Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes. - Ilya Minkin; Anand Patel; Mikhail Kolmogorov; Nikolay Vyahhi; Son K. Pham (WABI, 2013)

Ragout - a reference-assisted assembly tool for bacterial genomes. - Mikhail Kolmogorov; Brian J. Raney; Benedict Paten; Son K. Pham (Bioinform., 2014)

Assembly of long error-prone reads using de Bruijn graphs. - Yu Lin 001; Jeffrey Yuan; Mikhail Kolmogorov; Max W. Shen; Mark Chaisson; Pavel A. Pevzner (Proc. Natl. Acad. Sci. USA, 2016)

Single-molecule protein identification by sub-nanopore sensors. - Mikhail Kolmogorov; Eamonn Kennedy; Zhuxin Dong; Gregory Timp; Pavel A. Pevzner (PLoS Comput. Biol., 2017)

Assembly of Long Error-Prone Reads Using Repeat Graphs. - Mikhail Kolmogorov; Jeffrey Yuan; Yu Lin 001; Pavel A. Pevzner (RECOMB, 2018)

Synteny Paths for Assembly Graphs Comparison. - Evgeny Polevikov; Mikhail Kolmogorov (WABI, 2019)

Assembly Graph Browser: interactive visualization of assembly graphs. - Alla Mikheenko; Mikhail Kolmogorov (Bioinform., 2019)