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Pavel Pevzner

TitleProfessor
InstitutionUniversity of California San Diego
DepartmentComputer Science and Engineering
Address9500 Gilman Drive #0404
La Jolla CA 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. 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: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). PMID: 29795809.
      View in: PubMed
    2. Pu L, Lin Y, Pevzner P. Detection and analysis of ancient segmental duplications in mammalian genomes. Genome Res. 2018 May 07. PMID: 29735604.
      View in: PubMed
    3. Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner P. Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nat Microbiol. 2018 Mar; 3(3):319-327. PMID: 29358742.
      View in: PubMed
    4. Rozanov DV, Rozanov ND, Chiotti KE, Reddy A, Wilmarth PA, David LL, Cha SW, Woo S, Pevzner P, Bafna V, Burrows GG, Rantala JK, Levin T, Anur P, Johnson-Camacho K, Tabatabaei S, Munson DJ, Bruno TC, Slansky JE, Kappler JW, Hirano N, Boegel S, Fox BA, Egelston C, Simons DL, Jimenez G, Lee PP, Gray JW, Spellman PT. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics. 2018 Mar 30; 176:13-23. PMID: 29331515.
      View in: PubMed
    5. Cha SW, Bonissone S, Na S, Pevzner P, Bafna V. The Antibody Repertoire of Colorectal Cancer. Mol Cell Proteomics. 2017 Dec; 16(12):2111-2124. PMID: 29046389.
      View in: PubMed
    6. Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner P. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. J Immunol. 2017 11 01; 199(9):3369-3380. PMID: 28978691.
      View in: PubMed
    7. 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
    8. Nurk S, Meleshko D, Korobeynikov A, Pevzner P. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017 05; 27(5):824-834. PMID: 28298430.
      View in: PubMed
    9. 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 04 21; 159:67-76. PMID: 28242452.
      View in: PubMed
    10. 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
    11. 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 12 27; 113(52):E8396-E8405. PMID: 27956617.
      View in: PubMed
    12. Mohimani H, Gurevich A, Mikheenko A, Garg N, Nothias LF, Ninomiya A, Takada K, Dorrestein PC, Pevzner P. Dereplication of peptidic natural products through database search of mass spectra. Nat Chem Biol. 2017 Jan; 13(1):30-37. PMID: 27820803.
      View in: PubMed
    13. 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 08 09; 34(8):828-837. PMID: 27504778.
      View in: PubMed
    14. Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner P. plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics. 2016 11 15; 32(22):3380-3387. PMID: 27466620.
      View in: PubMed
    15. Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolic N, Luider TM, Paša-Tolic L, Pevzner P. Top-down analysis of protein samples by de novo sequencing techniques. Bioinformatics. 2016 09 15; 32(18):2753-9. PMID: 27187201.
      View in: PubMed
    16. 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].
    17. 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
    18. 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
    19. 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
    20. Antipov D, Korobeynikov A, McLean JS, Pevzner P. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics. 2016 04 01; 32(7):1009-15. PMID: 26589280; PMCID: PMC4907386 [Available on 04/01/17].
    21. 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.
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    22. 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.
    23. 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.
    24. 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.
    25. 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
    26. 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.
    27. Pandey A, Pevzner P. Proteogenomics. Proteomics. 2014 Dec; 14(23-24):2631-2. PMID: 25469796.
      View in: PubMed
    28. 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.
    29. 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.
    30. 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.
    31. 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
    32. 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.
    33. 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.
    34. 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
    35. 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.
      View in: PubMed
    36. 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
    37. 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.
    38. 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.
    39. 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.
    40. 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.
    41. 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.
    42. 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.
    43. 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.
    44. 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.
      View in: PubMed
    45. 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
    46. 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.
    47. 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.
    48. 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.
    49. 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.
    50. 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.
    51. 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
    52. 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
    53. 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.
    54. 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.
    55. 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.
    56. 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.
    57. 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.
    58. 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.
    59. 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.
    60. 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.
    61. 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.
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    62. 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.
    63. 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.
    64. 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.
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    65. 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.
    66. 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.
    67. 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.
    68. 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.
    69. 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.
    70. 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.
    71. 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.
    72. 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
    73. 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.
    74. 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.
    75. 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.
    76. 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
    77. 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.
    78. 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.
    79. 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.
    80. Alekseyev MA, Pevzner P. Breakpoint graphs and ancestral genome reconstructions. Genome Res. 2009 May; 19(5):943-57. PMID: 19218533; PMCID: PMC2675983.
    81. 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.
    82. 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.
      View in: PubMed
    83. 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
    84. 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.
    85. 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.
    86. Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner P. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics. 2008 Jul 01; 24(13):i416-23. PMID: 18785330; PMCID: PMC2718660.
    87. 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 P. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 2008 Jul; 18(7):1133-42. PMID: 18426904; PMCID: PMC2493402.
    88. Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner P. Interpreting top-down mass spectra using spectral alignment. Anal Chem. 2008 Apr 01; 80(7):2499-505. PMID: 18302345.
      View in: PubMed
    89. Ng J, Pevzner P. Algorithm for identification of fusion proteins via mass spectrometry. J Proteome Res. 2008 Jan; 7(1):89-95. PMID: 18173219.
      View in: PubMed
    90. Chaisson MJ, Pevzner P. Short read fragment assembly of bacterial genomes. Genome Res. 2008 Feb; 18(2):324-30. PMID: 18083777; PMCID: PMC2203630.
    91. Rodriguez J, Gupta N, Smith RD, Pevzner P. Does trypsin cut before proline? J Proteome Res. 2008 Jan; 7(1):300-5. PMID: 18067249.
      View in: PubMed
    92. Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner P. Clustering millions of tandem mass spectra. J Proteome Res. 2008 Jan; 7(1):113-22. PMID: 18067247; PMCID: PMC2533155.
    93. Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner P, Eichler EE. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet. 2007 Nov; 39(11):1361-8. PMID: 17922013.
      View in: PubMed
    94. Alekseyev MA, Pevzner P. Are there rearrangement hotspots in the human genome? PLoS Comput Biol. 2007 Nov; 3(11):e209. PMID: 17997591; PMCID: PMC2065889.
    95. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner P. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007 Sep; 17(9):1362-77. PMID: 17690205; PMCID: PMC1950905.
    96. Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A. 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. PMID: 17623296.
      View in: PubMed
    97. Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One. 2007 May 30; 2(5):e484. PMID: 17534434; PMCID: PMC1871613.
    98. Bandeira N, Clauser KR, Pevzner P. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics. 2007 Jul; 6(7):1123-34. PMID: 17446555.
      View in: PubMed
    99. Bandeira N, Tsur D, Frank A, Pevzner P. Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A. 2007 Apr 10; 104(15):6140-5. PMID: 17404225; PMCID: PMC1851064.
    100. Alekseyev MA, Pevzner P. Colored de Bruijn graphs and the genome halving problem. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):98-107. PMID: 17277417.
      View in: PubMed
    101. Zhi D, Keich U, Pevzner P, Heber S, Tang H. Correcting base-assignment errors in repeat regions of shotgun assembly. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):54-64. PMID: 17277413.
      View in: PubMed
    102. Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner P. De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res. 2007 Jan; 6(1):114-23. PMID: 17203955; PMCID: PMC2538556.
    103. Chong KF, Ning K, Leong HW, Pevzner P. Modeling and characterization of multi-charge mass spectra for peptide sequencing. J Bioinform Comput Biol. 2006 Dec; 4(6):1329-52. PMID: 17245817.
      View in: PubMed
    104. Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics. 2006 Oct 20; 7:460. PMID: 17052359; PMCID: PMC1626488.
    105. Wielsch N, Thomas H, Surendranath V, Waridel P, Frank A, Pevzner P, Shevchenko A. 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. PMID: 16944958.
      View in: PubMed
    106. Jones NC, Pevzner P. Comparative genomics reveals unusually long motifs in mammalian genomes. Bioinformatics. 2006 Jul 15; 22(14):e236-42. PMID: 16873477.
      View in: PubMed
    107. Bourque G, Tesler G, Pevzner P. The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 2006 Mar; 16(3):311-3. PMID: 16510896; PMCID: PMC1415205.
    108. Peng Q, Pevzner P, Tesler G. The fragile breakage versus random breakage models of chromosome evolution. PLoS Comput Biol. 2006 Feb; 2(2):e14. PMID: 16501665; PMCID: PMC1378107.
    109. 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. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res. 2006 Mar; 16(3):394-404. PMID: 16461635; PMCID: PMC1415204.
    110. Zhi D, Raphael BJ, Price AL, Tang H, Pevzner P. Identifying repeat domains in large genomes. Genome Biol. 2006; 7(1):R7. PMID: 16507140; PMCID: PMC1431705.
    111. Tanner S, Pevzner P, Bafna V. Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc. 2006; 1(1):67-72. PMID: 17406213.
      View in: PubMed
    112. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner P. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol. 2005 Dec; 23(12):1562-7. PMID: 16311586.
      View in: PubMed
    113. 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 P, Lewin HA. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 2005 Jul 22; 309(5734):613-7. PMID: 16040707.
      View in: PubMed
    114. Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner P, Bafna V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem. 2005 Jul 15; 77(14):4626-39. PMID: 16013882.
      View in: PubMed
    115. Frank A, Tanner S, Bafna V, Pevzner P. Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res. 2005 Jul-Aug; 4(4):1287-95. PMID: 16083278.
      View in: PubMed
    116. Price AL, Jones NC, Pevzner P. De novo identification of repeat families in large genomes. Bioinformatics. 2005 Jun; 21 Suppl 1:i351-8. PMID: 15961478.
      View in: PubMed
    117. Frank A, Pevzner P. PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem. 2005 Feb 15; 77(4):964-73. PMID: 15858974.
      View in: PubMed
    118. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner P. Identification of post-translational modifications via blind search of mass-spectra. Proc IEEE Comput Syst Bioinform Conf. 2005; 157-66. PMID: 16447973.
      View in: PubMed
    119. Bandeira N, Tang H, Bafna V, Pevzner P. Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem. 2004 Dec 15; 76(24):7221-33. PMID: 15595863.
      View in: PubMed
    120. Bourque G, Zdobnov EM, Bork P, Pevzner P, Tesler G. 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. PMID: 15590940; PMCID: PMC540283.
    121. Murphy WJ, Pevzner P, O'Brien SJ. Mammalian phylogenomics comes of age. Trends Genet. 2004 Dec; 20(12):631-9. PMID: 15522459.
      View in: PubMed
    122. Price AL, Eskin E, Pevzner P. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 2004 Nov; 14(11):2245-52. PMID: 15520288; PMCID: PMC525682.
    123. Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 2004 Nov; 14(11):2336-46. PMID: 15520295; PMCID: PMC525693.
    124. Pevzner PA, Pevzner PA, Tang H, Tesler G. De novo repeat classification and fragment assembly. Genome Res. 2004 Sep; 14(9):1786-96. PMID: 15342561; PMCID: PMC515325.
    125. Raphael BJ, Pevzner P. Reconstructing tumor amplisomes. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i265-73. PMID: 15262808.
      View in: PubMed
    126. Leipzig J, Pevzner P, Heber S. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res. 2004; 32(13):3977-83. PMID: 15292448; PMCID: PMC506815.
    127. Pevzner P. Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinformatics. 2004 Sep 22; 20(14):2159-61. PMID: 15073013.
      View in: PubMed
    128. 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. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 01; 428(6982):493-521. PMID: 15057822.
      View in: PubMed
    129. Chaisson M, Pevzner P, Tang H. Fragment assembly with short reads. Bioinformatics. 2004 Sep 01; 20(13):2067-74. PMID: 15059830.
      View in: PubMed
    130. Bourque G, Pevzner P, Tesler G. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 2004 Apr; 14(4):507-16. PMID: 15059991; PMCID: PMC383294.
    131. Kahng AB, Mandoiu II, Pevzner P, Reda S, Zelikovsky AZ. Scalable heuristics for design of DNA probe arrays. J Comput Biol. 2004; 11(2-3):429-47. PMID: 15285900.
      View in: PubMed
    132. Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics. 2003 Nov; 1(1):30-40. PMID: 15601531; PMCID: PMC3525001.
    133. Price A, Ramabhadran S, Pevzner P. Finding subtle motifs by branching from sample strings. Bioinformatics. 2003 Oct; 19 Suppl 2:ii149-55. PMID: 14534184.
      View in: PubMed
    134. Raphael BJ, Volik S, Collins C, Pevzner P. Reconstructing tumor genome architectures. Bioinformatics. 2003 Oct; 19 Suppl 2:ii162-71. PMID: 14534186.
      View in: PubMed
    135. Pevzner P, Tesler G. 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. PMID: 12810957; PMCID: PMC164646.
    136. Pevzner P, Tesler G. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res. 2003 Jan; 13(1):37-45. PMID: 12529304; PMCID: PMC430962.
    137. Eskin E, Keich U, Gelfand MS, Pevzner P. Genome-wide analysis of bacterial promoter regions. Pac Symp Biocomput. 2003; 29-40. PMID: 12603015.
      View in: PubMed
    138. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. PMID: 12466850.
      View in: PubMed
    139. Lunyak VV, Burgess R, Prefontaine GG, Nelson C, Sze SH, Chenoweth J, Schwartz P, Pevzner P, Glass C, Mandel G, Rosenfeld MG. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science. 2002 Nov 29; 298(5599):1747-52. PMID: 12399542.
      View in: PubMed
    140. Eskin E, Pevzner P. Finding composite regulatory patterns in DNA sequences. Bioinformatics. 2002; 18 Suppl 1:S354-63. PMID: 12169566.
      View in: PubMed
    141. Bourque G, Pevzner P. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 2002 Jan; 12(1):26-36. PMID: 11779828; PMCID: PMC155248.
    142. Mulyukov Z, Pevzner P. EULER-PCR: finishing experiments for repeat resolution. Pac Symp Biocomput. 2002; 199-210. PMID: 11928476.
      View in: PubMed
    143. Heber S, Alekseyev M, Sze SH, Tang H, Pevzner P. Splicing graphs and EST assembly problem. Bioinformatics. 2002; 18 Suppl 1:S181-8. PMID: 12169546.
      View in: PubMed
    144. Hannenhalli S, Hubell E, Lipshutz R, Pevzner P. Combinatorial algorithms for design of DNA arrays. Adv Biochem Eng Biotechnol. 2002; 77:1-19. PMID: 12227732.
      View in: PubMed
    145. Pevzner P, Tang H. Fragment assembly with double-barreled data. Bioinformatics. 2001; 17 Suppl 1:S225-33. PMID: 11473013.
      View in: PubMed