Li; Pontus Stenetorp; Lars Juhl Jensen (ACL (System Demonstrations), 2015)

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. - 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; et al. (Bioinform., 2015)

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes. - Alberto Santos; Rasmus Wernersson; Lars Juhl Jensen (Nucleic Acids Res., 2015)

STRING v10: protein-protein interaction networks, integrated over the tree of life. - Damian Szklarczyk; Andrea Franceschini; Stefan Wyder; Kristoffer Forslund; Davide Heller; Jaime Huerta-Cepas; Milan Simonovic; Alexander Roth 001; Alberto Santos; Kalliopi Tsafou; Michael Kuhn 004; Peer Bork; et al. (Nucleic Acids Res., 2015)

A dictionary- and rule-based system for identification of bacteria and habitats in text. - Helen Cook; Evangelos Pafilis; Lars Juhl Jensen (BioNLP (Shared Task), 2016)

One Tagger, Many Uses: Illustrating the Power of Ontologies in Dictionary-based Named Entity Recognition. - Lars Juhl Jensen (ICBO/BioCreative, 2016)

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. - Evangelos Pafilis; Pier Luigi Buttigieg; Barbra Ferrell; Emiliano Pereira; Julia Schnetzer; Christos Arvanitidis; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2016)

Overview of the interactive task in BioCreative V. - Qinghua Wang 003; Shabbir Syed-Abdul; Lara Almeida; Sophia Ananiadou; Yalbi I. Balderas-Martínez; Riza Batista-Navarro; David Campos 001; Lucy Chilton; Hui-Jou Chou; Gabriela Contreras; Laurel Cooper; Hong-Jie Dai; et al. (Database J. Biol. Databases Curation, 2016)

SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. - Andrea Franceschini; Jianyi Lin; Christian von Mering; Lars Juhl Jensen (Bioinform., 2016)

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. - Jaime Huerta-Cepas; Damian Szklarczyk; Kristoffer Forslund; Helen Cook; Davide Heller; Mathias C. Walter; Thomas Rattei; Daniel R. Mende; Shinichi Sunagawa; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2016)

The SIDER database of drugs and side effects. - Michael Kuhn 004; Ivica Letunic; Lars Juhl Jensen; Peer Bork (Nucleic Acids Res., 2016)

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. - Damian Szklarczyk; Alberto Santos; Christian von Mering; Lars Juhl Jensen; Peer Bork; Michael Kuhn 004 (Nucleic Acids Res., 2016)

Creation and evaluation of a dictionary-based tagger for virus species and proteins. - Helen Cook; Rudolfs Berzins; Cristina Leal Rodriguez; Juan Miguel Cejuela; Lars Juhl Jensen (BioNLP, 2017)

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

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

Drug target ontology to classify and integrate drug discovery data. - 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; et al. (J. Biomed. Semant., 2017)

Pharos: Collating protein information to shed light on the druggable genome. - 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; et al. (Nucleic Acids Res., 2017)

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. - Damian Szklarczyk; John H. Morris; Helen Cook; Michael Kuhn 004; Stefan Wyder; Milan Simonovic; Alberto Santos; Nadezhda T. Doncheva; Alexander Roth 001; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2017)

TISSUES 2.0: an integrative web resource on mammalian tissue expression. - Oana Palasca; Alberto Santos; Christian Stolte; Jan Gorodkin; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2018)

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

miRandola 2017: a curated knowledge base of non-invasive biomarkers. - Francesco Russo 004; Sebastiano Di Bella; Federica Vannini; Gabriele Berti; Flavia Scoyni; Helen Cook; Alberto Santos; Giovanni Nigita; Vincenzo Bonnici; Alessandro Laganà; Filippo Geraci; Alfredo Pulvirenti; et al. (Nucleic Acids Res., 2018)

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. - David Westergaard; Hans Henrik Stærfeldt; Christian Tønsberg; Lars Juhl Jensen; Søren Brunak (PLoS Comput. Biol., 2018)

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles. - Xiaoyong Pan; Lars Juhl Jensen; Jan Gorodkin (Bioinform., 2019)

Design, implementation, and operation of a rapid, robust named entity recognition web service. - Sune Pletscher-Frankild; Lars Juhl Jensen (J. Cheminformatics, 2019)

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

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

ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins. - Somnath Tagore; Alessandro Gorohovski; Lars Juhl Jensen; Milana Frenkel-Morgenstern (PLoS Comput. Biol., 2019)

Using National Electronic Health Care Registries to Analyse and Predict Alcoholic Liver Disease. - Dhouha Grissa; Ditlev Nytoft Rasmussen; Aleksander Krag; Søren Brunak; Lars Juhl Jensen (EGC, 2020)

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. - Alexander Junge; Lars Juhl Jensen (Bioinform., 2020)

Visualize omics data on networks with Omics Visualizer, a Cytoscape App. - Marc Legeay; Nadezhda T. Doncheva; John H. Morris; Lars Juhl Jensen (F1000Research, 2020)

Alcoholic liver disease: A registry view on comorbidities and disease prediction. - Dhouha Grissa; Ditlev Nytoft Rasmussen; Aleksander Krag; Søren Brunak; Lars Juhl Jensen (PLoS Comput. Biol., 2020)

TIGA: target illumination GWAS analytics. - Jeremy J. Yang; Dhouha Grissa; Christophe G. Lambert; Cristian Bologa; Stephen L. Mathias; Anna Waller; David J. Wild 001; Lars Juhl Jensen; Tudor I. Oprea (Bioinform., 2021)

TCRD and Pharos 2021: mining the human proteome for disease biology. - 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; et al. (Nucleic Acids Res., 2021)

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

Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration. - Dhouha Grissa; Alexander Junge; Tudor I. Oprea; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2022)

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

Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies. - Marie Locard-Paulet; Oana Palasca; Lars Juhl Jensen (PLoS Comput. Biol., 2022)

eggNOG 6.0: enabling comparative genomics across 12 535 organisms. - 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; et al. (Nucleic Acids Res., 2023)

Pharos 2023: an integrated resource for the understudied human proteome. - 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; et al. (Nucleic Acids Res., 2023)

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

Graph databases in systems biology: a systematic review. - Ilya Mazein; Adrien Rougny; Alexander Mazein; Ron Henkel; Lea Gütebier; Lea Michaelis; Marek Ostaszewski; Reinhard Schneider 002; Venkata P. Satagopam; Lars Juhl Jensen; Dagmar Waltemath; Judith A. H. Wodke; et al. (Briefings Bioinform., 2024)

ECCB2024: The 23rd European Conference on Computational Biology. - 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; et al. (Bioinform., 2024)

Improving dictionary-based named entity recognition with deep learning. - Katerina C. Nastou; Mikaela Koutrouli; Sampo Pyysalo; Lars Juhl Jensen (Bioinform., 2024)

RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature. - Katerina C. Nastou; Farrokh Mehryary; Tomoko Ohta; Jouni Luoma; Sampo Pyysalo; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2024)

FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data. - Mikaela Koutrouli; Katerina C. Nastou; Pau Piera Líndez; Robbin Bouwmeester; Simon Rasmussen; Lennart Martens; Lars Juhl Jensen (Bioinform., 2024)

LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations. - Esmaeil Nourani; Evangelia-Mantelena Makri; Xiqing Mao; Sampo Pyysalo; Søren Brunak; Katerina C. Nastou; Lars Juhl Jensen (Database J. Biol. Databases Curation, 2025)