XRate: a fast prototyping, training and annotation tool for phylo-grammars. - Peter S. Klosterman; Andrew V. Uzilov; Yuri R. Bendaña; Robert K. Bradley; Sharon Chao; Carolin Kosiol; Nick Goldman; Ian H. Holmes (BMC Bioinform., 2006)

Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome. - Carolin Kosiol; Lee Bofkin; Simon Whelan (J. Biomed. Informatics, 2006)

Gaussian process test for high-throughput sequencing time series: application to experimental evolution. - Hande Topa; Ágnes Jónás; Robert Kofler; Carolin Kosiol; Antti Honkela (Bioinform., 2015)

Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed). - Claus Vogl; Mariia Karapetiants; Burçin Yildirim; Hrönn Kjartansdóttir; Carolin Kosiol; Juraj Bergman; Michal Majka; Lynette Caitlin Mikula (BMC Bioinform., 2024)