Frameshift detection in prokaryotic genomic sequences. - Andrey Kislyuk; Alexandre Lomsadze; Alla L. Lapidus; Mark Borodovsky (Int. J. Bioinform. Res. Appl., 2009)

Identification of protein coding regions in RNA transcripts. - Shiyuyun Tang; Alexandre Lomsadze; Mark Borodovsky (BCB, 2014)

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. - Katharina Jasmin Hoff; Simone Lange; Alexandre Lomsadze; Mark Borodovsky; Mario Stanke (Bioinform., 2016)

StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. - Karl Gemayel; Alexandre Lomsadze; Mark Borodovsky (Frontiers Bioinform., 2021)