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

Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. - Sergey Nurk; Anton Bankevich; Dmitry Antipov; Alexey A. Gurevich; Anton I. Korobeynikov; Alla L. Lapidus; Andrey D. Prjibelsky; Alex Pyshkin; Alexander Sirotkin 001; Yakov Sirotkin; Ramunas Stepanauskas; Jeffrey S. McLean; et al. (RECOMB, 2013)

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. - Sergey Nurk; Anton Bankevich; Dmitry Antipov; Alexey A. Gurevich; Anton I. Korobeynikov; Alla L. Lapidus; Andrey D. Prjibelski; Alex Pyshkin; Alexander Sirotkin 001; Yakov Sirotkin; Ramunas Stepanauskas; Scott R. Clingenpeel; et al. (J. Comput. Biol., 2013)

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)

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. - Yana Safonova; Stefano Bonissone; Eugene Kurpilyansky; Ekaterina Starostina; Alla L. Lapidus; Jeremy Stinson; Laura DePalatis; Wendy Sandoval; Jennie Lill; Pavel A. Pevzner (Bioinform., 2015)

IgSimulator: a versatile immunosequencing simulator. - Yana Safonova; Alla L. Lapidus; Jennie Lill (Bioinform., 2015)

plasmidSPAdes: assembling plasmids from whole genome sequencing data. - Dmitry Antipov; Nolan Hartwick; Max W. Shen; Mikhail Raiko; Alla L. Lapidus; Pavel A. Pevzner (Bioinform., 2016)

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. - Elena Bushmanova; Dmitry Antipov; Alla L. Lapidus; Vladimir Suvorov; Andrey D. Prjibelski (Bioinform., 2016)

IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction. - Vasily Ershov; Artem Tarasov; Alla L. Lapidus; Anton I. Korobeynikov (J. Comput. Biol., 2019)

Sequence Analysis. - Andrey D. Prjibelski; Anton I. Korobeynikov; Alla L. Lapidus (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Metaviral SPAdes: assembly of viruses from metagenomic data. - Dmitry Antipov; Mikhail Raiko; Alla L. Lapidus; Pavel A. Pevzner (Bioinform., 2020)

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities. - Yulia Kondratenko; Anton I. Korobeynikov; Alla L. Lapidus (BMC Bioinform., 2020)

Correction to: CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities. - Yulia Kondratenko; Anton I. Korobeynikov; Alla L. Lapidus (BMC Bioinform., 2020)

Extending rnaSPAdes functionality for hybrid transcriptome assembly. - Andrey D. Prjibelski; Giuseppe D. Puglia; Dmitry Antipov; Elena Bushmanova; Daniela Giordano; Alla Mikheenko; Domenico Vitale; Alla L. Lapidus (BMC Bioinform., 2020)

MGnify: the microbiome analysis resource in 2020. - Alex L. Mitchell; Alexandre Almeida; Martin Beracochea; Miguel A. Boland; Josephine Burgin; Guy Cochrane; Michael R. Crusoe; Varsha Kale; Simon C. Potter; Lorna J. Richardson; Ekaterina A. Sakharova; Maxim Scheremetjew; et al. (Nucleic Acids Res., 2020)