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    Pavel Pevzner

    TitleResearcher
    SchoolUniversity of California, San Diego
    DepartmentComputer Science and Engineering
    Address9500 Gilman Drive #0404
    CA La Jolla 92093
    Phone858-822-4365
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      Collapse Research 
      Collapse Research Activities and Funding
      Integrated Active Learning Framework for Biomedical BD2K
      NIH/NIGMS R25GM114819Sep 29, 2014 - Aug 31, 2017
      Role: Principal Investigator
      New approaches to sequencing of complex peptides.
      NIH/NIGMS R01GM086283Sep 25, 2008 - Aug 31, 2012
      Role: Principal Investigator
      Center for Computational Mass Spectrometry
      NIH/NIGMS P41GM103484Sep 20, 2008 - Jun 30, 2019
      Role: Principal Investigator
      Center for Computational Mass-Spectrometry
      NIH/NCRR P41RR024851Sep 20, 2008 - Jun 30, 2013
      Role: Principal Investigator
      Algorithms &Software for Computational Mass Spectrometry
      NIH/NCRR R01RR016522Dec 1, 2001 - Aug 31, 2010
      Role: Principal Investigator
      A New Approach to Fragment Assembly in DNA Sequencing
      NIH/NHGRI R01HG002366Aug 24, 2001 - Jul 31, 2005
      Role: Principal Investigator
      Graduate Training Program in Bioinformatics
      NIH/NIGMS 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/NHGRI 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.
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      1. Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner P. Single-molecule protein identification by sub-nanopore sensors. PLoS Comput Biol. 2017 May; 13(5):e1005356. PMID: 28486472.
        View in: PubMed
      2. Nurk S, Meleshko D, Korobeynikov A, Pevzner P. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017 May; 27(5):824-834. PMID: 28298430.
        View in: PubMed
      3. Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner P, Makarov A, Beck A, Tsybin YO. Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer. J Proteomics. 2017 Apr 21; 159:67-76. PMID: 28242452.
        View in: PubMed
      4. Garg N, Zeng Y, Edlund A, Melnik AV, Sanchez LM, Mohimani H, Gurevich A, Miao V, Schiffler S, Lim YW, Luzzatto-Knaan T, Cai S, Rohwer F, Pevzner P, Cichewicz RH, Alexandrov T, Dorrestein PC. Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen. mSystems. 2016 Nov-Dec; 1(6). PMID: 28028548.
        View in: PubMed
      5. Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner P. Assembly of long error-prone reads using de Bruijn graphs. Proc Natl Acad Sci U S A. 2016 Dec 27; 113(52):E8396-E8405. PMID: 27956617.
        View in: PubMed
      6. Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 Aug 09; 34(8):828-837. PMID: 27504778.
        View in: PubMed
      7. Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner P. plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics. 2016 Nov 15; 32(22):3380-3387. PMID: 27466620.
        View in: PubMed
      8. Bonissone SR, Pevzner P. Immunoglobulin Classification Using the Colored Antibody Graph. J Comput Biol. 2016 Jun; 23(6):483-94. PMID: 27149636; PMCID: PMC4904161 [Available on 06/01/17].
      9. Bankevich A, Pevzner P. TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nat Methods. 2016 Mar; 13(3):248-50. PMID: 26828418.
        View in: PubMed
      10. Mohimani H, Pevzner P. Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. Nat Prod Rep. 2016 Jan; 33(1):73-86. PMID: 26497201.
        View in: PubMed
      11. Kolmogorov M, Liu X, Pevzner P. SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra. J Proteome Res. 2016 Jan 04; 15(1):144-51. PMID: 26629978.
        View in: PubMed
      12. Antipov D, Korobeynikov A, McLean JS, Pevzner P. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics. 2016 Apr 01; 32(7):1009-15. PMID: 26589280; PMCID: PMC4907386 [Available on 04/01/17].
      13. Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolic N, Dvorkin M, Alexandrova S, Luider TM, Paša-Tolic L, Pevzner P. De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra. J Proteome Res. 2015 Nov 06; 14(11):4450-62. PMID: 26412692.
        View in: PubMed
      14. León-Zayas R, Novotny M, Podell S, Shepard CM, Berkenpas E, Nikolenko S, Pevzner P, Lasken RS, Bartlett DH. Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages. Appl Environ Microbiol. 2015 Dec; 81(24):8265-76. PMID: 26386059; PMCID: PMC4644660.
      15. Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner P, Bafna V. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. J Proteome Res. 2015 Sep 04; 14(9):3555-67. PMID: 26139413; PMCID: PMC4868822.
      16. Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner P. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics. 2015 Jun 15; 31(12):i53-61. PMID: 26072509; PMCID: PMC4542777.
      17. Vasilinetc I, Prjibelski AD, Gurevich A, Korobeynikov A, Pevzner P. Assembling short reads from jumping libraries with large insert sizes. Bioinformatics. 2015 Oct 15; 31(20):3262-8. PMID: 26040456.
        View in: PubMed
      18. Safonova Y, Bankevich A, Pevzner P. dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. J Comput Biol. 2015 Jun; 22(6):528-45. PMID: 25734602; PMCID: PMC4449708.
      19. Pandey A, Pevzner P. Proteogenomics. Proteomics. 2014 Dec; 14(23-24):2631-2. PMID: 25469796.
        View in: PubMed
      20. Kim S, Pevzner P. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun. 2014 Oct 31; 5:5277. PMID: 25358478; PMCID: PMC5036525.
      21. Lin Y, Nurk S, Pevzner P. What is the difference between the breakpoint graph and the de Bruijn graph? BMC Genomics. 2014; 15 Suppl 6:S6. PMID: 25572416; PMCID: PMC4240671.
      22. Mohimani H, Liu WT, Kersten RD, Moore BS, Dorrestein PC, Pevzner P. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. J Nat Prod. 2014 Aug 22; 77(8):1902-9. PMID: 25116163; PMCID: PMC4143176.
      23. Liu X, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolic N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-Tolic L, Pevzner P. De novo protein sequencing by combining top-down and bottom-up tandem mass spectra. J Proteome Res. 2014 Jul 03; 13(7):3241-8. PMID: 24874765.
        View in: PubMed
      24. Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner P. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics. 2014 Jun 15; 30(12):i293-301. PMID: 24931996; PMCID: PMC4058921.
      25. Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner P, Dorrestein PC. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol. 2014 Jul 18; 9(7):1545-51. PMID: 24802639; PMCID: PMC4215869.
      26. Wu S, Brown JN, Tolic N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolic L. Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry. Proteomics. 2014 May; 14(10):1211-22. PMID: 24591407.
        View in: PubMed
      27. Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH. Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS One. 2014; 9(1):e85140. PMID: 24475038; PMCID: PMC3903477.
      28. Terterov I, Vyatkina K, Kononikhin AS, Boitsov V, Vyazmin S, Popov IA, Nikolaev EN, Pevzner P, Dubina M. Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms. Rapid Commun Mass Spectrom. 2014 Jan 15; 28(1):33-41. PMID: 24285388.
        View in: PubMed
      29. Liu X, Hengel S, Wu S, Tolic N, Pasa-Tolic L, Pevzner P. Identification of ultramodified proteins using top-down tandem mass spectra. J Proteome Res. 2013 Dec 06; 12(12):5830-8. PMID: 24188097; PMCID: PMC3905687.
      30. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner P. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013 Oct; 20(10):714-37. PMID: 24093227; PMCID: PMC3791033.
      31. Castellana NE, Lushnikov A, Rotkiewicz P, Sefcovic N, Pevzner P, Godzik A, Vyatkina K. MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms Mol Biol. 2013 Jul 11; 8(1):19. PMID: 23844614; PMCID: PMC3738870.
      32. Jeong K, Kim S, Pevzner P. UniNovo: a universal tool for de novo peptide sequencing. Bioinformatics. 2013 Aug 15; 29(16):1953-62. PMID: 23766417; PMCID: PMC3722526.
      33. McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner P, Friedman RM, Nealson KH, Venter JC, Lasken RS. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci U S A. 2013 Jun 25; 110(26):E2390-9. PMID: 23754396; PMCID: PMC3696752.
      34. Ansong C, Wu S, Meng D, Liu X, Brewer HM, Deatherage Kaiser BL, Nakayasu ES, Cort JR, Pevzner P, Smith RD, Heffron F, Adkins JN, Pasa-Tolic L. Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions. Proc Natl Acad Sci U S A. 2013 Jun 18; 110(25):10153-8. PMID: 23720318; PMCID: PMC3690903.
      35. McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, Torriani F, Nealson KH, Pevzner P, Friedman R, Venter JC, Lasken RS. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Res. 2013 May; 23(5):867-77. PMID: 23564253; PMCID: PMC3638142.
      36. Ivankov DN, Payne SH, Galperin MY, Bonissone S, Pevzner P, Frishman D. How many signal peptides are there in bacteria? Environ Microbiol. 2013 Apr; 15(4):983-90. PMID: 23556536; PMCID: PMC3621014.
      37. Mohimani H, Kim S, Pevzner P. A new approach to evaluating statistical significance of spectral identifications. J Proteome Res. 2013 Apr 05; 12(4):1560-8. PMID: 23343606.
        View in: PubMed
      38. Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolic L, Smith RD, Pevzner P. Unexpected diversity of signal peptides in prokaryotes. MBio. 2012 Nov 20; 3(6). PMID: 23169999; PMCID: PMC3509430.
      39. Bonissone S, Gupta N, Romine M, Bradshaw RA, Pevzner P. N-terminal protein processing: a comparative proteogenomic analysis. Mol Cell Proteomics. 2013 Jan; 12(1):14-28. PMID: 23001859; PMCID: PMC3536895.
      40. Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner P, Alekseyev MA. Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly. J Comput Biol. 2013 Apr; 20(4):359-71. PMID: 22803627; PMCID: PMC3619201.
      41. Ronen R, Boucher C, Chitsaz H, Pevzner P. SEQuel: improving the accuracy of genome assemblies. Bioinformatics. 2012 Jun 15; 28(12):i188-96. PMID: 22689760; PMCID: PMC3371851.
      42. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner P. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012 May; 19(5):455-77. PMID: 22506599; PMCID: PMC3342519.
      43. Anderson WA, Amasino RM, Ares M, Banerjee U, Bartel B, Corces VG, Drennan CL, Elgin SC, Epstein IR, Fanning E, Guillette LJ, Handelsman J, Hatfull GF, Hoy RR, Kelley D, Leinwand LA, Losick R, Lu Y, Lynn DG, Neuhauser C, O'Dowd DK, Olivera T, Pevzner P, Richards-Kortum RR, Rine J, Sah RL, Strobel SA, Walker GC, Walt DR, Warner IM, Wessler S, Willard HF, Zare RN. Competencies: a cure for pre-med curriculum. Science. 2011 Nov 11; 334(6057):760-1. PMID: 22076362.
        View in: PubMed
      44. Compeau PE, Pevzner P, Tesler G. How to apply de Bruijn graphs to genome assembly. Nat Biotechnol. 2011 Nov 08; 29(11):987-91. PMID: 22068540.
        View in: PubMed
      45. Mohimani H, Liu WT, Yang YL, Gaudêncio SP, Fenical W, Dorrestein PC, Pevzner P. Multiplex de novo sequencing of peptide antibiotics. J Comput Biol. 2011 Nov; 18(11):1371-81. PMID: 22035290; PMCID: PMC3216106.
      46. Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner P. Protein identification using top-down. Mol Cell Proteomics. 2012 Jun; 11(6):M111.008524. PMID: 22027200; PMCID: PMC3433905.
      47. Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P. Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J Comput Biol. 2011 Nov; 18(11):1625-34. PMID: 21999285; PMCID: PMC3216098.
      48. Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner P, Lasken RS. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol. 2011 Sep 18; 29(10):915-21. PMID: 21926975; PMCID: PMC3558281.
      49. Mohimani H, Liu WT, Mylne JS, Poth AG, Colgrave ML, Tran D, Selsted ME, Dorrestein PC, Pevzner P. Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases. J Proteome Res. 2011 Oct 07; 10(10):4505-12. PMID: 21851130; PMCID: PMC3242011.
      50. Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner P. Sequencing cyclic peptides by multistage mass spectrometry. Proteomics. 2011 Sep; 11(18):3642-50. PMID: 21751357; PMCID: PMC3398611.
      51. Medvedev P, Scott E, Kakaradov B, Pevzner P. Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics. 2011 Jul 01; 27(13):i137-41. PMID: 21685062; PMCID: PMC3117386.
      52. Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner P. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods. 2011 May 15; 8(7):587-91. PMID: 21572408; PMCID: PMC3128193.
      53. Pevzner P, Shamir R. Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). J Comput Biol. 2011 Jul; 18(7):865. PMID: 21563980.
        View in: PubMed
      54. Gupta N, Bandeira N, Keich U, Pevzner P. Target-decoy approach and false discovery rate: when things may go wrong. J Am Soc Mass Spectrom. 2011 Jul; 22(7):1111-20. PMID: 21953092; PMCID: PMC3220955.
      55. Mevers E, Liu WT, Engene N, Mohimani H, Byrum T, Pevzner P, Dorrestein PC, Spadafora C, Gerwick WH. Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera. J Nat Prod. 2011 May 27; 74(5):928-36. PMID: 21488639; PMCID: PMC3103610.
      56. Grindberg RV, Ishoey T, Brinza D, Esquenazi E, Coates RC, Liu WT, Gerwick L, Dorrestein PC, Pevzner P, Lasken R, Gerwick WH. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One. 2011 Apr 12; 6(4):e18565. PMID: 21533272; PMCID: PMC3075265.
      57. Jeong K, Kim S, Bandeira N, Pevzner P. Gapped spectral dictionaries and their applications for database searches of tandem mass spectra. Mol Cell Proteomics. 2011 Jun; 10(6):M110.002220. PMID: 21444829; PMCID: PMC3108828.
      58. Alekseyev MA, Pevzner P. Comparative genomics reveals birth and death of fragile regions in mammalian evolution. Genome Biol. 2010; 11(11):R117. PMID: 21118492; PMCID: PMC3156956.
      59. Gupta N, Bark SJ, Lu WD, Taupenot L, O'Connor DT, Pevzner P, Hook V. Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing. J Proteome Res. 2010 Oct 01; 9(10):5065-75. PMID: 20704348; PMCID: PMC3000314.
      60. Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner P. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics. 2010 Dec; 9(12):2772-82. PMID: 20855543; PMCID: PMC3101958.
      61. Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner P. 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. PMID: 20829449; PMCID: PMC3101864.
      62. Liu WT, Yang YL, Xu Y, Lamsa A, Haste NM, Yang JY, Ng J, Gonzalez D, Ellermeier CD, Straight PD, Pevzner P, Pogliano J, Nizet V, Pogliano K, Dorrestein PC. 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. PMID: 20805502; PMCID: PMC2941286.
      63. Pham SK, Pevzner P. DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics. 2010 Oct 15; 26(20):2509-16. PMID: 20736338.
        View in: PubMed
      64. Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O'Connor DT, Pevzner P. Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication. AAPS J. 2010 Dec; 12(4):635-45. PMID: 20734175; PMCID: PMC2976990.
      65. Gupta N, Hixson KK, Culley DE, Smith RD, Pevzner P. Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry. Proteomics. 2010 Aug; 10(15):2833-44. PMID: 20597098; PMCID: PMC3220954.
      66. Leão PN, Pereira AR, Liu WT, Ng J, Pevzner P, Dorrestein PC, König GM, Vasconcelos VM, Gerwick WH. Synergistic allelochemicals from a freshwater cyanobacterium. Proc Natl Acad Sci U S A. 2010 Jun 22; 107(25):11183-8. PMID: 20534563; PMCID: PMC2895120.
      67. Gupta N, Pevzner P. False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res. 2009 Sep; 8(9):4173-81. PMID: 19627159; PMCID: PMC3398614.
      68. Pevzner P, Shamir R. Computing has changed biology--biology education must catch up. Science. 2009 Jul 31; 325(5940):541-2. PMID: 19644094.
        View in: PubMed
      69. Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner P. Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods. 2009 Aug; 6(8):596-9. PMID: 19597502; PMCID: PMC2754211.
      70. Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner P, Dorrestein PC. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem. 2009 Jun 01; 81(11):4200-9. PMID: 19413302; PMCID: PMC2765223.
      71. Kim S, Bandeira N, Pevzner P. 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. PMID: 19254948; PMCID: PMC2690493.
      72. Alekseyev MA, Pevzner P. Breakpoint graphs and ancestral genome reconstructions. Genome Res. 2009 May; 19(5):943-57. PMID: 19218533; PMCID: PMC2675983.
      73. Chaisson MJ, Brinza D, Pevzner P. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res. 2009 Feb; 19(2):336-46. PMID: 19056694; PMCID: PMC2652199.
      74. Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR. Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol. 2008 Dec; 26(12):1336-8. PMID: 19060866; PMCID: PMC2891972.
      75. Pevzner P, Kim S, Ng J. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science. 2008 Aug 22; 321(5892):1040; author reply 1040. PMID: 18719266.
        View in: PubMed
      76. Kim S, Gupta N, Bandeira N, Pevzner P. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics. 2009 Jan; 8(1):53-69. PMID: 18703573; PMCID: PMC2621003.
      77. Kim S, Gupta N, Pevzner P. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res. 2008 Aug; 7(8):3354-63. PMID: 18597511; PMCID: PMC2689316.
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      166. Gelfand MS, Kozhukhin CG, Pevzner P. Extendable words in nucleotide sequences. Comput Appl Biosci. 1992 Apr; 8(2):129-35. PMID: 1375526.
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      167. Pevzner P, Khrapko KR, Belyavsky AV, Florentiev VL, Mirzabekov AD. Improved chips for sequencing by hybridization. J Biomol Struct Dyn. 1991 Oct; 9(2):399-410. PMID: 1741970.
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      168. Pevzner P, Lysov IuP, Khrapko KR, Beliavskii AV, Florent'ev VL, Mirzabekov AD. [Optimal chips for megabase DNA sequencing]. Mol Biol (Mosk). 1991 Mar-Apr; 25(2):552-62. PMID: 1881398.
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      169. Kozhukhin CG, Pevzner P. Genome inhomogeneity is determined mainly by WW and SS dinucleotides. Comput Appl Biosci. 1991 Jan; 7(1):39-49. PMID: 2004273.
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      170. Pevzner P. 1-Tuple DNA sequencing: computer analysis. J Biomol Struct Dyn. 1989 Aug; 7(1):63-73. PMID: 2684223.
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      171. Pevzner P, Veiko VP. [Paths in graphs and selection of oligonucleotide linkers]. Mol Biol (Mosk). 1989 Jul-Aug; 23(4):1075-9. PMID: 2555681.
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      172. Pevzner P, Mironov AA. 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. PMID: 2531597.
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      173. Pevzner P, Mironov AA. 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. PMID: 2531596.
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      174. Pevzner P, Mironov AA. [Effective method for physical mapping the DNA molecule]. Mol Biol (Mosk). 1987 May-Jun; 21(3):788-96. PMID: 3657777.
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