Pavel Pevzner

Title(s)Professor, Computer Science and Engineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research Activities and Funding
    DEVELOPMENT OF ONLINE COMPUTATIONAL GENOMICS SPECIALIZATION
    NIH R25HG011022May 8, 2020 - Feb 28, 2025
    Role: Principal Investigator
    Integrated Active Learning Framework for Biomedical BD2K
    NIH R25GM114819Sep 29, 2014 - Aug 31, 2019
    Role: Principal Investigator
    New approaches to sequencing of complex peptides.
    NIH R01GM086283Sep 25, 2008 - Aug 31, 2012
    Role: Principal Investigator
    Center for Computational Mass Spectrometry
    NIH P41GM103484Sep 20, 2008 - Jun 30, 2021
    Role: Principal Investigator
    Center for Computational Mass-Spectrometry
    NIH P41RR024851Sep 20, 2008 - Jun 30, 2013
    Role: Principal Investigator
    Algorithms &Software for Computational Mass Spectrometry
    NIH R01RR016522Dec 1, 2001 - Aug 31, 2010
    Role: Principal Investigator
    A New Approach to Fragment Assembly in DNA Sequencing
    NIH R01HG002366Aug 24, 2001 - Jul 31, 2005
    Role: Principal Investigator
    Graduate Training Program in Bioinformatics
    NIH T32GM008806Jul 1, 2001 - Jun 30, 2021
    Role: Principal Investigator
    Comprehensive Biology: Exploiting the Yeast Genome
    NIH P41RR011823Sep 30, 1996 - Jun 30, 2016
    Role: Co-Investigator
    NATIONAL BIOMEDICAL COMPUTATION RESOURCE
    NIH P41RR008605Apr 15, 1994 - Apr 30, 2014
    Role: Co-Investigator
    ALGORITHMS AND SOFTWARE FOR SEQUENCING BY HYBRIDIZATION
    NIH R01HG000987Feb 7, 1994 - Jul 31, 1997
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Complete sequencing of ape genomes. bioRxiv. 2024 Oct 05. Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Roha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. PMID: 39131277; PMCID: PMC11312596.
      View in: PubMed   Mentions:
    2. SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs. PeerJ. 2024; 12:e18050. Tolstoganov I, Chen Z, Pevzner P, Korobeynikov A. PMID: 39351368; PMCID: PMC11441382.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    3. Synthetic lethality and the minimal genome size problem. mSphere. 2024 Jul 30; 9(7):e0013924. Rahiminejad S, De Sanctis B, Pevzner P, Mushegian A. PMID: 38904396; PMCID: PMC11288024.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    4. UniAligner: a parameter-free framework for fast sequence alignment. Nat Methods. 2023 09; 20(9):1346-1354. Bzikadze AV, Pevzner PA. PMID: 37580559.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    5. Analyzing rare mutations in metagenomes assembled using long and accurate reads. Genome Res. 2022 Nov-Dec; 32(11-12):2119-2133. Fedarko MW, Kolmogorov M, Pevzner PA. PMID: 36418060; PMCID: PMC9808630.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    6. Fast and accurate mapping of long reads to complete genome assemblies with VerityMap. Genome Res. 2022 Nov-Dec; 32(11-12):2107-2118. Bzikadze AV, Mikheenko A, Pevzner PA. PMID: 36379716; PMCID: PMC9808623.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    7. Michael Waterman's Contributions to Computational Biology and Bioinformatics. J Comput Biol. 2022 07; 29(7):601-615. Pevzner P, Vingron M, Reidys C, Sun F, Istrail S. PMID: 35727100.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    8. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics. 2022 07; 21(7):100254. Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. PMID: 35654359; PMCID: PMC9256833.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    9. Gene prediction in the immunoglobulin loci. Genome Res. 2022 06; 32(6):1152-1169. Sirupurapu V, Safonova Y, Pevzner PA. PMID: 35545447; PMCID: PMC9248892.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    10. Automated annotation of human centromeres with HORmon. Genome Res. 2022 06; 32(6):1137-1151. Kunyavskaya O, Dvorkina T, Bzikadze AV, Alexandrov IA, Pevzner PA. PMID: 35545449; PMCID: PMC9248890.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    11. Complete genomic and epigenetic maps of human centromeres. Science. 2022 04; 376(6588):eabl4178. Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. PMID: 35357911; PMCID: PMC9233505.
      View in: PubMed   Mentions: 149     Fields:    Translation:HumansCells
    12. The complete sequence of a human genome. Science. 2022 04; 376(6588):44-53. Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sovic I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. PMID: 35357919; PMCID: PMC9186530.
      View in: PubMed   Mentions: 892     Fields:    Translation:HumansCells
    13. Variations in antibody repertoires correlate with vaccine responses. Genome Res. 2022 04; 32(4):791-804. Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. PMID: 35361626; PMCID: PMC8997358.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    14. Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads. Nat Biotechnol. 2022 07; 40(7):1075-1081. Bankevich A, Bzikadze AV, Kolmogorov M, Antipov D, Pevzner PA. PMID: 35228706.
      View in: PubMed   Mentions: 32     Fields:    Translation:Humans
    15. viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data. Genome Biol. 2022 02 21; 23(1):57. Antipov D, Rayko M, Kolmogorov M, Pevzner PA. PMID: 35189932; PMCID: PMC8862349.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    16. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nat Biotechnol. 2022 05; 40(5):711-719. Bickhart DM, Kolmogorov M, Tseng E, Portik DM, Korobeynikov A, Tolstoganov I, Uritskiy G, Liachko I, Sullivan ST, Shin SB, Zorea A, Andreu VP, Panke-Buisse K, Medema MH, Mizrahi I, Pevzner PA, Smith TPL. PMID: 34980911.
      View in: PubMed   Mentions: 67     Fields:    Translation:Animals
    17. CentromereArchitect: inference and analysis of the architecture of centromeres. Bioinformatics. 2021 07 12; 37(Suppl_1):i196-i204. Dvorkina T, Kunyavskaya O, Bzikadze AV, Alexandrov I, Pevzner PA. PMID: 34252949; PMCID: PMC8336445.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    18. Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun. 2021 Jul 08; 12(1):4318. Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. PMID: 34238936; PMCID: PMC8266848.
      View in: PubMed   Mentions:    Fields:    
    19. ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs. Microbiome. 2021 06 28; 9(1):149. Dvorkina T, Bankevich A, Sorokin A, Yang F, Adu-Oppong B, Williams R, Turner K, Pevzner PA. PMID: 34183047; PMCID: PMC8240309.
      View in: PubMed   Mentions: 3     Fields:    
    20. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun. 2021 05 28; 12(1):3225. Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. PMID: 34050176; PMCID: PMC8163882.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCellsPHPublic Health
    21. Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res. 2021 May; 31(5):934. Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. PMID: 33941606; PMCID: PMC8092014.
      View in: PubMed   Mentions:    Fields:    
    22. Thousands of previously unknown phages discovered in whole-community human gut metagenomes. Microbiome. 2021 03 29; 9(1):78. Benler S, Yutin N, Antipov D, Rayko M, Shmakov S, Gussow AB, Pevzner P, Koonin EV. PMID: 33781338; PMCID: PMC8008677.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansCells
    23. Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nat Commun. 2021 02 16; 12(1):1044. Yutin N, Benler S, Shmakov SA, Wolf YI, Tolstoy I, Rayko M, Antipov D, Pevzner PA, Koonin EV. PMID: 33594055; PMCID: PMC7886860.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansCells
    24. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Mar Drugs. 2021 Jan 06; 19(1). Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L. PMID: 33418911; PMCID: PMC7825088.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    25. Trace Reconstruction Problems in Computational Biology. IEEE Trans Inf Theory. 2021 Jun; 67(6):3295-3314. Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. PMID: 34176957; PMCID: PMC8224466.
      View in: PubMed   Mentions: 1  
    26. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods. 2020 11; 17(11):1103-1110. Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. PMID: 33020656; PMCID: PMC10699202.
      View in: PubMed   Mentions: 311     Fields:    Translation:HumansAnimals
    27. V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s. Genome Res. 2020 11; 30(11):1547-1558. Safonova Y, Pevzner PA. PMID: 32948615; PMCID: PMC7605257.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    28. Metaviral SPAdes: assembly of viruses from metagenomic data. Bioinformatics. 2020 08 15; 36(14):4126-4129. Antipov D, Raiko M, Lapidus A, Pevzner PA. PMID: 32413137.
      View in: PubMed   Mentions: 106     Fields:    Translation:Cells
    29. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020 09; 585(7823):79-84. Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM. PMID: 32663838; PMCID: PMC7484160.
      View in: PubMed   Mentions: 343     Fields:    Translation:HumansCells
    30. Automated assembly of centromeres from ultra-long error-prone reads. Nat Biotechnol. 2020 11; 38(11):1309-1316. Bzikadze AV, Pevzner PA. PMID: 32665660; PMCID: PMC10718184.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    31. TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics. 2020 07 01; 36(Suppl_1):i75-i83. Mikheenko A, Bzikadze AV, Gurevich A, Miga KH, Pevzner PA. PMID: 32657355; PMCID: PMC7355294.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    32. The string decomposition problem and its applications to centromere analysis and assembly. Bioinformatics. 2020 07 01; 36(Suppl_1):i93-i101. Dvorkina T, Bzikadze AV, Pevzner PA. PMID: 32657390; PMCID: PMC7428072.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    33. Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res. 2020 06; 30(6):898-909. Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. PMID: 32540955; PMCID: PMC7370886.
      View in: PubMed   Mentions: 50     Fields:    Translation:Humans
    34. Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLoS Comput Biol. 2020 04; 16(4):e1007837. Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. PMID: 32339161; PMCID: PMC7295240.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimals
    35. De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst. 2020 01 22; 10(1):99-108.e5. Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA. PMID: 31864964.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    36. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 2019 10 31; 20(1):226. Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. PMID: 31672156; PMCID: PMC6822431.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimals
    37. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst. 2019 12 18; 9(6):600-608.e4. Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. PMID: 31629686; PMCID: PMC6952069.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    38. cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. Bioinformatics. 2019 07 15; 35(14):i61-i70. Tolstoganov I, Bankevich A, Chen Z, Pevzner PA. PMID: 31510642; PMCID: PMC6612831.
      View in: PubMed   Mentions: 15     Fields:    
    39. BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs. Genome Res. 2019 08; 29(8):1352-1362. Meleshko D, Mohimani H, Tracanna V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA. PMID: 31160374; PMCID: PMC6673720.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    40. De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins. Front Immunol. 2019; 10:987. Safonova Y, Pevzner PA. PMID: 31134072; PMCID: PMC6516046.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    41. Plasmid detection and assembly in genomic and metagenomic data sets. Genome Res. 2019 06; 29(6):961-968. Antipov D, Raiko M, Lapidus A, Pevzner PA. PMID: 31048319; PMCID: PMC6581055.
      View in: PubMed   Mentions: 65     Fields:    Translation:Humans
    42. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 05; 37(5):540-546. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. PMID: 30936562.
      View in: PubMed   Mentions: 1922     Fields:    Translation:HumansCells
    43. How bioinformatics and open data can boost basic science in countries and universities with limited resources. Nat Biotechnol. 2019 03; 37(3):324-326. Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E. PMID: 30833765.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    44. Dereplication of microbial metabolites through database search of mass spectra. Nat Commun. 2018 10 02; 9(1):4035. Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA. PMID: 30279420; PMCID: PMC6168521.
      View in: PubMed   Mentions: 116     Fields:    Translation:Cells
    45. Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity. Cell Syst. 2018 08 22; 7(2):192-200.e3. Bankevich A, Pevzner PA. PMID: 30056005.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    46. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut Consortium , Knight R. PMID: 29795809; PMCID: PMC5954204.
      View in: PubMed   Mentions: 363     Fields:    
    47. Detection and analysis of ancient segmental duplications in mammalian genomes. Genome Res. 2018 06; 28(6):901-909. Pu L, Lin Y, Pevzner PA. PMID: 29735604; PMCID: PMC5991524.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    48. A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch. Plant Direct. 2018 Feb; 2(2). Fisher MF, Zhang J, Taylor NL, Howard MJ, Berkowitz O, Debowski AW, Behsaz B, Whelan J, Pevzner PA, Mylne JS. PMID: 30417166; PMCID: PMC6223261.
      View in: PubMed   Mentions: 12  
    49. Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nat Microbiol. 2018 03; 3(3):319-327. Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner PA. PMID: 29358742; PMCID: PMC5951390.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
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    114. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics. 2010 Dec; 9(12):2772-82. Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. PMID: 20855543; PMCID: PMC3101958.
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    115. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics. 2010 Dec; 9(12):2840-52. Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. PMID: 20829449; PMCID: PMC3101864.
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    116. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proc Natl Acad Sci U S A. 2010 Sep 14; 107(37):16286-90. Liu WT, Yang YL, Xu Y, Lamsa A, Haste NM, Yang JY, Ng J, Gonzalez D, Ellermeier CD, Straight PD, Pevzner PA, Pogliano J, Nizet V, Pogliano K, Dorrestein PC. PMID: 20805502; PMCID: PMC2941286.
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    117. Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication. AAPS J. 2010 Dec; 12(4):635-45. Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O'Connor DT, Pevzner P. PMID: 20734175; PMCID: PMC2976990.
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    118. DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics. 2010 Oct 15; 26(20):2509-16. Pham SK, Pevzner PA. PMID: 20736338.
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    119. Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry. Proteomics. 2010 Aug; 10(15):2833-44. Gupta N, Hixson KK, Culley DE, Smith RD, Pevzner PA. PMID: 20597098; PMCID: PMC3220954.
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    120. Synergistic allelochemicals from a freshwater cyanobacterium. Proc Natl Acad Sci U S A. 2010 Jun 22; 107(25):11183-8. Leão PN, Pereira AR, Liu WT, Ng J, Pevzner PA, Dorrestein PC, König GM, Vasconcelos VM, Gerwick WH. PMID: 20534563; PMCID: PMC2895120.
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    121. False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res. 2009 Sep; 8(9):4173-81. Gupta N, Pevzner PA. PMID: 19627159; PMCID: PMC3398614.
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    122. Computing has changed biology--biology education must catch up. Science. 2009 Jul 31; 325(5940):541-2. Pevzner P, Shamir R. PMID: 19644094.
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    123. Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods. 2009 Aug; 6(8):596-9. Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. PMID: 19597502; PMCID: PMC2754211.
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    124. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem. 2009 Jun 01; 81(11):4200-9. Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. PMID: 19413302; PMCID: PMC2765223.
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    125. Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Mol Cell Proteomics. 2009 Jun; 8(6):1391-400. Kim S, Bandeira N, Pevzner PA. PMID: 19254948; PMCID: PMC2690493.
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    126. Breakpoint graphs and ancestral genome reconstructions. Genome Res. 2009 May; 19(5):943-57. Alekseyev MA, Pevzner PA. PMID: 19218533; PMCID: PMC2675983.
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    127. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res. 2009 Feb; 19(2):336-46. Chaisson MJ, Brinza D, Pevzner PA. PMID: 19056694; PMCID: PMC2652199.
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    128. Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol. 2008 Dec; 26(12):1336-8. Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR. PMID: 19060866; PMCID: PMC2891972.
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    129. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science. 2008 Aug 22; 321(5892):1040; author reply 1040. Pevzner PA, Kim S, Ng J. PMID: 18719266.
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    130. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics. 2009 Jan; 8(1):53-69. Kim S, Gupta N, Bandeira N, Pevzner PA. PMID: 18703573; PMCID: PMC2621003.
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    131. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res. 2008 Aug; 7(8):3354-63. Kim S, Gupta N, Pevzner PA. PMID: 18597511; PMCID: PMC2689316.
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    132. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics. 2008 Jul 01; 24(13):i416-23. Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. PMID: 18785330; PMCID: PMC2718660.
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    133. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 2008 Jul; 18(7):1133-42. Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA. PMID: 18426904; PMCID: PMC2493402.
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    134. Interpreting top-down mass spectra using spectral alignment. Anal Chem. 2008 Apr 01; 80(7):2499-505. Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA. PMID: 18302345.
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    135. Algorithm for identification of fusion proteins via mass spectrometry. J Proteome Res. 2008 Jan; 7(1):89-95. Ng J, Pevzner PA. PMID: 18173219.
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    136. Short read fragment assembly of bacterial genomes. Genome Res. 2008 Feb; 18(2):324-30. Chaisson MJ, Pevzner PA. PMID: 18083777; PMCID: PMC2203630.
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    137. Does trypsin cut before proline? J Proteome Res. 2008 Jan; 7(1):300-5. Rodriguez J, Gupta N, Smith RD, Pevzner PA. PMID: 18067249.
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    138. Clustering millions of tandem mass spectra. J Proteome Res. 2008 Jan; 7(1):113-22. Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. PMID: 18067247; PMCID: PMC2533155.
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    139. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet. 2007 Nov; 39(11):1361-8. Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, Eichler EE. PMID: 17922013.
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    140. Are there rearrangement hotspots in the human genome? PLoS Comput Biol. 2007 Nov; 3(11):e209. Alekseyev MA, Pevzner PA. PMID: 17997591; PMCID: PMC2065889.
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    141. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007 Sep; 17(9):1362-77. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. PMID: 17690205; PMCID: PMC1950905.
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    142. Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics. 2007 Jul; 7(14):2318-29. Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A. PMID: 17623296.
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    143. Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One. 2007 May 30; 2(5):e484. Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. PMID: 17534434; PMCID: PMC1871613.
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    144. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics. 2007 Jul; 6(7):1123-34. Bandeira N, Clauser KR, Pevzner PA. PMID: 17446555.
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    145. Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A. 2007 Apr 10; 104(15):6140-5. Bandeira N, Tsur D, Frank A, Pevzner PA. PMID: 17404225; PMCID: PMC1851064.
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    146. Colored de Bruijn graphs and the genome halving problem. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):98-107. Alekseyev MA, Pevzner PA. PMID: 17277417.
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    147. Correcting base-assignment errors in repeat regions of shotgun assembly. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):54-64. Zhi D, Keich U, Pevzner P, Heber S, Tang H. PMID: 17277413.
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    148. De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res. 2007 Jan; 6(1):114-23. Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA. PMID: 17203955; PMCID: PMC2538556.
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    149. Microinversions in mammalian evolution. Proc Natl Acad Sci U S A. 2006 Dec 26; 103(52):19824-9. Chaisson MJ, Raphael BJ, Pevzner PA. PMID: 17189424; PMCID: PMC1750909.
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    150. Modeling and characterization of multi-charge mass spectra for peptide sequencing. J Bioinform Comput Biol. 2006 Dec; 4(6):1329-52. Chong KF, Ning K, Leong HW, Pevzner P. PMID: 17245817.
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    151. Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics. 2006 Oct 20; 7:460. Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. PMID: 17052359; PMCID: PMC1626488.
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    152. 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? J Proteome Res. 2006 Oct; 5(10):2554-66. Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. PMID: 17022627; PMCID: PMC2536618.
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    153. Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches. J Proteome Res. 2006 Sep; 5(9):2448-56. Wielsch N, Thomas H, Surendranath V, Waridel P, Frank A, Pevzner P, Shevchenko A. PMID: 16944958.
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    154. Comparative genomics reveals unusually long motifs in mammalian genomes. Bioinformatics. 2006 Jul 15; 22(14):e236-42. Jones NC, Pevzner PA. PMID: 16873477.
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    155. The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 2006 Mar; 16(3):311-3. Bourque G, Tesler G, Pevzner PA. PMID: 16510896; PMCID: PMC1415205.
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    156. The fragile breakage versus random breakage models of chromosome evolution. PLoS Comput Biol. 2006 Feb; 2(2):e14. Peng Q, Pevzner PA, Tesler G. PMID: 16501665; PMCID: PMC1378107.
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    157. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res. 2006 Mar; 16(3):394-404. Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C. PMID: 16461635; PMCID: PMC1415204.
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    158. Identifying repeat domains in large genomes. Genome Biol. 2006; 7(1):R7. Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. PMID: 16507140; PMCID: PMC1431705.
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    159. Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc. 2006; 1(1):67-72. Tanner S, Pevzner PA, Bafna V. PMID: 17406213.
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    160. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol. 2005 Dec; 23(12):1562-7. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. PMID: 16311586.
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    161. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 2005 Jul 22; 309(5734):613-7. Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O'brien SJ, Pevzner PA, Lewin HA. PMID: 16040707.
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    162. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem. 2005 Jul 15; 77(14):4626-39. Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. PMID: 16013882.
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    163. Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res. 2005 Jul-Aug; 4(4):1287-95. Frank A, Tanner S, Bafna V, Pevzner P. PMID: 16083278.
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    164. De novo identification of repeat families in large genomes. Bioinformatics. 2005 Jun; 21 Suppl 1:i351-8. Price AL, Jones NC, Pevzner PA. PMID: 15961478.
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    165. PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem. 2005 Feb 15; 77(4):964-73. Frank A, Pevzner P. PMID: 15858974.
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    166. Identification of post-translational modifications via blind search of mass-spectra. Proc IEEE Comput Syst Bioinform Conf. 2005; 157-66. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. PMID: 16447973.
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    167. Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem. 2004 Dec 15; 76(24):7221-33. Bandeira N, Tang H, Bafna V, Pevzner P. PMID: 15595863.
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    168. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 2005 Jan; 15(1):98-110. Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G. PMID: 15590940; PMCID: PMC540283.
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    169. Mammalian phylogenomics comes of age. Trends Genet. 2004 Dec; 20(12):631-9. Murphy WJ, Pevzner PA, O'Brien SJ. PMID: 15522459.
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    170. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 2004 Nov; 14(11):2245-52. Price AL, Eskin E, Pevzner PA. PMID: 15520288; PMCID: PMC525682.
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    171. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 2004 Nov; 14(11):2336-46. Raphael B, Zhi D, Tang H, Pevzner P. PMID: 15520295; PMCID: PMC525693.
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    172. De novo repeat classification and fragment assembly. Genome Res. 2004 Sep; 14(9):1786-96. Pevzner PA, Pevzner PA, Tang H, Tesler G. PMID: 15342561; PMCID: PMC515325.
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    173. Reconstructing tumor amplisomes. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i265-73. Raphael BJ, Pevzner PA. PMID: 15262808.
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    174. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res. 2004; 32(13):3977-83. Leipzig J, Pevzner P, Heber S. PMID: 15292448; PMCID: PMC506815.
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    175. Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements. Genomics. 2004 Jun; 83(6):1053-62. Andelfinger G, Hitte C, Etter L, Guyon R, Bourque G, Tesler G, Pevzner P, Kirkness E, Galibert F, Benson DW. PMID: 15177558.
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    176. Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinformatics. 2004 Sep 22; 20(14):2159-61. Pevzner PA. PMID: 15073013.
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    177. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 04 01; 428(6982):493-521. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium. PMID: 15057822.
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    178. Fragment assembly with short reads. Bioinformatics. 2004 Sep 01; 20(13):2067-74. Chaisson M, Pevzner P, Tang H. PMID: 15059830.
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    179. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 2004 Apr; 14(4):507-16. Bourque G, Pevzner PA, Tesler G. PMID: 15059991; PMCID: PMC383294.
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    180. Scalable heuristics for design of DNA probe arrays. J Comput Biol. 2004; 11(2-3):429-47. Kahng AB, Mandoiu II, Pevzner PA, Reda S, Zelikovsky AZ. PMID: 15285900.
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    181. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics. 2003 Nov; 1(1):30-40. Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ. PMID: 15601531; PMCID: PMC3525001.
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    182. Finding subtle motifs by branching from sample strings. Bioinformatics. 2003 Oct; 19 Suppl 2:ii149-55. Price A, Ramabhadran S, Pevzner PA. PMID: 14534184.
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    183. Reconstructing tumor genome architectures. Bioinformatics. 2003 Oct; 19 Suppl 2:ii162-71. Raphael BJ, Volik S, Collins C, Pevzner PA. PMID: 14534186.
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    184. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A. 2003 Jun 24; 100(13):7672-7. Pevzner P, Tesler G. PMID: 12810957; PMCID: PMC164646.
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    185. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res. 2003 Jan; 13(1):37-45. Pevzner P, Tesler G. PMID: 12529304; PMCID: PMC430962.
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    186. Genome-wide analysis of bacterial promoter regions. Pac Symp Biocomput. 2003; 29-40. Eskin E, Keich U, Gelfand MS, Pevzner PA. PMID: 12603015.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    187. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. PMID: 12466850.
      View in: PubMed   Mentions: 2864     Fields:    Translation:HumansAnimalsCells
    188. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science. 2002 Nov 29; 298(5599):1747-52. Lunyak VV, Burgess R, Prefontaine GG, Nelson C, Sze SH, Chenoweth J, Schwartz P, Pevzner PA, Glass C, Mandel G, Rosenfeld MG. PMID: 12399542.
      View in: PubMed   Mentions: 182     Fields:    Translation:HumansAnimalsCells
    189. Finding motifs in the twilight zone. Bioinformatics. 2002 Oct; 18(10):1374-81. Keich U, Pevzner PA. PMID: 12376382.
      View in: PubMed   Mentions: 25     Fields:    Translation:AnimalsCells
    190. Subtle motifs: defining the limits of motif finding algorithms. Bioinformatics. 2002 Oct; 18(10):1382-90. Keich U, Pevzner PA. PMID: 12376383.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    191. Finding composite regulatory patterns in DNA sequences. Bioinformatics. 2002; 18 Suppl 1:S354-63. Eskin E, Pevzner PA. PMID: 12169566.
      View in: PubMed   Mentions: 65     Fields:    Translation:Cells
    192. Splicing graphs and EST assembly problem. Bioinformatics. 2002; 18 Suppl 1:S181-8. Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA. PMID: 12169546.
      View in: PubMed   Mentions: 73     Fields:    Translation:HumansCells
    193. Combinatorial algorithms for design of DNA arrays. Adv Biochem Eng Biotechnol. 2002; 77:1-19. Hannenhalli S, Hubell E, Lipshutz R, Pevzner PA. PMID: 12227732.
      View in: PubMed   Mentions: 2     Fields:    
    194. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 2002 Jan; 12(1):26-36. Bourque G, Pevzner PA. PMID: 11779828; PMCID: PMC155248.
      View in: PubMed   Mentions: 127     Fields:    Translation:HumansAnimalsCells
    195. Finding weak motifs in DNA sequences. Pac Symp Biocomput. 2002; 235-46. Sze SH, Gelfand MS, Pevzner PA. PMID: 11928479.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    196. EULER-PCR: finishing experiments for repeat resolution. Pac Symp Biocomput. 2002; 199-210. Mulyukov Z, Pevzner PA. PMID: 11928476.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    197. Assembling puzzles from preassembled blocks. Genome Res. 2001 Sep; 11(9):1461-2. Pevzner PA. PMID: 11544188.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    198. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A. 2001 Aug 14; 98(17):9748-53. Pevzner PA, Tang H, Waterman MS. PMID: 11504945; PMCID: PMC55524.
      View in: PubMed   Mentions: 383     Fields:    Translation:Cells
    199. A new approach to sequence comparison: normalized sequence alignment. Bioinformatics. 2001 Apr; 17(4):327-37. Arslan AN, Egecioglu O, Pevzner PA. PMID: 11301301.
      View in: PubMed   Mentions: 10     Fields:    
    200. Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res. 2001 Feb; 11(2):290-9. Pevzner PA, Mulyukov Z, Dancik V, Tang CL. PMID: 11157792; PMCID: PMC544186.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    201. Fragment assembly with double-barreled data. Bioinformatics. 2001; 17 Suppl 1:S225-33. Pevzner PA, Tang H. PMID: 11473013.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    202. Combinatorial approaches to finding subtle signals in DNA sequences. Proc Int Conf Intell Syst Mol Biol. 2000; 8:269-78. Pevzner PA, Sze SH. PMID: 10977088.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansAnimals
    203. Mutation-tolerant protein identification by mass spectrometry. J Comput Biol. 2000; 7(6):777-87. Pevzner PA, Dancík V, Tang CL. PMID: 11382361.
      View in: PubMed   Mentions: 37     Fields:    
    204. De novo peptide sequencing via tandem mass spectrometry. J Comput Biol. 1999 Fall-Winter; 6(3-4):327-42. Dancík V, Addona TA, Clauser KR, Vath JE, Pevzner PA. PMID: 10582570.
      View in: PubMed   Mentions: 125     Fields:    Translation:Cells
    205. SST versus EST in gene recognition. Microb Comp Genomics. 1999; 4(3):167-72. Mironov AA, Pevzner PA. PMID: 10587944.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    206. Fidelity probes for DNA arrays. Proc Int Conf Intell Syst Mol Biol. 1999; 113-7. Hubbell E, Pevzner PA. PMID: 10786293.
      View in: PubMed   Mentions: 1     Fields:    
    207. Performance-guarantee gene predictions via spliced alignment. Genomics. 1998 Aug 01; 51(3):332-9. Mironov AA, Roytberg MA, Pevzner PA, Gelfand MS. PMID: 9721203.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    208. Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs. Genomics. 1998 Jan 15; 47(2):171-9. Xu G, Sze SH, Liu CP, Pevzner PA, Arnheim N. PMID: 9479489.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    209. Algorithms and software for support of gene identification experiments. Bioinformatics. 1998; 14(1):14-9. Sze SH, Roytberg MA, Gelfand MS, Mironov AA, Astakhova TV, Pevzner PA. PMID: 9520497.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    210. Software for DNA sequencing by hybridization. Comput Appl Biosci. 1997 Apr; 13(2):205-10. Belyi I, Pevzner PA. PMID: 9146969.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    211. Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. J Comput Biol. 1997; 4(3):297-309. Sze SH, Pevzner PA. PMID: 9278061.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    212. Gene recognition via spliced sequence alignment. Proc Natl Acad Sci U S A. 1996 Aug 20; 93(17):9061-6. Gelfand MS, Mironov AA, Pevzner PA. PMID: 8799154; PMCID: PMC38595.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    213. Positional sequencing by hybridization. Comput Appl Biosci. 1996 Feb; 12(1):19-24. Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA. PMID: 8670615.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    214. Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics. 1995 Nov 20; 30(2):299-311. Hannenhalli S, Chappey C, Koonin EV, Pevzner PA. PMID: 8586431.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    215. DNASUN: a package of computer programs for the biotechnology laboratory. Comput Appl Biosci. 1995 Jun; 11(3):331-5. Mironov AA, Alexandrov NN, Grigorjev A, Lebedev VF, Lunovskaya LV, Truchan ME, Pevzner PA. PMID: 7583703.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    216. Combinatorial methods for DNA mapping and sequencing. J Comput Biol. 1995; 2(2):153-8. Pevzner PA. PMID: 7497124.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    217. Gray code masks for sequencing by hybridization. Genomics. 1994 Sep 01; 23(1):233-5. Feldman W, Pevzner P. PMID: 7829077.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    218. Rearrangements of DNA sequences and SBH. Comput Chem. 1994 Sep; 18(3):221-3. Pevzner PA. PMID: 7952892.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    219. Extendable words in nucleotide sequences. Comput Appl Biosci. 1992 Apr; 8(2):129-35. Gelfand MS, Kozhukhin CG, Pevzner PA. PMID: 1375526.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    220. Statistical distance between texts and filtration methods in sequence comparison. Comput Appl Biosci. 1992 Apr; 8(2):121-7. Pevzner PA. PMID: 1591607.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    221. Improved chips for sequencing by hybridization. J Biomol Struct Dyn. 1991 Oct; 9(2):399-410. Pevzner PA, Khrapko KR, Belyavsky AV, Florentiev VL, Mirzabekov AD. PMID: 1741970.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    222. [Optimal chips for megabase DNA sequencing]. Mol Biol (Mosk). 1991 Mar-Apr; 25(2):552-62. Pevzner PA, Lysov IuP, Khrapko KR, Beliavskii AV, Florent'ev VL, Mirzabekov AD. PMID: 1881398.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    223. Genome inhomogeneity is determined mainly by WW and SS dinucleotides. Comput Appl Biosci. 1991 Jan; 7(1):39-49. Kozhukhin CG, Pevzner PA. PMID: 2004273.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    224. 1-Tuple DNA sequencing: computer analysis. J Biomol Struct Dyn. 1989 Aug; 7(1):63-73. Pevzner PA. PMID: 2684223.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    225. [Paths in graphs and selection of oligonucleotide linkers]. Mol Biol (Mosk). 1989 Jul-Aug; 23(4):1075-9. Pevzner PA, Veiko VP. PMID: 2555681.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    226. Linguistics of nucleotide sequences. II: Stationary words in genetic texts and the zonal structure of DNA. J Biomol Struct Dyn. 1989 Apr; 6(5):1027-38. Pevzner PA, Mironov AA. PMID: 2531597.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    227. Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words. J Biomol Struct Dyn. 1989 Apr; 6(5):1013-26. Pevzner PA, Mironov AA. PMID: 2531596.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    228. [Effective method for physical mapping the DNA molecule]. Mol Biol (Mosk). 1987 May-Jun; 21(3):788-96. Pevzner PA, Mironov AA. PMID: 3657777.
      View in: PubMed   Mentions:    Fields:    
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