Automatic clustering of orthologs and inparalogs shared by multiple proteomes. - Andrey Alexeyenko; Ivica Tamas; Gang Liu; Erik L. L. Sonnhammer (ISMB (Supplement of Bioinformatics), 2006)

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. - Andrey Alexeyenko; Woojoo Lee; Maria Pernemalm; Justin Guegan; Philippe Dessen; Vladimir Lazar; Janne Lehtiö; Yudi Pawitan (BMC Bioinform., 2012)

Comparative interactomics with Funcoup 2.0. - Andrey Alexeyenko; Thomas Schmitt 003; Andreas Tjärnberg; Dimitri Guala; Oliver Frings; Erik L. L. Sonnhammer (Nucleic Acids Res., 2012)

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis. - Simon Kebede Merid; Daria Goranskaya; Andrey Alexeyenko (BMC Bioinform., 2014)

NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis. - Ashwini Jeggari; Andrey Alexeyenko (BMC Bioinform., 2017)

Using Erlang in Research and Education in a Technical University. - Iurii Petrov; Andrey Alexeyenko; Galina Ivanova (Comput. Sci., 2018)

EviNet: a web platform for network enrichment analysis with flexible definition of gene sets. - Ashwini Jeggari; Zhanna Alekseenko; Iurii Petrov; José M. Dias; Johan Ericson; Andrey Alexeyenko (Nucleic Acids Res., 2018)