2020

• 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 2020 Nucleic Acids Research, 2020
• Dmitry Antipov, Mikhail Rayko, Alla L. Lapidus, and Pavel A. Pevzner metaviralSPAdes: assembly of viruses from metagenomic data Bioinformatics, 2020
• Alla Mikheenko , Andrey V Bzikadze, Alexey Gurevich , Karen H Miga, Pavel A Pevzner TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats Bioinformatics, 2020
• Tatiana Dvorkina , Andrey V Bzikadze, Pavel A Pevzner The string decomposition problem and its applications to centromere analysis and assembly Bioinformatics, 2020

2019

• Azat M Tagirdzhanov, Alexander Shlemov, Alexey Gurevich NPS: scoring and evaluating the statistical significance of peptidic natural product–spectrum matches Bioinformatics, 2019
• 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 Mohimani MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities Cell Systems, 2019
• Alla Mikheenko, Mikhail Kolmogorov Assembly Graph Browser: interactive visualization of assembly graphs Bioinformatics, 2019
• Alexander Shlemov, Anton Korobeynikov PathRacer: Racing Profile HMM Paths on Assembly Graph Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2019
• Dmitry Antipov , Mikhail Raiko , Alla Lapidus , and Pavel A. Pevzner Plasmid detection and assembly in genomic and metagenomic data sets Genome Research, 2019
• Dmitry Meleshko , Hosein Mohimani, Vittorio Tracanna, Iman Hajirasouliha, Marnix H. Medema, Anton Korobeynikov , and Pavel A. Pevzner BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs Genome Research, 2019
• Ivan Tolstoganov , Anton Bankevich, Zhoutao Chen, Pavel A Pevzner cloudSPAdes: Assembly of Synthetic Long Reads Using de Bruijn graphs Bioinformatics, 2019

2018

• Elena Bushmanova, Dmitry Antipov, Alla Lapidus, Andrey D Prjibelski rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data GigaScience, 2019
• Gurevich A, Mikheenko A., Shlemov A., Korobeynikov A., Mohimani H., Pevzner P. A. Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nature Microbiology, 2018
• Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich Versatile genome assembly evaluation with QUAST-LG Bioinformatics, 2018
• Hosein Mohimani, Alexey Gurevich, Alexander Shlemov, Alla Mikheenko, Anton Korobeynikov, Liu Cao, Egor Shcherbin, Louis-Felix Nothias, Pieter Dorrestein, Pavel Pevzner Dereplication of Microbial Metabolites Through Database Search of Mass Spectra Nature Communications, 2018
• Olga Kunyavskaya , Andrey D. Prjibelski SGTK: a toolkit for visualization and assessment of scaffold graphs. Bioinformatics, 2018

2017

• Nurk S., Meleshko D., Korobeynikov A., Pevzner P. A. metaSPAdes: a new versatile de novo metagenomics assembler. Genome Research, 2017
• Hosein Mohimani, Alexey Gurevich, Alla Mikheenko, Neha Garg, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Pieter C Dorrestein, and Pavel A. Pevzner Dereplication of peptidic natural products through database search of mass spectra. Nature Chemical Biology, 2017
• Alexander Shlemov , Sergey Bankevich , Andrey Bzikadze , Maria A. Turchaninova, Yana Safonova , and Pavel A. Pevzner Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. The Journal of Immunology, 2017

2016

• Vyatkina K., Wu S., Dekker L. J., VanDuijn M. M., Liu X., Tolić N., Dvorkin M., Alexandrova S., Luider T. M., Paša-Tolić L., Pevzner P. A. Top-down analysis of protein samples by de novo sequencing techniques. Bioinformatics, 2016
• Bankevich A., Pevzner P. A. TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nature Methods, 2016
• Mikheenko A., Valin G., Prjibelski A., Saveliev V., Gurevich A. Icarus: visualizer for de novo assembly evaluation. Bioinformatics, 2016
• Mikheenko A., Saveliev V., Gurevich A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics, 2016
• Antipov D., Korobeynikov A., McLean J. S., Pevzner P. A. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics, 2016
• Bushmanova E., Antipov D., Lapidus A., Suvorov V., Prjibelski A. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. Bioinformatics, 2016
• 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

2015

• Safonova Y., Bonissone S., Kurpilyansky E., Starostina E., Lapidus A., Stinson J., DePalatis L., Sandoval W., Lill J., Pevzner P. A. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics, 2015
• Safonova Y., Lapidus A., Lill J. IgSimulator: a versatile immunosequencing simulator. Bioinformatics, 2015
• Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. Journal of Computational Biology, 2015
• Vyatkina K., Wu S., Dekker L. J., VanDuijn M. M., Liu X., Tolić N., Dvorkin M., Alexandrova S., Luider T.M., Paša-Tolić L., Pevzner P. A. De novo sequencing of peptides from top-down tandem mass spectra. Journal of Proteome Research, 2015
• Vasilinetc I., Prjibelski A., Gurevich A., Korobeynikov A., Pevzner P. A. Assembling Short Reads from Jumping Libraries with Large Insert Sizes. Bioinformatics, 2015
• Guzman G. I., Utrilla J., Nurk S., Brunk E., Monk J. M., Ebrahim A., Palsson B. A., Feist A. M. Model-driven discovery of underground metabolic functions in Escherichia coli. Proceedings of the National Academy of Sciences, 2015

2014

• Prjibelski A., Vasilinetc I., Bankevich A., Gurevich A., Krivosheeva T., Nurk S., Pham S., Korobeynikov A., Lapidus A., Pevzner P. A. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics, 2014
• Coates R. C., Podell S., Korobeynikov A., Lapidus A., Pevzner P. A., Sherman D. H., Allen E. E., Gerwick L., Gerwick W. H. Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways. PLoS One, 2014
• Lin Y., Nurk S., Pevzner P. A. What is the difference between the breakpoint graph and the de Bruijn graph? BMC Genomics, 2014
• 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
• McLean J. S., Lombardo M.-J., Ziegler M. G., Novotny M., Yee-Greenbaum J., Badger J. H., Tesler G., Nurk S., Lesin V., Brami D., Hall A. P., Edlund A., Allen L. Z., Durkin S., Reed S., Torriani F., Nealson K. H., Pevzner P. A., Friedman R. M., Venter J. C., Lasken R. S. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research, 2013
• Gurevich A., Saveliev V., Vyahhi N., Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics, 2013
• Pham S., Antipov D., Sirotkin A., Tesler G., Pevzner P. A., Alekseyev M. A. Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. 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
• Nikolenko S., Korobeynikov A., Pevzner P. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013

2012

• Bankevich A., Nurk S., Antipov D., Gurevich A., Dvorkin M., Kulikov A. S., Lesin V., Nikolenko S., Pham S., Prjibelski A., Pyshkin A., Sirotkin A., Vyahhi N., Tesler G., Alekseyev M. A., Pevzner P. A. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 2012
• Aganezov S. Jr., Alekseyev M. A. On pairwise distances and median score of three genomes under DCJ. BMC Bioinformatics, 2012
• Vyahhi N., Pyshkin A., Pham S., Pevzner P. A. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. Lecture Notes in Bioinformatics, 2012
• Monroe E. A., Choi H., Lesin V., Sirotkin A., Dvorkin M., Pevzner P. A., Gerwick W. H., Gerwick L. Genomic insights into secondary metabolism of the natural product-rich cyanobacterium Moorea bouillonii. Planta Medica, 2012
• 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