Assembly reconciliation. - Aleksey V. Zimin; Douglas R. Smith; Granger G. Sutton; James A. Yorke (Bioinform., 2008)

The MaSuRCA genome assembler. - Aleksey V. Zimin; Guillaume Marçais; Daniela Puiu; Michael Roberts; Steven L. Salzberg; James A. Yorke (Bioinform., 2013)

MUMmer4: A fast and versatile genome alignment system. - Guillaume Marçais; Arthur L. Delcher; Adam M. Phillippy; Rachel Coston; Steven L. Salzberg; Aleksey V. Zimin (PLoS Comput. Biol., 2018)

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. - Aleksey V. Zimin; Steven L. Salzberg (PLoS Comput. Biol., 2020)

The SAMBA tool uses long reads to improve the contiguity of genome assemblies. - Aleksey V. Zimin; Steven L. Salzberg (PLoS Comput. Biol., 2022)

Metagenomic classification with KrakenUniq on low-memory computers. - Christopher Pockrandt; Aleksey V. Zimin; Steven L. Salzberg (J. Open Source Softw., 2022)

JASPER: A fast genome polishing tool that improves accuracy of genome assemblies. - Alina Guo; Steven L. Salzberg; Aleksey V. Zimin (PLoS Comput. Biol., 2023)