DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. - Son K. Pham; Pavel A. Pevzner (Bioinform., 2010)

Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. - Paul Medvedev; Son K. Pham; Mark Chaisson; Glenn Tesler; Pavel A. Pevzner (J. Comput. Biol., 2011)

From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. - Nikolay Vyahhi; Alex Pyshkin; Son K. Pham; Pavel A. Pevzner (WABI, 2012)

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. - Anton Bankevich; Sergey Nurk; Dmitry Antipov; Alexey A. Gurevich; Mikhail Dvorkin; Alexander S. Kulikov; Valery M. Lesin; Sergey I. Nikolenko; Son K. Pham; Andrey D. Prjibelski; Alex Pyshkin; Alexander Sirotkin 001; et al. (J. Comput. Biol., 2012)

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)

Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. - Son K. Pham; Dmitry Antipov; Alexander Sirotkin 001; Glenn Tesler; Pavel A. Pevzner; Max A. Alekseyev (J. Comput. Biol., 2013)

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

ExSPAnder: a universal repeat resolver for DNA fragment assembly. - Andrey D. Prjibelski; Irina Vasilinetc; Anton Bankevich; Alexey A. Gurevich; Tatiana Krivosheeva; Sergey Nurk; Son K. Pham; Anton I. Korobeynikov; Alla L. Lapidus; Pavel A. Pevzner (Bioinform., 2014)

TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes. - Ilya Minkin; Son K. Pham; Paul Medvedev (Bioinform., 2017)