Pavel A. Pevzner

Publication Activity (10 Years)

Years Active: 1991-2022
Publications (10 Years): 30

Top Venues

Bioinform.

RECOMB

J. Comput. Biol.

CoRR

Publications

Sorin Istrail, Pavel A. Pevzner, Fengzhu Sun, Martin Vingron
Special Issue: Professor Michael Waterman's 80th Birthday, Part 1. J. Comput. Biol. 29 (7) (2022)
Pavel A. Pevzner, Martin Vingron, Christian M. Reidys, Fengzhu Sun, Sorin Istrail
Michael Waterman's Contributions to Computational Biology and Bioinformatics. J. Comput. Biol. 29 (7) (2022)
Tatiana Dvorkina, Olga Kunyavskaya, Andrey V. Bzikadze, Ivan V. Alexandrov, Pavel A. Pevzner
CentromereArchitect: inference and analysis of the architecture of centromeres. Bioinform. 37 (Supplement) (2021)
Vinnu Bhardwaj, Pavel A. Pevzner, Cyrus Rashtchian, Yana Safonova
Trace Reconstruction Problems in Computational Biology. IEEE Trans. Inf. Theory 67 (6) (2021)
Dmitry Antipov, Mikhail Raiko, Alla L. Lapidus, Pavel A. Pevzner
Metaviral SPAdes: assembly of viruses from metagenomic data. Bioinform. 36 (14) (2020)
Tatiana Dvorkina, Andrey V. Bzikadze, Pavel A. Pevzner
The string decomposition problem and its applications to centromere analysis and assembly. Bioinform. 36 (Supplement-1) (2020)
Vinnu Bhardwaj, Pavel A. Pevzner, Cyrus Rashtchian, Yana Safonova
Trace Reconstruction Problems in Computational Biology. CoRR (2020)
Anton Bankevich, Pavel A. Pevzner
MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads. RECOMB (2020)
Vinnu Bhardwaj, Massimo Franceschetti, Ramesh Rao, Pavel A. Pevzner, Yana Safonova
Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLoS Comput. Biol. 16 (4) (2020)
Alla Mikheenko, Andrey V. Bzikadze, Alexey A. Gurevich, Karen H. Miga, Pavel A. Pevzner
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinform. 36 (Supplement-1) (2020)
Pavel A. Pevzner
Bioinformatics: a Servant or the Queen of Molecular Biology? BIBM (2019)
Ivan Tolstoganov, Anton Bankevich, Zhoutao Chen, Pavel A. Pevzner
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. Bioinform. 35 (14) (2019)
Bahar Behsaz, Hosein Mohimani, Alexey A. Gurevich, Andrey D. Prjibelski, Mark F. Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner
De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments. RECOMB (2019)
Anton Bankevich, Pavel A. Pevzner
Long Reads Enable Accurate Estimates of Complexity of Metagenomes. RECOMB (2018)
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner
Assembly of Long Error-Prone Reads Using Repeat Graphs. RECOMB (2018)
Alexander Shlemov, Sergey Bankevich, Andrey V. Bzikadze, Yana Safonova, Pavel A. Pevzner
Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Datasets. RECOMB (2017)
Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp, Pavel A. Pevzner
Single-molecule protein identification by sub-nanopore sensors. PLoS Comput. Biol. 13 (5) (2017)
Dmitry Antipov, Anton I. Korobeynikov, Jeffrey S. McLean, Pavel A. Pevzner
hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinform. 32 (7) (2016)
Kira Vyatkina, Si Wu, Lennard J. Dekker, Martijn M. VanDuijn, Xiaowen Liu, Nikola Tolic, Theo M. Luider, Ljiljana Pasa-Tolic, Pavel A. Pevzner
sequencing techniques. Bioinform. 32 (18) (2016)
Sergey Nurk, Dmitry Meleshko, Anton I. Korobeynikov, Pavel A. Pevzner
metaSPAdes: A New Versatile de novo Metagenomics Assembler. RECOMB (2016)
Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp, Pavel A. Pevzner
Single-Molecule Protein Identification by Sub-Nanopore Sensors. CoRR (2016)
Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W. Shen, Mark Chaisson, Pavel A. Pevzner
Assembly of long error-prone reads using de Bruijn graphs. Proc. Natl. Acad. Sci. USA 113 (52) (2016)
Yu Lin, Max W. Shen, Jeffrey Yuan, Mark Chaisson, Pavel A. Pevzner
Assembly of Long Error-Prone Reads Using de Bruijn Graphs. RECOMB (2016)
Dmitry Antipov, Nolan Hartwick, Max W. Shen, Mikhail Raiko, Alla L. Lapidus, Pavel A. Pevzner
plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinform. 32 (22) (2016)
Stefano Bonissone, Pavel A. Pevzner
Immunoglobulin Classification Using the Colored Antibody Graph. J. Comput. Biol. 23 (6) (2016)
Yana Safonova, Stefano Bonissone, Eugene Kurpilyansky, Ekaterina Starostina, Alla L. Lapidus, Jeremy Stinson, Laura DePalatis, Wendy Sandoval, Jennie Lill, Pavel A. Pevzner
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinform. 31 (12) (2015)
Yana Safonova, Anton Bankevich, Pavel A. Pevzner
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. J. Comput. Biol. 22 (6) (2015)
Stefano Bonissone, Pavel A. Pevzner
Immunoglobulin Classification Using the Colored Antibody Graph. RECOMB (2015)
Irina Vasilinetc, Andrey D. Prjibelski, Alexey A. Gurevich, Anton I. Korobeynikov, Pavel A. Pevzner
Assembling short reads from jumping libraries with large insert sizes. Bioinform. 31 (20) (2015)
Phillip Compeau, Pavel A. Pevzner
Life after MOOCs. Commun. ACM 58 (10) (2015)
Yu Lin, Pavel A. Pevzner
Manifold de Bruijn Graphs. WABI (2014)
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
ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinform. 30 (12) (2014)
Yana Safonova, Anton Bankevich, Pavel A. Pevzner
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. RECOMB (2014)
Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton I. Korobeynikov, Alla L. Lapidus, Andrey D. Prjibelski, Alex Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Scott R. Clingenpeel, Tanja Woyke, Jeffrey S. McLean, Roger Lasken, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. J. Comput. Biol. 20 (10) (2013)
Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, Adam Godzik, Kira Vyatkina
MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms Mol. Biol. 8 (2013)
Kyowon Jeong, Sangtae Kim, Pavel A. Pevzner
peptide sequencing. Bioinform. 29 (16) (2013)
Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic, Pavel A. Pevzner
Identification of Ultramodified Proteins Using Top-Down Spectra. RECOMB (2013)
Kyowon Jeong, Sangtae Kim, Pavel A. Pevzner
UniNovo: A Universal Tool for de Novo Peptide Sequencing. RECOMB (2013)
Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. J. Comput. Biol. 20 (4) (2013)
Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton I. Korobeynikov, Alla L. Lapidus, Andrey D. Prjibelsky, Alex Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey S. McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. RECOMB (2013)
Pavel A. Pevzner
Keynote: De novo sequencing of novel peptide antibiotics by tandem mass spectrometry. ICCABS (2012)
Nikolay Vyahhi, Alex Pyshkin, Son K. Pham, Pavel A. Pevzner
From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. WABI (2012)
Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev
Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. RECOMB (2012)
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son K. Pham, Andrey D. Prjibelski, Alex Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol. 19 (5) (2012)
Hosein Mohimani, Sangtae Kim, Pavel A. Pevzner
MS-DPR: An Algorithm for Computing Statistical Significance of Spectral Identifications of Non-linear Peptides. WABI (2012)
Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner
SEQuel: improving the accuracy of genome assemblies. Bioinform. 28 (12) (2012)
Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, Adam Godzik, Kira Vyatkina
MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing. WABI (2012)
Pavel A. Pevzner, Ron Shamir
Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). J. Comput. Biol. 18 (7) (2011)
Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. J. Comput. Biol. 18 (11) (2011)
Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudêncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner
Multiplex De Novo Sequencing of Peptide Antibiotics. RECOMB (2011)
Julio Ng, Amihood Amir, Pavel A. Pevzner
Blocked Pattern Matching Problem and Its Applications in Proteomics. RECOMB (2011)
Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner
Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinform. 27 (13) (2011)
Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudêncio, William Fenical, Pieter C. Dorrestein, Pavel A. Pevzner
Multiplex De Novo Sequencing of Peptide Antibiotics. J. Comput. Biol. 18 (11) (2011)
Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. RECOMB (2011)
Kyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner
Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra. RECOMB (2010)
Son K. Pham, Pavel A. Pevzner
DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinform. 26 (20) (2010)
Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff
Session Introduction. Pacific Symposium on Biocomputing (2010)
Max A. Alekseyev, Qian Peng, Pavel A. Pevzner, Glenn Tesler
Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-scale Duplications. Commun. Inf. Syst. 10 (1) (2010)
Max A. Alekseyev, Pavel A. Pevzner
Limited Lifespan of Fragile Regions in Mammalian Evolution. RECOMB-CG (2010)
Qian Peng, Max A. Alekseyev, Glenn Tesler, Pavel A. Pevzner
Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. WABI (2009)
Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff
Session Introduction. Pacific Symposium on Biocomputing (2009)
Max A. Alekseyev, Pavel A. Pevzner
Multi-break rearrangements and chromosomal evolution. Theor. Comput. Sci. 395 (2-3) (2008)
Nuno Bandeira, Jesper V. Olsen, Matthias Mann, Pavel A. Pevzner
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. ISMB (2008)
Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger G. Linington, Pieter C. Dorrestein, Pavel A. Pevzner
De Novo Sequencing of Nonribosomal Peptides. RECOMB (2008)
Pavel A. Pevzner
Shotgun Protein Sequencing. WABI (2007)
Max A. Alekseyev, Pavel A. Pevzner
Colored de Bruijn Graphs and the Genome Halving Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Max A. Alekseyev, Pavel A. Pevzner
Whole genome duplications, multi-break rearrangements, and genome halving problem. SODA (2007)
Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner
Protein identification by spectral networks analysis. Proc. Natl. Acad. Sci. USA 104 (15) (2007)
Pavel A. Pevzner
Protein Identification via Spectral Networks Analysis. APBC (2007)
Max A. Alekseyev, Pavel A. Pevzner
Whole Genome Duplications and Contracted Breakpoint Graphs. SIAM J. Comput. 36 (6) (2007)
Degui Zhi, Uri Keich, Pavel A. Pevzner, Steffen Heber, Haixu Tang
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir
Special issue on computational molecular biology. J. Comput. Syst. Sci. 73 (7) (2007)
Max A. Alekseyev, Pavel A. Pevzner
Are There Rearrangement Hotspots in the Human Genome? PLoS Comput. Biol. 3 (11) (2007)
Sorin Istrail, Pavel A. Pevzner, Ron Shamir
Preface. Discret. Appl. Math. 155 (6-7) (2007)
Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik
Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinform. 7 (2006)
Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner
Characterization of Multi-Charge Mass Spectra for Peptide Sequencing. APBC (2006)
Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner
A New Approach to Protein Identification. RECOMB (2006)
Neil C. Jones, Pavel A. Pevzner
Comparative genomics reveals unusually long motifs in mammalian genomes. ISMB (Supplement of Bioinformatics) (2006)
Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner
Modeling and Characterization of Multi-charge Mass Spectra for Peptide Sequencing. J. Bioinform. Comput. Biol. 4 (6) (2006)
Mark Chaisson, Benjamin J. Raphael, Pavel A. Pevzner
Microinversions in mammalian evolution. Proc. Natl. Acad. Sci. USA 103 (52) (2006)
Qian Peng, Pavel A. Pevzner, Glenn Tesler
The Fragile Breakage versus Random Breakage Models of Chromosome Evolution. PLoS Comput. Biol. 2 (2) (2006)
Alkes L. Price, Neil C. Jones, Pavel A. Pevzner
identification of repeat families in large genomes. ISMB (Supplement of Bioinformatics) (2005)
Ari Frank, Stephen Tanner, Pavel A. Pevzner
Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. RECOMB (2005)
Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir
Guest Editors' foreword. J. Comput. Syst. Sci. 70 (3) (2005)
Dekel Tsur, Stephen Tanner, Ebrahim Zandi, Vineet Bafna, Pavel A. Pevzner
Identification of Post-Translational Modifications via Blind Search of Mass-Spectra. CSB (2005)
Max A. Alekseyev, Pavel A. Pevzner
Genome Halving Problem Revisited. FSTTCS (2004)
Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky
Scalable Heuristics for Design of DNA Probe Arrays. J. Comput. Biol. 11 (2/3) (2004)
Pavel A. Pevzner, Haixu Tang, Glenn Tesler
repeat classification and fragment assembly. RECOMB (2004)
Pavel A. Pevzner
Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinform. 20 (14) (2004)
Mark Chaisson, Pavel A. Pevzner, Haixu Tang
Fragment assembly with short reads. Bioinform. 20 (13) (2004)
Benjamin J. Raphael, Pavel A. Pevzner
Reconstructing tumor amplisomes. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Pavel A. Pevzner, Glenn Tesler
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited. RECOMB (2003)
Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner
Reconstructing tumor genome architectures. ECCB (2003)
Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky
Engineering a scalable placement heuristic for DNA probe arrays. RECOMB (2003)
Alkes L. Price, Sriram Ramabhadran, Pavel A. Pevzner
Finding subtle motifs by branching from sample strings. ECCB (2003)
Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner
Genome-Wide Analysis of Bacterial Promoter Regions. Pacific Symposium on Biocomputing (2003)
Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky
Border Length Minimization in DNA Array Design. WABI (2002)
Uri Keich, Pavel A. Pevzner
U Subtle motifs: defining the limits of motif finding algorithms. Bioinform. 18 (10) (2002)
Uri Keich, Pavel A. Pevzner
Finding motifs in the twilight zone. Bioinform. 18 (10) (2002)
Zufar Mulyukov, Pavel A. Pevzner
EULER-PCR: Finishing Experiments for Repeat Resolution. Pacific Symposium on Biocomputing (2002)

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Publication Activity (10 Years)

Top Topics

Top Venues

Pavel A. Pevzner