Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G, Crusoe MR, Kale V, Potter SC, Richardson LJ, Sakharova E, Scheremetjew M, Korobeynikov A, Shlemov A, Kunyavskaya O, Lapidus A and Finn RD.MGnify: the microbiome analysis resource in 2020Nucleic Acids Research,
2020
Liu Cao, Alexey Gurevich , Kelsey L Alexander, C. Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Robby Quinn, Amina Bouslimani, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo A S Benitez, Luke R Thompson, Md-Nafiz Hamid, James T Morton, Alla Mikheenko , Alexander Shlemov , Anton Korobeynikov , Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Peter C. Dorrestein, Pavel A. Pevzner , Hosein MohimaniMetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial CommunitiesCell Systems,
2019
Alexander Shlemov, Anton KorobeynikovPathRacer: Racing Profile HMM Paths on Assembly GraphLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
2019
Antipov D., Hartwick N., Shen M., Raiko M., Lapidus A., Pevzner P. A.plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data.Bioinformatics,
2016
Shlemov A., Bzikadze A., Bankevich S., Safonova Y.IgReC 2.0: New algorithmic challenges of adaptive immune repertoire construction.Proceedings of RECOMBSeq,
2016
Safonova Y., Shlemov A., Bzikadze A., Bankevich S., Pevzner P. A.A novel toolkit for analysis of adaptive immune repertoires using immunosequencing and mass spectra data.Poster.,
2016
Safonova Y., Bankevich A., Pevzner P. A.dipSPAdes: assembler for highly polymorphic diploid genomes.In Sharan, Roded (eds.) RECOMB 2014, LNCS (8394). pp. 265-279. Springer, Heidelberg,
2014
2013
Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelski A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., Clingenpeel S. R., Woyke T., Mclean J. S., Lasken R., Tesler G., Alekseyev M. A., Pevzner P. A.Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.Journal of Computational Biology,
2013
Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelski A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., McLean J., Lasken R., Clingenpeel S., Woyke T., Tesler G., Alekseyev M. A., Pevzner P. A.Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads.Lecture Notes in Computer Science,
2013
Pham S., Antipov D., Sirotkin A., Tesler G., Pevzner P. A., Alekseyev M. A.Pathset Graphs: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly.Lecture Notes in Computer Science,
2012