Pavel A. Pevzner

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. Journal of Computational Biology 20(4): 359-371 (2013)

Kyowon Jeong, Sangtae Kim, Pavel A. Pevzner: UniNovo: A Universal Tool for de Novo Peptide Sequencing. RECOMB 2013: 100-117

Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic, Pavel A. Pevzner: Identification of Ultramodified Proteins Using Top-Down Spectra. RECOMB 2013: 132-144

Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alex Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey 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: 158-170

Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel A. Pevzner: SEQuel: improving the accuracy of genome assemblies. Bioinformatics 28(12): 188-196 (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. Journal of Computational Biology 19(5): 455-477 (2012)

Pavel A. Pevzner: Keynote: De novo sequencing of novel peptide antibiotics by tandem mass spectrometry. ICCABS 2012: 1

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: 200-212

Nikolay Vyahhi, Alex Pyshkin, Son K. Pham, Pavel A. Pevzner: From de Bruijn Graphs to Rectangle Graphs for Genome Assembly. WABI 2012: 249-261

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: 262-273

Hosein Mohimani, Sangtae Kim, Pavel A. Pevzner: MS-DPR: An Algorithm for Computing Statistical Significance of Spectral Identifications of Non-linear Peptides. WABI 2012: 301-313

Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner: Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics [ISMB/ECCB] 27(13): 137-141 (2011)

Pavel A. Pevzner, Ron Shamir: Preface: 2^nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). Journal of Computational Biology 18(7): 865 (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. Journal of Computational Biology 18(11): 1371-1381 (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. Journal of Computational Biology 18(11): 1625-1634 (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: 238-251

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: 267-281

Julio Ng, Amihood Amir, Pavel A. Pevzner: Blocked Pattern Matching Problem and Its Applications in Proteomics. RECOMB 2011: 298-319

Son K. Pham, Pavel A. Pevzner: DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics 26(20): 2509-2516 (2010)

Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff: Session Introduction. Pacific Symposium on Biocomputing 2010: 1-2

Max A. Alekseyev, Pavel A. Pevzner: Limited Lifespan of Fragile Regions in Mammalian Evolution. RECOMB-CG 2010: 198-215

Kyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner: Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra. RECOMB 2010: 208-232

Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff: Session Introduction. Pacific Symposium on Biocomputing 2009: 111-113

Qian Peng, Max A. Alekseyev, Glenn Tesler, Pavel A. Pevzner: Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. WABI 2009: 220-232

Max A. Alekseyev, Pavel A. Pevzner: Multi-break rearrangements and chromosomal evolution. Theor. Comput. Sci. 395(2-3): 193-202 (2008)

Nuno Bandeira, Jesper V. Olsen, Matthias Mann, Pavel A. Pevzner: Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. ISMB 2008: 416-423

Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger G. Linington, Pieter C. Dorrestein, Pavel A. Pevzner: De Novo Sequencing of Nonribosomal Peptides. RECOMB 2008: 181-195

Sorin Istrail, Pavel A. Pevzner, Ron Shamir: Preface. Discrete Applied Mathematics 155(6-7): 673-674 (2007)

Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir: Special issue on computational molecular biology. J. Comput. Syst. Sci. 73(7): 1023 (2007)

Max A. Alekseyev, Pavel A. Pevzner: Are There Rearrangement Hotspots in the Human Genome? PLoS Computational Biology 3(11) (2007)

Max A. Alekseyev, Pavel A. Pevzner: Whole Genome Duplications and Contracted Breakpoint Graphs. SIAM J. Comput. 36(6): 1748-1763 (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. Biology Bioinform. 4(1): 54-64 (2007)

Max A. Alekseyev, Pavel A. Pevzner: Colored de Bruijn Graphs and the Genome Halving Problem. IEEE/ACM Trans. Comput. Biology Bioinform. 4(1): 98-107 (2007)

Pavel A. Pevzner: Protein Identification via Spectral Networks Analysis. APBC 2007: 5

Max A. Alekseyev, Pavel A. Pevzner: Whole genome duplications, multi-break rearrangements, and genome halving problem. SODA 2007: 665-679

Pavel A. Pevzner: Shotgun Protein Sequencing. WABI 2007: 1

Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik: Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics 7: 460 (2006)

Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner: Modeling and Characterization of Multi-charge Mass Spectra for Peptide Sequencing. J. Bioinformatics and Computational Biology 4(6): 1329-1352 (2006)

Qian Peng, Pavel A. Pevzner, Glenn Tesler: The Fragile Breakage versus Random Breakage Models of Chromosome Evolution. PLoS Computational Biology 2(2) (2006)

Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner: Characterization of Multi-Charge Mass Spectra for Peptide Sequencing. APBC 2006: 109-119

Neil C. Jones, Pavel A. Pevzner: Comparative genomics reveals unusually long motifs in mammalian genomes. ISMB (Supplement of Bioinformatics) 2006: 236-242

Nuno Bandeira, Dekel Tsur, Ari Frank, Pavel A. Pevzner: A New Approach to Protein Identification. RECOMB 2006: 363-378

Alberto Apostolico, Concettina Guerra, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman (Eds.): Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings. Lecture Notes in Computer Science 3909, Springer 2006, isbn 3-540-33295-2

Richard M. Karp, Ming Li, Pavel A. Pevzner, Ron Shamir: Guest Editors' foreword. J. Comput. Syst. Sci. 70(3): 283- (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: 157-166

Alkes L. Price, Neil C. Jones, Pavel A. Pevzner: De novo identification of repeat families in large genomes. ISMB (Supplement of Bioinformatics) 2005: 351-358

Ari Frank, Stephen Tanner, Pavel A. Pevzner: Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. RECOMB 2005: 326-341

Satoru Miyano, Jill P. Mesirov, Simon Kasif, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman (Eds.): Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings. Lecture Notes in Computer Science 3500, Springer 2005, isbn 3-540-25866-3

Mark Chaisson, Pavel A. Pevzner, Haixu Tang: Fragment assembly with short reads. Bioinformatics 20(13): 2067-2074 (2004)

Pavel A. Pevzner: Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinformatics 20(14): 2159-2161 (2004)

Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky: Scalable Heuristics for Design of DNA Probe Arrays. Journal of Computational Biology 11(2/3): 429-447 (2004)

Max A. Alekseyev, Pavel A. Pevzner: Genome Halving Problem Revisited. FSTTCS 2004: 1-15

Benjamin J. Raphael, Pavel A. Pevzner: Reconstructing tumor amplisomes. ISMB/ECCB (Supplement of Bioinformatics) 2004: 265-273

Pavel A. Pevzner, Haixu Tang, Glenn Tesler: De novo repeat classification and fragment assembly. RECOMB 2004: 213-222

Alkes L. Price, Sriram Ramabhadran, Pavel A. Pevzner: Finding subtle motifs by branching from sample strings. ECCB 2003: 149-155

Benjamin J. Raphael, Stanislav Volik, Colin Collins, Pavel A. Pevzner: Reconstructing tumor genome architectures. ECCB 2003: 162-171

Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner: Genome-Wide Analysis of Bacterial Promoter Regions. Pacific Symposium on Biocomputing 2003: 29-40

Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky: Engineering a scalable placement heuristic for DNA probe arrays. RECOMB 2003: 148-156

Pavel A. Pevzner, Glenn Tesler: Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited. RECOMB 2003: 247-256

Uri Keich, Pavel A. Pevzner: Finding motifs in the twilight zone. Bioinformatics 18(10): 1374-1381 (2002)

Uri Keich, Pavel A. Pevzner: U Subtle motifs: defining the limits of motif finding algorithms. Bioinformatics 18(10): 1382-1390 (2002)

Ming Li, Pavel A. Pevzner, Ron Shamir: Foreword. J. Comput. Syst. Sci. 65(3): 441 (2002)

Steffen Heber, Max A. Alekseyev, Sing-Hoi Sze, Haixu Tang, Pavel A. Pevzner: Splicing graphs and EST assembly problem. ISMB 2002: 181-188

Eleazar Eskin, Pavel A. Pevzner: Finding composite regulatory patterns in DNA sequences. ISMB 2002: 354-363

Zufar Mulyukov, Pavel A. Pevzner: EULER-PCR: Finishing Experiments for Repeat Resolution. Pacific Symposium on Biocomputing 2002: 199-210

Sing-Hoi Sze, Mikhail S. Gelfand, Pavel A. Pevzner: Finding Weak Motifs in DNA Sequences. Pacific Symposium on Biocomputing 2002: 235-246

Uri Keich, Pavel A. Pevzner: Finding motifs in the twilight zone. RECOMB 2002: 195-204

Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky: Border Length Minimization in DNA Array Design. WABI 2002: 435-448

Abdullah N. Arslan, Ömer Egecioglu, Pavel A. Pevzner: A new approach to sequence comparison: normalized sequence alignment. Bioinformatics 17(4): 327-337 (2001)

Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk: The Complexity of Gene Placement. J. Algorithms 41(2): 225-243 (2001)

Pavel A. Pevzner, Haixu Tang: Fragment assembly with double-barreled data. ISMB (Supplement of Bioinformatics) 2001: 225-233

Abdullah N. Arslan, Ömer Egecioglu, Pavel A. Pevzner: A new approach to sequence comparison: normalized sequence alignment. RECOMB 2001: 2-11

Pavel A. Pevzner, Haixu Tang, Michael S. Waterman: A new approach to fragment assembly in DNA sequencing. RECOMB 2001: 256-267

Pavel A. Pevzner: Computational molecular biology - an algorithmic approach. MIT Press 2000, isbn 978-0-262-16197-8, pp. I-XVIII, 1-314

Sorin Istrail, Pavel A. Pevzner, Ron Shamir: Foreword. Discrete Applied Mathematics 104(1-3): 1-2 (2000)

Pavel A. Pevzner, Vlado Dancík, Chris L. Tang: Mutation-Tolerant Protein Identification by Mass Spectrometry. Journal of Computational Biology 7(6): 777-787 (2000)

Pavel A. Pevzner, Sing-Hoi Sze: Combinatorial Approaches to Finding Subtle Signals in DNA Sequences. ISMB 2000: 269-278

Pavel A. Pevzner, Vlado Dancík, Chris L. Tang: Mutation-tolerant protein identification by mass-spectrometry. RECOMB 2000: 231-236

Sridhar Hannenhalli, Pavel A. Pevzner: Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals. J. ACM 46(1): 1-27 (1999)

Vlado Dancík, Theresa A. Addona, Karl R. Clauser, James E. Vath, Pavel A. Pevzner: De Novo Peptide Sequencing via Tandem Mass Spectrometry. Journal of Computational Biology 6(3/4): 327-342 (1999)

Earl Hubbell, Pavel A. Pevzner: Fidelity Probes for DNA Arrays. ISMB 1999: 113-117

Leslie Ann Goldberg, Paul W. Goldberg, Mike Paterson, Pavel A. Pevzner, Süleyman Cenk Sahinalp, Elizabeth Sweedyk: The Complexity of Gene Placement. SODA 1999: 386-395

Sing-Hoi Sze, Mikhail A. Roytberg, Mikhail S. Gelfand, Andrey A. Mironov, Tatiana V. Astakhova, Pavel A. Pevzner: Algorithms and software for support of gene identification experiments. Bioinformatics 14(1): 14-19 (1998)

Sorin Istrail, Pavel A. Pevzner, Ron Shamir: Foreword. Discrete Applied Mathematics 88(1-3): 3-6 (1998)

Vineet Bafna, Pavel A. Pevzner: Sorting by Transpositions. SIAM J. Discrete Math. 11(2): 224-240 (1998)

Andrey A. Mironov, Pavel A. Pevzner: SST versus EST in Gene Recognition (Invited Paper). SPIRE 1998: 60-64

I. Belyi, Pavel A. Pevzner: Software for DNA sequencing by hybridization. Computer Applications in the Biosciences 13(2): 205-210 (1997)

Michael S. Waterman, Sorin Istrail, Pavel A. Pevzner: Selected Papers from RECOMB'97 - Preface. Journal of Computational Biology 4(3): 215-216 (1997)

Sing-Hoi Sze, Pavel A. Pevzner: Las Vegas Algorithms for Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment. Journal of Computational Biology 4(3): 297-309 (1997)

Alfred V. Aho, David S. Johnson, Richard M. Karp, S. Rao Kosaraju, Catherine C. McGeoch, Christos H. Papadimitriou, Pavel A. Pevzner: Emerging opportunities for theoretical computer science. SIGACT News 28(3): 65-74 (1997)

Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner: Approximation Algorithms for Multiple Sequence Alignment. Theor. Comput. Sci. 182(1-2): 233-244 (1997)

Guorong Xu, Sing-Hoi Sze, Cheng-Pin Liu, Pavel A. Pevzner, Norman Arnheim: Gene Hunting without Sequencing Genomis Clones: the "Twenty Questions" game with genes. German Conference on Bioinformatics 1997: 17

Sing-Hoi Sze, Pavel A. Pevzner: Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. RECOMB 1997: 300-309

Sridhar Hannenhalli, W. Feldman, H. F. Lewis, Steven Skiena, Pavel A. Pevzner: Positional sequencing by hybridization. Computer Applications in the Biosciences 12(1): 19-24 (1996)

Vineet Bafna, Pavel A. Pevzner: Genome Rearrangements and Sorting by Reversals. SIAM J. Comput. 25(2): 272-289 (1996)

Mikhail S. Gelfand, Andrey A. Mironov, Pavel A. Pevzner: Spliced Alignment: A New Approach to Gene Recognition. CPM 1996: 141-158

Sridhar Hannenhalli, Pavel A. Pevzner: To Cut... or Not to Cut (Applications of Comparative Physical Maps in Molecular Evolution). SODA 1996: 304-313

Pavel A. Pevzner: DNA Physical Mapping and Alternating Eulerian Cycles in Colored Graphs. Algorithmica 13(1/2): 77-105 (1995)

Pavel A. Pevzner, Michael S. Waterman: Multiple Filtration and Approximate Pattern Matching. Algorithmica 13(1/2): 135-154 (1995)

Andrey A. Mironov, N. N. Alexandrov, N. Yu. Bogodarova, A. Grigorjev, V. F. Lebedev, L. V. Lunovskaya, M. E. Truchan, Pavel A. Pevzner: DNASUN: a package of computer programs for the biotechnology laboratory. Computer Applications in the Biosciences 11(3): 331-335 (1995)

Sridhar Hannenhalli, Pavel A. Pevzner: Towards a Computational Theory of Genome Rearrangements. Computer Science Today 1995: 184-202

Sridhar Hannenhalli, Pavel A. Pevzner: Transforming Men into Mice (Polynomial Algorithm for Genomic Distance Problem). FOCS 1995: 581-592

Pavel A. Pevzner, Michael S. Waterman: Open Combinatorial Problems in Computational Molecular Biology. ISTCS 1995: 158-173

Vineet Bafna, Pavel A. Pevzner: Sorting Permutations by Transpositions. SODA 1995: 614-623

Sridhar Hannenhalli, Pavel A. Pevzner: Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. STOC 1995: 178-189

Pavel A. Pevzner: Rearrangements of DNA Sequences and SBH. Computers & Chemistry 18(3): 221-223 (1994)

Vineet Bafna, Eugene L. Lawler, Pavel A. Pevzner: Approximation Algorithms for Multiple Sequence Alignment. CPM 1994: 43-53

Xiaoqiu Huang, Pavel A. Pevzner, Webb Miller: Parametric Recomuting in Alignment Graphs. CPM 1994: 87-101

Pavel A. Pevzner, Robert J. Lipshutz: Towards DNA Sequencing Chips. MFCS 1994: 143-158

Pavel A. Pevzner, Michael S. Waterman: A Fast Filtration Algorithm for the Substring Matching Problem. CPM 1993: 197-214

Martin Vingron, Pavel A. Pevzner: Multiple Sequence Comparison and n-Dimensional Image Reconstruction. CPM 1993: 243-253

Vineet Bafna, Pavel A. Pevzner: Genome Rearrangements and Sorting by Reversals. FOCS 1993: 148-157

Pavel A. Pevzner: Statistical distance between texts and filtration methods in sequence comparison. Computer Applications in the Biosciences 8(2): 121-127 (1992)

Mikhail S. Gelfand, C. G. Kozhukhin, Pavel A. Pevzner: Extendable words in nucleotide sequences. Computer Applications in the Biosciences 8(2): 129-135 (1992)

Pavel A. Pevzner: Nucleotide Sequences Versus Markov Models. Computers & Chemistry 16(2): 103-106 (1992)

Pavel A. Pevzner, Michael S. Waterman: Matrix Longest Common Subsequence Problem, Duality and Hibert Bases. CPM 1992: 79-89

Pavel A. Pevzner: Multiple Alignment with Guaranteed Error Bounds and Communication Cost. CPM 1992: 205-213

C. G. Kozhukhin, Pavel A. Pevzner: Genome inhomogeneity is determined mainly by WW and SS dinucleotides. Computer Applications in the Biosciences 7(1): 39-49 (1991)