Publications

1. 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 (talk), 2020
2. Tatiana Dvorkina , Andrey V Bzikadze, Pavel A Pevzner The String Decomposition problem and its applications to centromere analysis and assembly (talk), 2020
3. Tatiana Dvorkina , Andrey V Bzikadze, Pavel A Pevzner The string decomposition problem and its applications to centromere analysis and assembly Bioinformatics, 2020
4. 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
5. Tolstoganov I. , Pevzner P. A. cloudSPAdes: Assembly of Synthetic Long Reads Using de Bruijn graphs (talk), 2019
6. Dmitry Antipov , Mikhail Raiko , Alla Lapidus , and Pavel A. Pevzner Plasmid detection and assembly in genomic and metagenomic data sets Genome Research, 2019
7. 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
8. Ivan Tolstoganov , Anton Bankevich, Zhoutao Chen, Pavel A Pevzner cloudSPAdes: Assembly of Synthetic Long Reads Using de Bruijn graphs Bioinformatics, 2019
9. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. L. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , and Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: Current Status (poster), 2018
10. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2018
11. Gurevich A. , Mikheenko A. , Shlemov A. , Korobeynikov A. , Pevzner P. A. Variable Identification and De Novo Sequencing of Cyclopeptides via Computational Processing of Tandem Mass Spectra (talk), 2018
12. Lapidus A. , Antipov D. , Bankevich A. , Bushmanova E. , Korobeynikov A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
13. Nurk S., Meleshko D., Korobeynikov A., Pevzner P. A. metaSPAdes: a new versatile de novo metagenomics assembler. Genome Research, 2017
14. 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
15. 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
16. Bankevich S. , Shlemov A., Safonova Y., Bzikadze A. , Pevzner P. A. Reconstructing antibody repertoires from error-prone immunosequencing datasets (talk), 2017
17. Shlemov A., Bankevich S. , Safonova Y., Bzikadze A. , Pevzner P. A. Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017
18. Bzikadze A. , Shlemov A., Bankevich S. , Safonova Y., Pevzner P. A. AntEvolo: a novel approach for clonal analysis of antibody repertoires (poster), 2017
19. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes: is there anything new we could develop? (talk), 2017
20. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. VarQuest: modification-tolerant identification of novel variants of peptidic antibiotics and other natural products. (poster), 2017
21. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017
22. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
23. Pevzner P. A. From Metagenome Sequencing to Genome Mining for New Antibiotics (talk), 2017
24. Nurk S., Pevzner P. A. SPArcle: Identifying Microbial Genome Variations with Colored de Bruijn Graphs. Manuscript in preparation., 2016
25. 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
26. Antipov D., Hartwick N., Shen M., Raiko M., Lapidus A., Pevzner P. A. plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data. Bioinformatics, 2016
27. Antipov D., Korobeynikov A., McLean J. S., Pevzner P. A. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics, 2016
28. 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
29. Bankevich A., Pevzner P. A. TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nature Methods, 2016
30. Vasilinetc I., Prjibelski A., Gurevich A., Korobeynikov A., Pevzner P. A. Assembling Short Reads from Jumping Libraries with Large Insert Sizes. Bioinformatics, 2015
31. 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
32. Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. Journal of Computational Biology, 2015
33. 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
34. Safonova Y., Shlemov A., Starostina E., Bzikadze A., Lapidus A., Pevzner P. A. IgTools: a toolkit for analysis of antibody repertoire from immunosequencing and mass spectra data. Poster on Immunogenomics 2015. Huntsville, USA, 2015
35. Lapidus A., Antipov D., Bankevich A., Gurevich A., Korobeynikov A., Nurk S., Prjibelski A., Safonova Y., Vasilinetc I., Pevzner P. A. New Frontiers of Genome Assembly with SPAdes 3.0. (poster), 2014
36. Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. Talk., 2014
37. 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
38. 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
39. Lin Y., Nurk S., Pevzner P. A. What is the difference between the breakpoint graph and the de Bruijn graph? BMC Genomics, 2014
40. 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
41. Nikolenko S., Korobeynikov A., Pevzner P. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013
42. Antipov D., Krasheninnikova K., Pevzner P. A. Using uneven coverage depth in bacterial single-cell repeat resolution. (poster), 2013
43. 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
44. Castellana N. E., Lushnikov A., Rotkiewicz P., Sefcovic N., Pevzner P. A., Godzik A., Vyatkina K. MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms for molecular biology, 2013
45. 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
46. 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
47. McLean J. S., Lombardo M.-J., Badger J. H., Edlund A., Novotny M., Yee-Greenbaum J., Vyahhi N., Hall A. P., Yang Y., Dupont C. L., Ziegler M. G., Chitsaz H., Allen A. E., Yooseph S., Tesler G., Pevzner P. A., Friedman R. M., Nealson K. H., Venter J. C., Lasken R. S. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences, 2013
48. Nikolenko S., Korobeynikov A., Pevzner P. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013
49. 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
50. 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
51. 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
52. Prjibelski A., Krivosheeva T., Bankevich A., Nurk S., Pham S., Pevzner P. A. Path-Extend: An Approach for Repeat Resolution in de novo Genome Assembly. , 2012
53. Sirotkin Y., Liu X., Gladkikh M., Pevzner P. A., Vyatkina K. Peptide Sequence Tags for Top-Down Spectra. (talk), 2012
54. 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
55. Pevzner P. A. BioInformatics and genome assemblies — Challenges for Russia and for the world community. , 2012
56. Sirotkin Y., Liu X., Gladkikh M., Pevzner P. A., Vyatkina K. Peptide Sequence Tags for Top-Down Spectra. (poster, session TP25), 2012
57. Vyahhi N., Pyshkin A., Pham S., Pevzner P. A. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. Lecture Notes in Bioinformatics, 2012
58. Pevzner P. A. Вычислительная протеомика. , 2011
59. Pevzner P. A. Genome rearrangements: from biological problems to combinatorial algorithms (and back). , 2011
60. Nikolenko S., Alekseyev M. A., Pevzner P. A. Bayesian Evaluation of de novo Genome Assembly. (poster), 2011
61. Pevzner P. A. De novo sequencing of peptide antibiotics. (talk), 2011
62. Alekseyev M. A., Pevzner P. A. The Birth and Death of Fragile Regions in Human Genome. (highlight track paper), 2011
63. Pevzner P. A. How Will the Human Genome Evolve in the Next Million Years? (talk), 2011
64. Medvedev P., Pham S., Chaisson M., Tesler G., Pevzner P. A. Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. (paper, talk), 2011
65. Ng J., Amir A., Pevzner P. A. Blocked Pattern Matching Problem and its Applications in Proteomics. (paper, talk), 2011
66. Mohimani H., Liu W. T., Yang Y. L., Gaudencio S., Fenical W., Dorrestein P., Pevzner P. A. Multiplex De Novo Sequencing of Peptide Antibiotics. (paper, talk), 2011
67. Liu X., Sirotkin Y., Shen Y., Anderson G., Tsai Y. S., Ting Y. S., Goodlett D. R., Smith R. D., Bafna V., Pevzner P. A. Protein Identification Using Top-Down Spectra. (poster), 2011
68. Nikolenko S., Nurk S., Bankevich A., Alekseyev M. A., Pevzner P. A. Expandable de novo genome assembler for short-read sequence data. (HiTSeq poster), 2011
69. Pevzner P. A. Genome Rearrangements: from Biological Problems to Combinatorial Algorithms. , 2010