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Pavel Pevzner
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Network (preview)
11
Tesler, Glenn
10
Tang, Haixu
9
Bafna, Vineet
8
Tanner, Stephen
7
Bourque, Guillaume
7
Sze, Sing-Hoi
5
Raphael, Benjamin
4
Smith, Richard
4
Zhi, Degui
4
Keich, Uri
3
Heber, Steffen
3
Eskin, Eleazar
3
Frank, Ari
3
Zandi, Ebrahim
3
Gelfand, Mikhail
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All Publications
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2009: Gupta Nitin; Pevzner Pavel A
False discovery rates of protein identifications: a strike against the two-peptide rule.
Journal of proteome research 2009;8(9):4173-81.
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2009: Ng Julio; Bandeira Nuno; Liu Wei-Ting; Ghassemian Majid; Simmons Thomas L; Gerwick William H; Linington Roger; Dorrestein Pieter C; Pevzner Pavel A
Dereplication and de novo sequencing of nonribosomal peptides.
Nature methods 2009;6(8):596-9.
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2009: Liu Wei-Ting; Ng Julio; Meluzzi Dario; Bandeira Nuno; Gutierrez Marcelino; Simmons Thomas L; Schultz Andrew W; Linington Roger G; Moore Bradley S; Gerwick William H; Pevzner Pavel A; Dorrestein Pieter C
Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides.
Analytical chemistry 2009;81(11):4200-9.
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2009: Kim Sangtae; Bandeira Nuno; Pevzner Pavel A
Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification.
Molecular & cellular proteomics : MCP 2009;8(6):1391-400.
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2009: Alekseyev Max A; Pevzner Pavel A
Breakpoint graphs and ancestral genome reconstructions.
Genome research 2009;19(5):943-57.
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2009: Chaisson Mark J; Brinza Dumitru; Pevzner Pavel A
De novo fragment assembly with short mate-paired reads: Does the read length matter?
Genome research 2009;19(2):336-46.
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2009: Kim Sangtae; Gupta Nitin; Bandeira Nuno; Pevzner Pavel A
Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra.
Molecular & cellular proteomics : MCP 2009;8(1):53-69.
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2008: Bandeira Nuno; Pham Victoria; Pevzner Pavel; Arnott David; Lill Jennie R
Automated de novo protein sequencing of monoclonal antibodies.
Nature biotechnology 2008;26(12):1336-8.
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2008: Pevzner Pavel A; Kim Sangtae; Ng Julio
Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".
Science (New York, N.Y.) 2008;321(5892):1040; author reply 1040.
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2008: Kim Sangtae; Gupta Nitin; Pevzner Pavel A
Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.
Journal of proteome research 2008;7(8):3354-63.
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2008: Bandeira Nuno; Olsen Jesper V; Mann Jesper V; Mann Matthias; Pevzner Pavel A
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry.
Bioinformatics (Oxford, England) 2008;24(13):i416-23.
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2008: Gupta Nitin; Benhamida Jamal; Bhargava Vipul; Goodman Daniel; Kain Elisabeth; Kerman Ian; Nguyen Ngan; Ollikainen Noah; Rodriguez Jesse; Wang Jian; Lipton Mary S; Romine Margaret; Bafna Vineet; Smith Richard D; Pevzner Pavel A
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.
Genome research 2008;18(7):1133-42.
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2008: Frank Ari M; Pesavento James J; Mizzen Craig A; Kelleher Neil L; Pevzner Pavel A
Interpreting top-down mass spectra using spectral alignment.
Analytical chemistry 2008;80(7):2499-505.
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2008: Chaisson Mark J; Pevzner Pavel A
Short read fragment assembly of bacterial genomes.
Genome research 2008;18(2):324-30.
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2008: Ng Julio; Pevzner Pavel A
Algorithm for identification of fusion proteins via mass spectrometry.
Journal of proteome research 2008;7(1):89-95.
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2008: Rodriguez Jesse; Gupta Nitin; Smith Richard D; Pevzner Pavel A
Does trypsin cut before proline?
Journal of proteome research 2008;7(1):300-5.
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2008: Frank Ari M; Bandeira Nuno; Shen Zhouxin; Tanner Stephen; Briggs Steven P; Smith Richard D; Pevzner Pavel A
Clustering millions of tandem mass spectra.
Journal of proteome research 2008;7(1):113-22.
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2007: Alekseyev Max A; Pevzner Pavel A
Are there rearrangement hotspots in the human genome?
PLoS computational biology 2007;3(11):e209.
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2007: Gupta Nitin; Tanner Stephen; Jaitly Navdeep; Adkins Joshua N; Lipton Mary; Edwards Robert; Romine Margaret; Osterman Andrei; Bafna Vineet; Smith Richard D; Pevzner Pavel A
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.
Genome research 2007;17(9):1362-77.
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2007: Bandeira Nuno; Clauser Karl R; Pevzner Pavel A
Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.
Molecular & cellular proteomics : MCP 2007;6(7):1123-34.
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2007: Bandeira Nuno; Tsur Dekel; Frank Ari; Pevzner Pavel A
Protein identification by spectral networks analysis.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(15):6140-5.
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2007: Alekseyev Max A; Pevzner Pavel A
Colored de Bruijn graphs and the genome halving problem.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2007;4(1):98-107.
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2007: Zhi Degui; Keich Uri; Pevzner Pavel; Heber Steffen; Tang Haixu
Correcting base-assignment errors in repeat regions of shotgun assembly.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2007;4(1):54-64.
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2007: Frank Ari M; Savitski Mikhail M; Nielsen Michael L; Zubarev Roman A; Pevzner Pavel A
De novo peptide sequencing and identification with precision mass spectrometry.
Journal of proteome research 2007;6(1):114-23.
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2006: Chaisson M J; Raphael B J; Pevzner P A
Microinversions in mammalian evolution.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(52):19824-9.
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2006: Wilmarth P A; Tanner S; Dasari S; Nagalla S R; Riviere M A; Bafna V; Pevzner P A; David L L
Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?
Journal of proteome research 2006;5(10):2554-66.
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2006: Jones Neil C; Pevzner Pavel A
Comparative genomics reveals unusually long motifs in mammalian genomes.
Bioinformatics (Oxford, England) 2006;22(14):e236-42.
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2006: Bourque Guillaume; Tesler Glenn; Pevzner Pavel A
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction.
Genome research 2006;16(3):311-3.
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2006: Volik Stanislav; Raphael Benjamin J; Huang Guiqing; Stratton Michael R; Bignel Graham; Murnane John; Brebner John H; Bajsarowicz Krystyna; Paris Pamela L; Tao Quanzhou; Kowbel David; Lapuk Anna; Shagin Dmitri A; Shagina Irina A; Gray Joe W; Cheng Jan-Fang; de Jong Pieter J; Pevzner Pavel; Collins Colin
Decoding the fine-scale structure of a breast cancer genome and transcriptome.
Genome research 2006;16(3):394-404.
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2006: Peng Qian; Pevzner Pavel A; Tesler Glenn
The fragile breakage versus random breakage models of chromosome evolution.
PLoS computational biology 2006;2(2):e14.
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2006: Tanner Stephen; Pevzner Pavel A; Bafna Vineet
Unrestrictive identification of post-translational modifications through peptide mass spectrometry.
Nature protocols 2006;1(1):67-72.
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2006: Zhi Degui; Krishna S Sri; Cao Haibo; Pevzner Pavel; Godzik Adam
Representing and comparing protein structures as paths in three-dimensional space.
BMC bioinformatics 2006;7():460.
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2006: Zhi Degui; Raphael Benjamin J; Price Alkes L; Tang Haixu; Pevzner Pavel A
Identifying repeat domains in large genomes.
Genome biology 2006;7(1):R7.
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2005: Tsur Dekel; Tanner Stephen; Zandi Ebrahim; Bafna Vineet; Pevzner Pavel A
Identification of post-translational modifications by blind search of mass spectra.
Nature biotechnology 2005;23(12):1562-7.
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2005: Frank Ari; Tanner Stephen; Bafna Vineet; Pevzner Pavel
Peptide sequence tags for fast database search in mass-spectrometry.
Journal of proteome research 2005;4(4):1287-95.
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2005: Murphy William J; Larkin Denis M; Everts-van der Wind Annelie; Bourque Guillaume; Tesler Glenn; Auvil Loretta; Beever Jonathan E; Chowdhary Bhanu P; Galibert Francis; Gatzke Lisa; Hitte Christophe; Meyers Stacey N; Milan Denis; Ostrander Elaine A; Pape Greg; Parker Heidi G; Raudsepp Terje; Rogatcheva Margarita B; Schook Lawrence B; Skow Loren C; Welge Michael; Womack James E; O'brien Stephen J; Pevzner Pavel A; Lewin Harris A
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps.
Science (New York, N.Y.) 2005;309(5734):613-7.
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2005: Tanner Stephen; Shu Hongjun; Frank Ari; Wang Ling-Chi; Zandi Ebrahim; Mumby Marc; Pevzner Pavel A; Bafna Vineet
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra.
Analytical chemistry 2005;77(14):4626-39.
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2005: Price Alkes L; Jones Neil C; Pevzner Pavel A
De novo identification of repeat families in large genomes.
Bioinformatics (Oxford, England) 2005;21 Suppl 1():i351-8.
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2005: Frank Ari; Pevzner Pavel
PepNovo: de novo peptide sequencing via probabilistic network modeling.
Analytical chemistry 2005;77(4):964-73.
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2005: Bourque Guillaume; Zdobnov Evgeny M; Bork Peer; Pevzner Pavel A; Tesler Glenn
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Genome research 2005;15(1):98-110.
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2005: Tsur Dekel; Tanner Stephen; Zandi Ebrahim; Bafna Vineet; Pevzner Pavel A
Identification of post-translational modifications via blind search of mass-spectra.
Proceedings / IEEE Computational Systems Bioinformatics Conference, CSB. IEEE Computational Systems Bioinformatics Conference 2005;():157-66.
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2004: Bandeira Nuno; Tang Haixu; Bafna Vineet; Pevzner Pavel
Shotgun protein sequencing by tandem mass spectra assembly.
Analytical chemistry 2004;76(24):7221-33.
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2004: Raphael Benjamin; Zhi Degui; Tang Haixu; Pevzner Pavel
A novel method for multiple alignment of sequences with repeated and shuffled elements.
Genome research 2004;14(11):2336-46.
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2004: Price Alkes L; Eskin Eleazar; Pevzner Pavel A
Whole-genome analysis of Alu repeat elements reveals complex evolutionary history.
Genome research 2004;14(11):2245-52.
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2004: Pevzner Pavel A; Tang Haixu; Tesler Glenn
De novo repeat classification and fragment assembly.
Genome research 2004;14(9):1786-96.
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2004: Pevzner Pavel A; Tang Haixu; Tesler Glenn
De novo repeat classification and fragment assembly.
Genome research 2004;14(9):1786-96.
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2004: Chaisson Mark; Pevzner Pavel; Tang Haixu
Fragment assembly with short reads.
Bioinformatics (Oxford, England) 2004;20(13):2067-74.
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2004: Raphael Benjamin J; Pevzner Pavel A
Reconstructing tumor amplisomes.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i265-73.
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2004: Andelfinger G; Hitte C; Etter L; Guyon R; Bourque G; Tesler G; Pevzner P; Kirkness E; Galibert F; Benson D W
Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements.
Genomics 2004;83(6):1053-62.
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2004: Bourque Guillaume; Pevzner Pavel A; Tesler Glenn
Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes.
Genome research 2004;14(4):507-16.
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2004: Leipzig Jeremy; Pevzner Pavel; Heber Steffen
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome.
Nucleic acids research 2004;32(13):3977-83.
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2004: Kahng Andrew B; Mandoiu Ion I; Pevzner Pavel A; Reda Sherief; Zelikovsky Alexander Z
Scalable heuristics for design of DNA probe arrays.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(2-3):429-47.
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2003: Murphy William J; Bourque Guillaume; Tesler Glenn; Pevzner Pavel; O'Brien Stephen J
Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.
Human genomics 2003;1(1):30-40.
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2003: Raphael Benjamin J; Volik Stanislav; Collins Colin; Pevzner Pavel A
Reconstructing tumor genome architectures.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii162-71.
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2003: Price Alkes; Ramabhadran Sriram; Pevzner Pavel A
Finding subtle motifs by branching from sample strings.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii149-55.
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2003: Pevzner Pavel; Tesler Glenn
Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(13):7672-7.
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2003: Pevzner Pavel; Tesler Glenn
Genome rearrangements in mammalian evolution: lessons from human and mouse genomes.
Genome research 2003;13(1):37-45.
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2003: Eskin Eleazar; Keich Uri; Gelfand Mikhail S; Pevzner Pavel A
Genome-wide analysis of bacterial promoter regions.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003;():29-40.
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2002: Lunyak Victoria V; Burgess Robert; Prefontaine Gratien G; Nelson Charles; Sze Sing-Hoi; Chenoweth Josh; Schwartz Phillip; Pevzner Pavel A; Glass Christopher; Mandel Gail; Rosenfeld Michael G
Corepressor-dependent silencing of chromosomal regions encoding neuronal genes.
Science (New York, N.Y.) 2002;298(5599):1747-52.
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2002: Keich U; Pevzner P A
Subtle motifs: defining the limits of motif finding algorithms.
Bioinformatics (Oxford, England) 2002;18(10):1382-90.
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2002: Keich U; Pevzner P A
Finding motifs in the twilight zone.
Bioinformatics (Oxford, England) 2002;18(10):1374-81.
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2002: Bourque Guillaume; Pevzner Pavel A
Genome-scale evolution: reconstructing gene orders in the ancestral species.
Genome research 2002;12(1):26-36.
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2002: Hannenhalli Sridhar; Hubell Earl; Lipshutz Robert; Pevzner Pavel A
Combinatorial algorithms for design of DNA arrays.
Advances in biochemical engineering/biotechnology 2002;77():1-19.
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2002: Eskin Eleazar; Pevzner Pavel A
Finding composite regulatory patterns in DNA sequences.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S354-63.
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2002: Heber Steffen; Alekseyev Max; Sze Sing-Hoi; Tang Haixu; Pevzner Pavel A
Splicing graphs and EST assembly problem.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S181-8.
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2002: Sze S H; Gelfand M S; Pevzner P A
Finding weak motifs in DNA sequences.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():235-46.
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2002: Mulyukov Zufar; Pevzner Pavel A
EULER-PCR: finishing experiments for repeat resolution.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():199-210.
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2001: Pevzner P A
Assembling puzzles from preassembled blocks.
Genome research 2001;11(9):1461-2.
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2001: Pevzner P A; Tang H; Waterman M S
An Eulerian path approach to DNA fragment assembly.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(17):9748-53.
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2001: Arslan A N; Egecioglu O; Pevzner P A
A new approach to sequence comparison: normalized sequence alignment.
Bioinformatics (Oxford, England) 2001;17(4):327-37.
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2001: Pevzner P A; Mulyukov Z; Dancik V; Tang C L
Efficiency of database search for identification of mutated and modified proteins via mass spectrometry.
Genome research 2001;11(2):290-9.
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2001: Pevzner P A; Tang H
Fragment assembly with double-barreled data.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S225-33.
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2000: Pevzner P A; Dancík V; Tang C L
Mutation-tolerant protein identification by mass spectrometry.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(6):777-87.
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2000: Pevzner P A; Sze S H
Combinatorial approaches to finding subtle signals in DNA sequences.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 2000;8():269-78.
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1999: Hubbell E; Pevzner P A
Fidelity probes for DNA arrays.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():113-7.
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1999: Mironov A A; Pevzner P A
SST versus EST in gene recognition.
Microbial & comparative genomics 1999;4(3):167-72.
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1999: Dancík V; Addona T A; Clauser K R; Vath J E; Pevzner P A
De novo peptide sequencing via tandem mass spectrometry.
Journal of computational biology : a journal of computational molecular cell biology 1999;6(3-4):327-42.
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1998: Mironov A A; Roytberg M A; Pevzner P A; Gelfand M S
Performance-guarantee gene predictions via spliced alignment.
Genomics 1998;51(3):332-9.
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1998: Xu G; Sze S H; Liu C P; Pevzner P A; Arnheim N
Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs.
Genomics 1998;47(2):171-9.
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1998: Sze S H; Roytberg M A; Gelfand M S; Mironov A A; Astakhova T V; Pevzner P A
Algorithms and software for support of gene identification experiments.
Bioinformatics (Oxford, England) 1998;14(1):14-9.
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1997: Sze S H; Pevzner P A
Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(3):297-309.
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1996: Gelfand M S; Mironov A A; Pevzner P A
Gene recognition via spliced sequence alignment.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(17):9061-6.
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1995: Mironov A A; Alexandrov N N; Bogodarova NYu; Grigorjev A; Lebedev V F; Lunovskaya L V; Truchan M E; Pevzner P A
DNASUN: a package of computer programs for the biotechnology laboratory.
Computer applications in the biosciences : CABIOS 1995;11(3):331-5.
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1992: Pevzner P A
Statistical distance between texts and filtration methods in sequence comparison.
Computer applications in the biosciences : CABIOS 1992;8(2):121-7.
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1992: Gelfand M S; Kozhukhin C G; Pevzner P A
Extendable words in nucleotide sequences.
Computer applications in the biosciences : CABIOS 1992;8(2):129-35.
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1991: Kozhukhin C G; Pevzner P A
Genome inhomogeneity is determined mainly by WW and SS dinucleotides.
Computer applications in the biosciences : CABIOS 1991;7(1):39-49.
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