JCoast - A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. - Michael Richter; Thierry Lombardot; Ivaylo Kostadinov; Renzo Kottmann; Melissa Beth Duhaime; Jörg Peplies; Frank Oliver Glöckner (BMC Bioinform., 2008)

Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function. - Wolfgang Hankeln; Pier Luigi Buttigieg; Ivaylo Kostadinov; Renzo Kottmann; Pelin Yilmaz; Melissa Beth Duhaime; Frank Oliver Glöckner (BCB, 2010)

Megx.net: integrated database resource for marine ecological genomics. - Renzo Kottmann; Ivaylo Kostadinov; Melissa Beth Duhaime; Pier Luigi Buttigieg; Pelin Yilmaz; Wolfgang Hankeln; Jost Waldmann; Frank Oliver Glöckner (Nucleic Acids Res., 2010)

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. - Geoffrey D. Hannigan; Melissa Beth Duhaime; Danai Koutra; Patrick D. Schloss (PLoS Comput. Biol., 2018)

Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks. - G. Eric Bastien; Rachel N. Cable; Cecelia Batterbee; A. J. Wing; Luis Zaman; Melissa Beth Duhaime (PLoS Comput. Biol., 2024)