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)

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)

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)

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)

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)

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)

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)

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)

WeGET: predicting new genes for molecular systems by weighted co-expression. - Radek Szklarczyk; Wout Megchelenbrink; Pavel Cizek; Marie Ledent; Gonny Velemans; Damian Szklarczyk; Martijn A. Huynen (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)

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)

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. - Davide Heller; Damian Szklarczyk; Christian von Mering (BMC Bioinform., 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)

The Quest for Orthologs benchmark service and consensus calls in 2020. - Adrian M. Altenhoff; Javier Garrayo-Ventas; Salvatore Cosentino; David Emms; Natasha M. Glover; Ana Hernández-Plaza; Yannis Nevers; Vicky Sundesha; Damian Szklarczyk; José María Fernández 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

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)

Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments. - Annika L. Gable; Damian Szklarczyk; David Lyon; João F. Matias Rodrigues; Christian von Mering (Briefings Bioinform., 2022)

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. - Anthony Fullam; Ivica Letunic; Thomas S. B. Schmidt; Quinten R. Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn 004; Martin Larralde; Oleksandr M. Maistrenko; Lukas Malfertheiner; Alessio Milanese; João F. Matias Rodrigues; et al. (Nucleic Acids Res., 2023)

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)

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)