Proteome Analysis: Application of InterPro and CluSTr for the Functional Classification of Proteins in Whole Genomes. - Margaret Biswas; Rolf Apweiler; Wolfgang Fleischmann; Alexander Kanapin; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Thomas M. Oinn; Isabelle Phan; Evgeni M. Zdobnov (German Conference on Bioinformatics, 2000)

InterPro-an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Bioinform., 2000)

InterProScan - an integration platform for the signature-recognition methods in InterPro. - Evgeni M. Zdobnov; Rolf Apweiler (Bioinform., 2001)

The InterPro database, an integrated documentation resource for protein families, domains and functional sites. - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Nucleic Acids Res., 2001)

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. - Rolf Apweiler; Margaret Biswas; Wolfgang Fleischmann; Alexander Kanapin; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Isabelle Phan; Evgeni M. Zdobnov (Nucleic Acids Res., 2001)

CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins. - Evgenia V. Kriventseva; Wolfgang Fleischmann; Evgeni M. Zdobnov; Rolf Apweiler (Nucleic Acids Res., 2001)

Bioinformatics: Using the Molecular Biology Data. - Evgeni M. Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold (Essentials of Genomics and Bioinformatics, 2002)

Interactive InterPro-based comparisons of proteins in whole genomes. - Alexander Kanapin; Rolf Apweiler; Margaret Biswas; Wolfgang Fleischmann; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Thomas M. Oinn; Isabelle Phan; Florence Servant; et al. (Bioinform., 2002)

The EBI SRS server-recent developments. - Evgeni M. Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold (Bioinform., 2002)

The EBI SRS server-new features. - Evgeni M. Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold (Bioinform., 2002)

The InterPro Database, 2003 brings increased coverage and new features. - Nicola J. Mulder; Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Philipp Bucher; Richard R. Copley; et al. (Nucleic Acids Res., 2003)

VectorBase: a home for invertebrate vectors of human pathogens. - Daniel Lawson; Peter Arensburger; Peter Atkinson; Nora J. Besansky; Robert V. Bruggner; Ryan Butler; Kathryn S. Campbell; George K. Christophides; Scott Christley; Emmanuel Dialynas; David B. Emmert; Martin Hammond; et al. (Nucleic Acids Res., 2007)

OrthoDB: the hierarchical catalog of eukaryotic orthologs. - Evgenia V. Kriventseva; Nazim Rahman; Octavio Espinosa; Evgeni M. Zdobnov (Nucleic Acids Res., 2008)

miROrtho: computational survey of microRNA genes. - Daniel Gerlach; Evgenia V. Kriventseva; Nazim Rahman; Charles E. Vejnar; Evgeni M. Zdobnov (Nucleic Acids Res., 2009)

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. - Thomas Junier; Evgeny M. Zdobnov (Bioinform., 2010)

Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances. - Jaebum Kim; Ryan Cunningham; Brian James; Stefan Wyder; Joshua D. Gibson; Oliver Niehuis; Evgeny M. Zdobnov; Hugh M. Robertson; Gene E. Robinson; John H. Werren; Saurabh Sinha (PLoS Comput. Biol., 2010)

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. - Robert M. Waterhouse; Evgeny M. Zdobnov; Fredrik Tegenfeldt; Jia Li; Evgenia V. Kriventseva (Nucleic Acids Res., 2011)

miRmap web: comprehensive microRNA target prediction online. - Charles E. Vejnar; Matthias Blum; Evgeny M. Zdobnov (Nucleic Acids Res., 2013)

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. - Robert M. Waterhouse; Fredrik Tegenfeldt; Jia Li; Evgeny M. Zdobnov; Evgenia V. Kriventseva (Nucleic Acids Res., 2013)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. - Felipe A. Simão; Robert M. Waterhouse; Panagiotis Ioannidis 001; Evgenia V. Kriventseva; Evgeny M. Zdobnov (Bioinform., 2015)

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. - Evgenia V. Kriventseva; Fredrik Tegenfeldt; Tom J. Petty; Robert M. Waterhouse; Felipe A. Simão; Igor A. Pozdnyakov; Panagiotis Ioannidis 001; Evgeny M. Zdobnov (Nucleic Acids Res., 2015)

CEGA - a catalog of conserved elements from genomic alignments. - Aline Dousse; Thomas Junier; Evgeny M. Zdobnov (Nucleic Acids Res., 2016)

Understanding key features of bacterial restriction-modification systems through quantitative modeling. - Andjela Rodic; Bojana Blagojevic; Evgeny M. Zdobnov; Magdalena Djordjevic; Marko Djordjevic (BMC Syst. Biol., 2017)

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. - Evgeny M. Zdobnov; Fredrik Tegenfeldt; Dmitry Kuznetsov; Robert M. Waterhouse; Felipe A. Simão; Panagiotis Ioannidis 001; Mathieu Seppey; Alexis Loetscher; Evgenia V. Kriventseva (Nucleic Acids Res., 2017)

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. - Evgenia V. Kriventseva; Dmitry Kuznetsov; Fredrik Tegenfeldt; Mosè Manni; Renata Dias; Felipe A. Simão; Evgeny M. Zdobnov (Nucleic Acids Res., 2019)

Phigaro: high-throughput prophage sequence annotation. - Elizaveta V. Starikova; Polina O. Tikhonova; Nikita A. Prianichnikov; Chris M. Rands; Evgeny M. Zdobnov; Elena N. Ilina; Vadim M. Govorun (Bioinform., 2020)

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. - Silas Kieser; Joseph Brown; Evgeny M. Zdobnov; Mirko Trajkovski; Lee Ann McCue (BMC Bioinform., 2020)

OrthoDB in 2020: evolutionary and functional annotations of orthologs. - Evgeny M. Zdobnov; Dmitry Kuznetsov; Fredrik Tegenfeldt; Mosè Manni; Matthew Berkeley; Evgenia V. Kriventseva (Nucleic Acids Res., 2021)

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart. - Silas Kieser; Evgeny M. Zdobnov; Mirko Trajkovski (PLoS Comput. Biol., 2022)

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. - Dmitry Kuznetsov; Fredrik Tegenfeldt; Mosè Manni; Mathieu Seppey; Matthew Berkeley; Evgenia V. Kriventseva; Evgeny M. Zdobnov (Nucleic Acids Res., 2023)