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)

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)

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)

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)

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)

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)