Pavel Pevzner

Chief Advisor

Software

Publications

  1. Tatiana Dvorkina , Andrey V Bzikadze, Pavel A Pevzner The String Decomposition problem and its applications to centromere analysis and assembly (talk), 2020
  2. 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
  3. Tolstoganov I. , Pevzner P. A. cloudSPAdes: Assembly of Synthetic Long Reads Using de Bruijn graphs (talk), 2019
  4. 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
  5. 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
  6. 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
  7. Bankevich S. , Shlemov A., Safonova Y., Bzikadze A. , Pevzner P. A. Reconstructing antibody repertoires from error-prone immunosequencing datasets (talk), 2017
  8. 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
  9. Bzikadze A. , Shlemov A., Bankevich S. , Safonova Y., Pevzner P. A. AntEvolo: a novel approach for clonal analysis of antibody repertoires (poster), 2017
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Pevzner P. A. From Metagenome Sequencing to Genome Mining for New Antibiotics (talk), 2017
  16. Nurk S., Pevzner P. A. SPArcle: Identifying Microbial Genome Variations with Colored de Bruijn Graphs. Manuscript in preparation., 2016
  17. Antipov D., Hartwick N., Shen M., Raiko M., Lapidus A., Pevzner P. A. plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data. Bioinformatics, 2016
  18. 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
  19. 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
  20. 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
  21. Safonova Y., Bankevich A., Pevzner P. A. dipSPAdes: assembler for highly polymorphic diploid genomes. Talk., 2014
  22. 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
  23. Antipov D., Krasheninnikova K., Pevzner P. A. Using uneven coverage depth in bacterial single-cell repeat resolution. (poster), 2013
  24. Nikolenko S., Korobeynikov A., Pevzner P. A. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013
  25. Vyahhi N., Pyshkin A., Pham S., Pevzner P. A. From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. Lecture Notes in Bioinformatics, 2012
  26. 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
  27. Sirotkin Y., Liu X., Gladkikh M., Pevzner P. A., Vyatkina K. Peptide Sequence Tags for Top-Down Spectra. (poster, session TP25), 2012
  28. 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
  29. Sirotkin Y., Liu X., Gladkikh M., Pevzner P. A., Vyatkina K. Peptide Sequence Tags for Top-Down Spectra. (talk), 2012
  30. Pevzner P. A. De novo sequencing of peptide antibiotics. (talk), 2011
  31. Alekseyev M. A., Pevzner P. A. The Birth and Death of Fragile Regions in Human Genome. (highlight track paper), 2011
  32. Nikolenko S., Alekseyev M. A., Pevzner P. A. Bayesian Evaluation of de novo Genome Assembly. (poster), 2011
  33. 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
  34. 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
  35. 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
  36. Ng J., Amir A., Pevzner P. A. Blocked Pattern Matching Problem and its Applications in Proteomics. (paper, talk), 2011
  37. 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
  38. Pevzner P. A. How Will the Human Genome Evolve in the Next Million Years? (talk), 2011