Pavel A. Pevzner - Publications

Affiliations: 
University of California, San Diego, La Jolla, CA 
Area:
Bioinformatics, proteomics, mass spectrometry

206 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Antipov D, Raiko M, Lapidus A, Pevzner PA. metaviralSPAdes: assembly of viruses from metagenomic data. Bioinformatics (Oxford, England). PMID 32413137 DOI: 10.1093/Bioinformatics/Btaa490  0.44
2019 Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA. De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Systems. PMID 31864964 DOI: 10.1016/J.Cels.2019.11.007  0.6
2019 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, ... ... Pevzner PA, et al. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Systems. PMID 31629686 DOI: 10.1016/J.Cels.2019.09.004  0.6
2019 Meleshko D, Mohimani H, Traccana V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA. BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs. Genome Research. PMID 31160374 DOI: 10.1101/Gr.243477.118  0.6
2019 Antipov D, Raiko M, Lapidus A, Pevzner PA. Plasmid detection and assembly in genomic and metagenomic datasets. Genome Research. PMID 31048319 DOI: 10.1101/Gr.241299.118  0.44
2018 Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA. Dereplication of microbial metabolites through database search of mass spectra. Nature Communications. 9: 4035. PMID 30279420 DOI: 10.1038/S41467-018-06082-8  0.6
2018 Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner PA. Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nature Microbiology. PMID 29358742 DOI: 10.1038/S41564-017-0094-2  0.6
2018 Rozanov DV, Rozanov ND, Chiotti K, 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, et al. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. Journal of Proteomics. PMID 29331515 DOI: 10.1016/J.Jprot.2018.01.004  0.96
2017 Cha SW, Bonissone S, Na S, Pevzner PA, Bafna V. The antibody repertoire of colorectal cancer. Molecular & Cellular Proteomics : McP. PMID 29046389 DOI: 10.1074/Mcp.Ra117.000397  0.96
2016 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 PA, Cichewicz RH, et al. Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen. Msystems. 1. PMID 28028548 DOI: 10.1128/mSystems.00139-16  0.6
2016 Mohimani H, Gurevich A, Mikheenko A, Garg N, Nothias LF, Ninomiya A, Takada K, Dorrestein PC, Pevzner PA. Dereplication of peptidic natural products through database search of mass spectra. Nature Chemical Biology. PMID 27820803 DOI: 10.1038/Nchembio.2219  0.6
2016 Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA. plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data. Bioinformatics (Oxford, England). PMID 27466620 DOI: 10.1093/Bioinformatics/Btw493  0.44
2016 Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolić N, Luider TM, Paša-Tolić L, Pevzner PA. Top-down analysis of protein samples by de novo sequencing techniques. Bioinformatics (Oxford, England). PMID 27187201 DOI: 10.1093/Bioinformatics/Btw307  0.32
2015 Kolmogorov M, Liu X, Pevzner PA. SpectroGene: a tool for proteogenomic annotations using top-down spectra. Journal of Proteome Research. PMID 26629978 DOI: 10.1021/Acs.Jproteome.5B00610  1
2015 Antipov D, Korobeynikov A, McLean JS, Pevzner PA. hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics (Oxford, England). PMID 26589280 DOI: 10.1093/Bioinformatics/Btv688  0.44
2015 Mohimani H, Pevzner PA. Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. Natural Product Reports. PMID 26497201 DOI: 10.1039/C5Np00050E  1
2015 Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolić N, Dvorkin M, Alexandrova S, Luider TM, Paša-Tolić L, Pevzner PA. De novo sequencing of peptides from top-down tandem mass spectra. Journal of Proteome Research. PMID 26412692 DOI: 10.1021/Pr501244V  1
2015 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. Applied and Environmental Microbiology. 81: 8265-76. PMID 26386059 DOI: 10.1128/Aem.01659-15  0.4
2015 Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. Journal of Proteome Research. 14: 3555-67. PMID 26139413 DOI: 10.1021/Acs.Jproteome.5B00264  0.4
2015 Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics (Oxford, England). 31: i53-61. PMID 26072509 DOI: 10.1093/Bioinformatics/Btv238  0.48
2015 Vasilinetc I, Prjibelski AD, Gurevich A, Korobeynikov A, Pevzner PA. Assembling short reads from jumping libraries with large insert sizes. Bioinformatics (Oxford, England). 31: 3262-8. PMID 26040456 DOI: 10.1093/Bioinformatics/Btv337  0.4
2015 Safonova Y, Bankevich A, Pevzner PA. dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 528-45. PMID 25734602 DOI: 10.1089/Cmb.2014.0153  1
2015 Compeau P, Pevzner PA. Viewpoint: Life after MOOCs Communications of the Acm. 58: 41-44. DOI: 10.1145/2686871  1
2015 Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, Depalatis L, Sandoval W, Lill J, Pevzner PA. Ig Repertoire Constructor: A novel algorithm for antibody repertoire construction and immunoproteogenomics analysis Bioinformatics. 31: i53-i61. DOI: 10.1093/bioinformatics/btv238  1
2015 Bonissone SR, Pevzner PA. Immunoglobulin classification using the colored antibody graph Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 44-59. DOI: 10.1007/978-3-319-16706-0_7  1
2014 Kim S, Pevzner PA. MS-GF+ makes progress towards a universal database search tool for proteomics. Nature Communications. 5: 5277. PMID 25358478 DOI: 10.1038/Ncomms6277  1
2014 Mohimani H, Liu WT, Kersten RD, Moore BS, Dorrestein PC, Pevzner PA. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. Journal of Natural Products. PMID 25116163 DOI: 10.1021/Np500370C  1
2014 Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner PA. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics (Oxford, England). 30: i293-301. PMID 24931996 DOI: 10.1093/Bioinformatics/Btu266  1
2014 Liu X, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolić N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, PaÅ¡a-Tolić L, Pevzner PA. De novo protein sequencing by combining top-down and bottom-up tandem mass spectra. Journal of Proteome Research. 13: 3241-8. PMID 24874765 DOI: 10.1021/Pr401300M  1
2014 Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC. Automated genome mining of ribosomal peptide natural products. Acs Chemical Biology. 9: 1545-51. PMID 24802639 DOI: 10.1021/Cb500199H  1
2014 Wu S, Brown JN, Tolić N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolić L. Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry. Proteomics. 14: 1211-22. PMID 24591407 DOI: 10.1002/Pmic.201300378  1
2014 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. 9: e85140. PMID 24475038 DOI: 10.1371/Journal.Pone.0085140  1
2014 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 Communications in Mass Spectrometry : Rcm. 28: 33-41. PMID 24285388 DOI: 10.1002/Rcm.6757  1
2014 Lin Y, Pevzner PA. Manifold de Bruijn graphs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8701: 296-310. DOI: 10.1007/978-3-662-44753-6-22  1
2013 Liu X, Hengel S, Wu S, Tolić N, Pasa-Tolić L, Pevzner PA. Identification of ultramodified proteins using top-down tandem mass spectra. Journal of Proteome Research. 12: 5830-8. PMID 24188097 DOI: 10.1021/Pr400849Y  1
2013 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, ... ... Pevzner PA, et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 714-37. PMID 24093227 DOI: 10.1089/Cmb.2013.0084  1
2013 Castellana NE, Lushnikov A, Rotkiewicz P, Sefcovic N, Pevzner PA, Godzik A, Vyatkina K. MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms For Molecular Biology : Amb. 8: 19. PMID 23844614 DOI: 10.1186/1748-7188-8-19  1
2013 Jeong K, Kim S, Pevzner PA. UniNovo: a universal tool for de novo peptide sequencing. Bioinformatics (Oxford, England). 29: 1953-62. PMID 23766417 DOI: 10.1093/Bioinformatics/Btt338  1
2013 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 PA, et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences of the United States of America. 110: E2390-9. PMID 23754396 DOI: 10.1073/Pnas.1219809110  1
2013 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. Proceedings of the National Academy of Sciences of the United States of America. 110: 10153-8. PMID 23720318 DOI: 10.1073/Pnas.1221210110  1
2013 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, ... ... Pevzner PA, et al. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research. 23: 867-77. PMID 23564253 DOI: 10.1101/Gr.150433.112  1
2013 Ivankov DN, Payne SH, Galperin MY, Bonissone S, Pevzner PA, Frishman D. How many signal peptides are there in bacteria? Environmental Microbiology. 15: 983-90. PMID 23556536 DOI: 10.1111/1462-2920.12105  1
2013 Mohimani H, Kim S, Pevzner PA. A new approach to evaluating statistical significance of spectral identifications. Journal of Proteome Research. 12: 1560-8. PMID 23343606 DOI: 10.1021/Pr300453T  1
2013 Bonissone S, Gupta N, Romine M, Bradshaw RA, Pevzner PA. N-terminal protein processing: a comparative proteogenomic analysis. Molecular & Cellular Proteomics : McP. 12: 14-28. PMID 23001859 DOI: 10.1074/Mcp.M112.019075  1
2013 Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA. Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 359-71. PMID 22803627 DOI: 10.1089/Cmb.2012.0098  1
2013 Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, McLean J, Lasken R, Clingenpeel SR, Woyke T, ... ... Pevzner PA, et al. Assembling genomes and mini-metagenomes from highly chimeric reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 158-170. DOI: 10.1007/978-3-642-37195-0_13  1
2013 Liu X, Hengel S, Wu S, Tolić N, Pasa-Tolić L, Pevzner PA. Identification of ultramodified proteins using top-down spectra Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 132-144. DOI: 10.1007/978-3-642-37195-0_11  1
2012 Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolić L, Smith RD, Pevzner PA. Unexpected diversity of signal peptides in prokaryotes. Mbio. 3. PMID 23169999 DOI: 10.1128/Mbio.00339-12  1
2012 Ronen R, Boucher C, Chitsaz H, Pevzner P. sEQuel: Improving the accuracy of genome assemblies Bioinformatics. 28: i188-i196. PMID 22689760 DOI: 10.1093/Bioinformatics/Bts219  1
2012 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 PA, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 455-77. PMID 22506599 DOI: 10.1089/Cmb.2012.0021  1
2012 Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, Day ME, Farcas C, Heintzman ND, Jiang X, Kim H, Kim J, Matheny ME, Resnic FS, Vinterbo SA, et al. iDASH: integrating data for analysis, anonymization, and sharing. Journal of the American Medical Informatics Association : Jamia. 19: 196-201. PMID 22081224 DOI: 10.1136/Amiajnl-2011-000538  1
2012 Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. Protein identification using top-down. Molecular & Cellular Proteomics : McP. 11: M111.008524. PMID 22027200 DOI: 10.1074/Mcp.M111.008524  1
2012 Mohimani H, Kim S, Pevzner PA. MS-DPR: An algorithm for computing statistical significance of spectral identifications of non-linear peptides Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7534: 301-313. DOI: 10.1007/978-3-642-33122-0_24  1
2012 Vyahhi N, Pyshkin A, Pham S, Pevzner PA. From de Bruijn graphs to rectangle graphs for genome assembly Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7534: 249-261. DOI: 10.1007/978-3-642-33122-0_20  1
2011 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, ... ... Pevzner P, et al. Competencies: a cure for pre-med curriculum. Science (New York, N.Y.). 334: 760-1. PMID 22076362 DOI: 10.1126/Science.334.6057.760-B  1
2011 Compeau PE, Pevzner PA, Tesler G. How to apply de Bruijn graphs to genome assembly. Nature Biotechnology. 29: 987-91. PMID 22068540 DOI: 10.1038/Nbt.2023  1
2011 Mohimani H, Liu WT, Yang YL, Gaudêncio SP, Fenical W, Dorrestein PC, Pevzner PA. Multiplex de novo sequencing of peptide antibiotics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1371-81. PMID 22035290 DOI: 10.1089/Cmb.2011.0158  1
2011 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. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1625-34. PMID 21999285 DOI: 10.1089/Cmb.2011.0151  1
2011 Gupta N, Bandeira N, Keich U, Pevzner PA. Target-decoy approach and false discovery rate: when things may go wrong. Journal of the American Society For Mass Spectrometry. 22: 1111-20. PMID 21953092 DOI: 10.1007/S13361-011-0139-3  1
2011 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 PA, Lasken RS. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnology. 29: 915-21. PMID 21926975 DOI: 10.1038/Nbt.1966  1
2011 Mohimani H, Liu WT, Mylne JS, Poth AG, Colgrave ML, Tran D, Selsted ME, Dorrestein PC, Pevzner PA. Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases. Journal of Proteome Research. 10: 4505-12. PMID 21851130 DOI: 10.1021/Pr200323A  1
2011 Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner PA. Sequencing cyclic peptides by multistage mass spectrometry. Proteomics. 11: 3642-50. PMID 21751357 DOI: 10.1002/Pmic.201000697  1
2011 Medvedev P, Scott E, Kakaradov B, Pevzner P. Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics (Oxford, England). 27: i137-41. PMID 21685062 DOI: 10.1093/bioinformatics/btr208  1
2011 Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nature Methods. 8: 587-91. PMID 21572408 DOI: 10.1038/Nmeth.1609  1
2011 Pevzner PA, Shamir R. Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 865. PMID 21563980 DOI: 10.1089/Cmb.2011.007P  1
2011 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. 6: e18565. PMID 21533272 DOI: 10.1371/Journal.Pone.0018565  1
2011 Mevers E, Liu WT, Engene N, Mohimani H, Byrum T, Pevzner PA, Dorrestein PC, Spadafora C, Gerwick WH. Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera. Journal of Natural Products. 74: 928-36. PMID 21488639 DOI: 10.1021/Np200077F  1
2011 Jeong K, Kim S, Bandeira N, Pevzner PA. Gapped spectral dictionaries and their applications for database searches of tandem mass spectra. Molecular & Cellular Proteomics : McP. 10: M110.002220. PMID 21444829 DOI: 10.1074/Mcp.M110.002220  1
2011 Ng J, Amir A, Pevzner PA. Blocked pattern matching problem and its applications in proteomics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 298-319. DOI: 10.1007/978-3-642-20036-6_27  1
2010 Alekseyev MA, Pevzner PA. Comparative genomics reveals birth and death of fragile regions in mammalian evolution. Genome Biology. 11: R117. PMID 21118492 DOI: 10.1186/Gb-2010-11-11-R117  1
2010 Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Molecular & Cellular Proteomics : McP. 9: 2772-82. PMID 20855543 DOI: 10.1074/Mcp.M110.002766  1
2010 Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Molecular & Cellular Proteomics : McP. 9: 2840-52. PMID 20829449 DOI: 10.1074/Mcp.M110.003731  1
2010 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. Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 107: 16286-90. PMID 20805502 DOI: 10.1073/Pnas.1008368107  1
2010 Pham SK, Pevzner PA. DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics (Oxford, England). 26: 2509-16. PMID 20736338 DOI: 10.1093/Bioinformatics/Btq465  1
2010 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. The Aaps Journal. 12: 635-45. PMID 20734175 DOI: 10.1208/S12248-010-9223-Z  1
2010 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. Journal of Proteome Research. 9: 5065-75. PMID 20704348 DOI: 10.1021/Pr100358B  1
2010 Gupta N, Hixson KK, Culley DE, Smith RD, Pevzner PA. Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry. Proteomics. 10: 2833-44. PMID 20597098 DOI: 10.1002/Pmic.200900821  1
2010 Leão PN, Pereira AR, Liu WT, Ng J, Pevzner PA, Dorrestein PC, König GM, Vasconcelos VM, Gerwick WH. Synergistic allelochemicals from a freshwater cyanobacterium. Proceedings of the National Academy of Sciences of the United States of America. 107: 11183-8. PMID 20534563 DOI: 10.1073/Pnas.0914343107  1
2010 Alekseyev MA, Pevzner PA. Limited lifespan of fragile regions in mammalian evolution Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6398: 198-215. DOI: 10.1007/978-3-642-16181-0_17  1
2010 Moret BME, Miller WC, Pevzner PA, Sankoff D. Computational challenges in comparative genomics session introduction Pacific Symposium On Biocomputing 2010, Psb 2010. 1-2.  1
2009 Pevzner P, Shamir R. Computing has changed biology-biology education must catch up Science. 325: 541-542. PMID 19644094 DOI: 10.1126/Science.1173876  1
2009 Gupta N, Pevzner PA. False discovery rates of protein identifications: a strike against the two-peptide rule. Journal of Proteome Research. 8: 4173-81. PMID 19627159 DOI: 10.1021/Pr9004794  1
2009 Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA. Dereplication and de novo sequencing of nonribosomal peptides. Nature Methods. 6: 596-9. PMID 19597502 DOI: 10.1038/Nmeth.1350  1
2009 Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Analytical Chemistry. 81: 4200-9. PMID 19413302 DOI: 10.1021/Ac900114T  1
2009 Kim S, Bandeira N, Pevzner PA. Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Molecular & Cellular Proteomics : McP. 8: 1391-400. PMID 19254948 DOI: 10.1074/Mcp.M800535-Mcp200  1
2009 Alekseyev MA, Pevzner PA. Breakpoint graphs and ancestral genome reconstructions. Genome Research. 19: 943-57. PMID 19218533 DOI: 10.1101/Gr.082784.108  1
2009 Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Research. 19: 336-46. PMID 19056694 DOI: 10.1101/Gr.079053.108  1
2009 Kim S, Gupta N, Bandeira N, Pevzner PA. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Molecular & Cellular Proteomics : McP. 8: 53-69. PMID 18703573 DOI: 10.1074/Mcp.M800103-Mcp200  1
2009 Peng Q, Alekseyev MA, Tesler G, Pevzner PA. Decoding synteny blocks and large-scale duplications in mammalian and plant genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5724: 220-232. DOI: 10.1007/978-3-642-04241-6_19  1
2009 Moret BME, Miller W, Pevzner PA, Sankoff D. Computational challenges in comparative genomics: Gene family evolution, ancestral genome reconstruction, and applications to human genetics Pacific Symposium On Biocomputing 2009, Psb 2009. 111-113.  1
2009 Istrail S, Pevzner P, Waterman M, Rajasekaran S. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5462: v-vi.  1
2008 Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR. Automated de novo protein sequencing of monoclonal antibodies Nature Biotechnology. 26: 1336-1338. PMID 19060866 DOI: 10.1038/Nbt1208-1336  1
2008 Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics (Oxford, England). 24: i416-23. PMID 18785330 DOI: 10.1093/bioinformatics/btn184  1
2008 Pevzner PA, Kim S, Ng J. Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science (New York, N.Y.). 321: 1040; author reply 1. PMID 18719266 DOI: 10.1126/Science.1155006  1
2008 Kim S, Gupta N, Pevzner PA. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. Journal of Proteome Research. 7: 3354-63. PMID 18597511 DOI: 10.1021/Pr8001244  1
2008 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. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Research. 18: 1133-42. PMID 18426904 DOI: 10.1101/Gr.074344.107  1
2008 Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA. Interpreting top-down mass spectra using spectral alignment. Analytical Chemistry. 80: 2499-505. PMID 18302345 DOI: 10.1021/Ac702324U  1
2008 Ng J, Pevzner PA. Algorithm for identification of fusion proteins via mass spectrometry. Journal of Proteome Research. 7: 89-95. PMID 18173219 DOI: 10.1021/Pr070214G  1
2008 Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Research. 18: 324-30. PMID 18083777 DOI: 10.1101/Gr.7088808  1
2008 Rodriguez J, Gupta N, Smith RD, Pevzner PA. Does trypsin cut before proline? Journal of Proteome Research. 7: 300-5. PMID 18067249 DOI: 10.1021/Pr0705035  1
2008 Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. Clustering millions of tandem mass spectra. Journal of Proteome Research. 7: 113-22. PMID 18067247 DOI: 10.1021/Pr070361E  1
2008 Alekseyev MA, Pevzner PA. Multi-break rearrangements and chromosomal evolution Theoretical Computer Science. 395: 193-202. DOI: 10.1016/J.Tcs.2008.01.013  1
2008 Bandeira N, Ng J, Meluzzi D, Linington RG, Dorrestein P, Pevzner PA. De novo sequencing of nonribosomal peptides Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 181-195. DOI: 10.1007/978-3-540-78839-3_16  1
2007 Alekseyev MA, Pevzner PA. Are there rearrangement hotspots in the human genome? Plos Computational Biology. 3: e209. PMID 17997591 DOI: 10.1371/Journal.Pcbi.0030209  1
2007 Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, Eichler EE. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nature Genetics. 39: 1361-8. PMID 17922013 DOI: 10.1038/Ng.2007.9  1
2007 Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Research. 17: 1362-77. PMID 17690205 DOI: 10.1101/Gr.6427907  1
2007 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. 7: 2318-29. PMID 17623296 DOI: 10.1002/Pmic.200700003  1
2007 Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. Whole-genome sequencing and assembly with high-throughput, short-read technologies. Plos One. 2: e484. PMID 17534434 DOI: 10.1371/Journal.Pone.0000484  1
2007 Bandeira N, Clauser KR, Pevzner PA. Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Molecular & Cellular Proteomics : McP. 6: 1123-34. PMID 17446555 DOI: 10.1074/Mcp.M700001-Mcp200  1
2007 Bandeira N, Tsur D, Frank A, Pevzner PA. Protein identification by spectral networks analysis. Proceedings of the National Academy of Sciences of the United States of America. 104: 6140-5. PMID 17404225 DOI: 10.1073/Pnas.0701130104  1
2007 Alekseyev MA, Pevzner PA. Colored de Bruijn graphs and the genome halving problem. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 4: 98-107. PMID 17277417 DOI: 10.1109/Tcbb.2007.1002  1
2007 Zhi D, Keich U, Pevzner P, Heber S, Tang H. Correcting base-assignment errors in repeat regions of shotgun assembly. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 4: 54-64. PMID 17277413 DOI: 10.1109/Tcbb.2007.1005  1
2007 Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA. De novo peptide sequencing and identification with precision mass spectrometry. Journal of Proteome Research. 6: 114-23. PMID 17203955 DOI: 10.1021/Pr060271U  1
2007 Alekseyev MA, Pevzner PA. Whole genome duplications and contracted breakpoint graphs Siam Journal On Computing. 36: 1748-1763. DOI: 10.1137/05064727X  1
2007 Karp R, Li M, Pevzner P, Shamir R. Special issue on computational molecular biology Journal of Computer and System Sciences. 73: 1023. DOI: 10.1016/J.Jcss.2007.03.010  1
2006 Tanner S, Pevzner PA, Bafna V. Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nature Protocols. 1: 67-72. PMID 17406213 DOI: 10.1038/Nprot.2006.10  1
2006 Chong KF, Ning K, Leong HW, Pevzner P. Modeling and characterization of multi-charge mass spectra for peptide sequencing. Journal of Bioinformatics and Computational Biology. 4: 1329-52. PMID 17245817 DOI: 10.1142/S021972000600248X  1
2006 Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. Representing and comparing protein structures as paths in three-dimensional space. Bmc Bioinformatics. 7: 460. PMID 17052359 DOI: 10.1186/1471-2105-7-460  1
2006 Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility? Journal of Proteome Research. 5: 2554-66. PMID 17022627 DOI: 10.1021/Pr050473A  1
2006 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. Journal of Proteome Research. 5: 2448-56. PMID 16944958 DOI: 10.1021/Pr060200V  1
2006 Jones NC, Pevzner PA. Comparative genomics reveals unusually long motifs in mammalian genomes. Bioinformatics (Oxford, England). 22: e236-42. PMID 16873477 DOI: 10.1093/Bioinformatics/Btl265  1
2006 Bourque G, Tesler G, Pevzner PA. The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Research. 16: 311-3. PMID 16510896 DOI: 10.1101/Gr.4631806  1
2006 Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. Identifying repeat domains in large genomes. Genome Biology. 7: R7. PMID 16507140 DOI: 10.1186/Gb-2006-7-1-R7  1
2006 Peng Q, Pevzner PA, Tesler G. The fragile breakage versus random breakage models of chromosome evolution. Plos Computational Biology. 2: e14. PMID 16501665 DOI: 10.1371/Journal.Pcbi.0020014  1
2006 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, ... ... Pevzner P, et al. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Research. 16: 394-404. PMID 16461635 DOI: 10.1101/Gr.4247306  1
2006 Bandeira N, Tsur D, Frank A, Pevzner P. A new approach to protein identification Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 363-378. DOI: 10.1007/11732990_31  1
2006 Chong KF, Ning K, Leong HW, Pevzner P. Characterization of multi-charge mass spectra for peptide sequencing Series On Advances in Bioinformatics and Computational Biology. 3: 109-119.  1
2005 Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. Identification of post-translational modifications via blind search of mass-spectra. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 157-66. PMID 16447973 DOI: 10.1109/CSB.2005.34  1
2005 Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. Identification of post-translational modifications by blind search of mass spectra. Nature Biotechnology. 23: 1562-7. PMID 16311586 DOI: 10.1038/Nbt1168  1
2005 Frank A, Tanner S, Bafna V, Pevzner P. Peptide sequence tags for fast database search in mass-spectrometry. Journal of Proteome Research. 4: 1287-95. PMID 16083278 DOI: 10.1021/Pr050011X  1
2005 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, ... ... Pevzner PA, et al. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science (New York, N.Y.). 309: 613-7. PMID 16040707 DOI: 10.1126/Science.1111387  1
2005 Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Analytical Chemistry. 77: 4626-39. PMID 16013882 DOI: 10.1021/Ac050102D  1
2005 Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics (Oxford, England). 21: i351-8. PMID 15961478 DOI: 10.1093/Bioinformatics/Bti1018  1
2005 Frank A, Pevzner P. PepNovo: De novo peptide sequencing via probabilistic network modeling Analytical Chemistry. 77: 964-973. PMID 15858974 DOI: 10.1021/Ac048788H  1
2005 Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Research. 15: 98-110. PMID 15590940 DOI: 10.1101/Gr.3002305  1
2004 Bandeira N, Tang H, Bafna V, Pevzner P. Shotgun protein sequencing by tandem mass spectra assembly. Analytical Chemistry. 76: 7221-33. PMID 15595863 DOI: 10.1021/Ac0489162  1
2004 Murphy WJ, Pevzner PA, O'Brien SJ. Mammalian phylogenomics comes of age. Trends in Genetics : Tig. 20: 631-9. PMID 15522459 DOI: 10.1016/J.Tig.2004.09.005  1
2004 Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Research. 14: 2336-46. PMID 15520295 DOI: 10.1101/Gr.2657504  1
2004 Price AL, Eskin E, Pevzner PA. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Research. 14: 2245-52. PMID 15520288 DOI: 10.1101/Gr.2693004  1
2004 Pevzner PA, Pevzner PA, Tang H, Tesler G. De novo repeat classification and fragment assembly. Genome Research. 14: 1786-96. PMID 15342561 DOI: 10.1101/Gr.2395204  1
2004 Kahng AB, Măndoiu II, Pevzner PA, Reda S, Zelikovsky AZ. Scalable heuristics for design of DNA probe arrays. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 429-47. PMID 15285900 DOI: 10.1089/1066527041410391  1
2004 Raphael BJ, Pevzner PA. Reconstructing tumor amplisomes. Bioinformatics (Oxford, England). 20: i265-73. PMID 15262808 DOI: 10.1093/bioinformatics/bth931  1
2004 Pevzner PA. Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinformatics (Oxford, England). 20: 2159-61. PMID 15073013 DOI: 10.1093/Bioinformatics/Bth217  1
2004 Bourque G, Pevzner PA, Tesler G. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Research. 14: 507-16. PMID 15059991 DOI: 10.1101/Gr.1975204  1
2004 Chaisson M, Pevzner P, Tang H. Fragment assembly with short reads. Bioinformatics (Oxford, England). 20: 2067-74. PMID 15059830 DOI: 10.1093/Bioinformatics/Bth205  1
2004 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, ... ... Pevzner PA, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  1
2004 Alekseyev MA, Pevzner PA. Genome halving problem revisited Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3328: 1-15.  1
2003 Raphael BJ, Volik S, Collins C, Pevzner PA. Reconstructing tumor genome architectures. Bioinformatics (Oxford, England). 19: ii162-71. PMID 14534186 DOI: 10.1093/bioinformatics/btg1074  1
2003 Price A, Ramabhadran S, Pevzner PA. Finding subtle motifs by branching from sample strings. Bioinformatics (Oxford, England). 19: ii149-55. PMID 14534184 DOI: 10.1093/bioinformatics/btg1072  1
2003 Eskin E, Keich U, Gelfand MS, Pevzner PA. Genome-wide analysis of bacterial promoter regions. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 29-40. PMID 12603015  1
2003 Kahng AB, Mǎndoiu I, Pevzner P, Reda S, Zelikovsky A. Engineering a scalable placement heuristic for DNA probe arrays Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 148-156.  1
2002 Lunyak VV, Burgess R, Prefontaine GG, Nelson C, Sze SH, Chenoweth J, Schwartz P, Pevzner PA, Glass C, Mandel G, Rosenfeld MG. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science (New York, N.Y.). 298: 1747-52. PMID 12399542 DOI: 10.1126/Science.1076469  1
2002 Keich U, Pevzner PA. Subtle motifs: defining the limits of motif finding algorithms. Bioinformatics (Oxford, England). 18: 1382-90. PMID 12376383 DOI: 10.1093/Bioinformatics/18.10.1382  1
2002 Keich U, Pevzner PA. Finding motifs in the twilight zone. Bioinformatics (Oxford, England). 18: 1374-81. PMID 12376382 DOI: 10.1093/Bioinformatics/18.10.1374  1
2002 Hannenhalli S, Hubell E, Lipshutz R, Pevzner PA. Combinatorial algorithms for design of DNA arrays. Advances in Biochemical Engineering/Biotechnology. 77: 1-19. PMID 12227732 DOI: 10.1007/3-540-45713-5_1  1
2002 Eskin E, Pevzner PA. Finding composite regulatory patterns in DNA sequences. Bioinformatics (Oxford, England). 18: S354-63. PMID 12169566  1
2002 Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA. Splicing graphs and EST assembly problem. Bioinformatics (Oxford, England). 18: S181-8. PMID 12169546  1
2002 Sze SH, Gelfand MS, Pevzner PA. Finding weak motifs in DNA sequences. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 235-46. PMID 11928479  1
2002 Mulyukov Z, Pevzner PA. EULER-PCR: finishing experiments for repeat resolution. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 199-210. PMID 11928476  1
2002 Bourque G, Pevzner PA. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Research. 12: 26-36. PMID 11779828  1
2002 Kahng AB, Măndoiu II, Pevzner PA, Reda S, Zelikovsky AZ. Border length minimization in dna array design Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2452: 435-448.  1
2001 Pevzner PA. Assembling puzzles from preassembled blocks. Genome Research. 11: 1461-2. PMID 11544188 DOI: 10.1101/Gr.206301  1
2001 Pevzner PA, Tang H, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proceedings of the National Academy of Sciences of the United States of America. 98: 9748-53. PMID 11504945 DOI: 10.1073/Pnas.171285098  1
2001 Pevzner PA, Tang H. Fragment assembly with double-barreled data. Bioinformatics (Oxford, England). 17: S225-33. PMID 11473013 DOI: 10.1093/Bioinformatics/17.Suppl_1.S225  1
2001 Arslan AN, EÄŸecioÄŸlu O, Pevzner PA. A new approach to sequence comparison: normalized sequence alignment. Bioinformatics (Oxford, England). 17: 327-37. PMID 11301301 DOI: 10.1093/Bioinformatics/17.4.327  1
2001 Pevzner PA, Mulyukov Z, Dancik V, Tang CL. Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Research. 11: 290-9. PMID 11157792 DOI: 10.1101/Gr.154101  1
2001 Goldberg LA, Goldberg PW, Paterson M, Pevzner P, Sahinalp SC, Sweedyk E. The Complexity of Gene Placement Journal of Algorithms. 41: 225-243. DOI: 10.1006/Jagm.2001.1172  1
2001 Pevzner PA, Tang H, Waterman MS. A new approach to fragment assembly in DNA sequencing Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 256-267.  1
2000 Pevzner PA, Dancík V, Tang CL. Mutation-tolerant protein identification by mass spectrometry. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 777-87. PMID 11382361 DOI: 10.1089/10665270050514927  1
2000 Pevzner PA, Sze SH. Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 269-78. PMID 10977088  1
1999 Hubbell E, Pevzner PA. Fidelity probes for DNA arrays. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 113-7. PMID 10786293  1
1999 Mironov AA, Pevzner PA. SST versus EST in gene recognition. Microbial & Comparative Genomics. 4: 167-72. PMID 10587944  1
1999 Dancík V, Addona TA, Clauser KR, Vath JE, Pevzner PA. De novo peptide sequencing via tandem mass spectrometry. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 327-42. PMID 10582570 DOI: 10.1089/106652799318300  1
1999 Hannenhalli S, Pevzner PA. Transforming Cabbage into Turnip: Polynomial Algorithm for Sorting Signed Permutations by Reversals Journal of the Acm. 46: 1-22. DOI: 10.1145/300515.300516  1
1998 Mironov AA, Roytberg MA, Pevzner PA, Gelfand MS. Performance-guarantee gene predictions via spliced alignment. Genomics. 51: 332-9. PMID 9721203 DOI: 10.1006/Geno.1998.5251  1
1998 Sze SH, Roytberg MA, Gelfand MS, Mironov AA, Astakhova TV, Pevzner PA. Algorithms and software for support of gene identification experiments. Bioinformatics (Oxford, England). 14: 14-9. PMID 9520497 DOI: 10.1093/Bioinformatics/14.1.14  1
1998 Xu G, Sze SH, Liu CP, Pevzner PA, Arnheim N. Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs. Genomics. 47: 171-9. PMID 9479489 DOI: 10.1006/Geno.1997.5072  1
1998 Bafna V, Pevzner PA. Sorting by transpositions Siam Journal On Discrete Mathematics. 11: 224-240. DOI: 10.1137/S089548019528280X  1
1998 Pevzner PA. Second Annual International Conference on Computational Biology, RECOMB'98, New York, 22-25 March 1998: Preface Journal of Computational Biology. 5: 367.  1
1997 Sze SH, Pevzner PA. Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 4: 297-309. PMID 9278061 DOI: 10.1089/Cmb.1997.4.297  0.36
1997 Belyi I, Pevzner PA. Software for DNA sequencing by hybridization. Computer Applications in the Biosciences : Cabios. 13: 205-10. PMID 9146969 DOI: 10.1093/Bioinformatics/13.2.205  1
1997 Bafna V, Lawler EL, Pevzner PA. Approximation algorithms for multiple sequence alignment Theoretical Computer Science. 182: 233-244. DOI: 10.1016/S0304-3975(97)00023-6  1
1996 Gelfand MS, Mironov AA, Pevzner PA. Gene recognition via spliced sequence alignment. Proceedings of the National Academy of Sciences of the United States of America. 93: 9061-6. PMID 8799154 DOI: 10.1073/Pnas.93.17.9061  1
1996 Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA. Positional sequencing by hybridization. Computer Applications in the Biosciences : Cabios. 12: 19-24. PMID 8670615  1
1996 Bafna V, Pevzner PA. Genome rearrangements and sorting by reversals Siam Journal On Computing. 25: 272-289. DOI: 10.1137/S0097539793250627  1
1995 Hannenhalli S, Chappey C, Koonin EV, Pevzner PA. Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics. 30: 299-311. PMID 8586431 DOI: 10.1006/Geno.1995.9873  1
1995 Mironov AA, Alexandrov NN, Bogodarova NYu, Grigorjev A, Lebedev VF, Lunovskaya LV, Truchan ME, Pevzner PA. DNASUN: a package of computer programs for the biotechnology laboratory. Computer Applications in the Biosciences : Cabios. 11: 331-5. PMID 7583703 DOI: 10.1093/Bioinformatics/11.3.331  1
1995 Pevzner PA. Combinatorial methods for DNA mapping and sequencing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 2: 153-8. PMID 7497124 DOI: 10.1089/Cmb.1995.2.153  1
1995 Bafna V, Pevzner PA. Sorting by reversals: Genome rearrangements in plant organelles and evolutionary history of X chromosome Molecular Biology and Evolution. 12: 239-246. DOI: 10.1093/Oxfordjournals.Molbev.A040208  1
1995 Pevzner PA, Waterman MS. Multiple filtration and approximate pattern matching Algorithmica. 13: 135-154. DOI: 10.1007/Bf01188584  1
1995 Pevzner PA. DNA physical mapping and alternating Eulerian cycles in colored graphs Algorithmica. 13: 77-105. DOI: 10.1007/Bf01188582  1
1995 Vingron M, Pevzner PA. Multiple Sequence Comparison and Consistency on Multipartite Graphs Advances in Applied Mathematics. 16: 1-22. DOI: 10.1006/Aama.1995.1001  1
1994 Pevzner PA. Rearrangements of DNA sequences and SBH. Computers & Chemistry. 18: 221-3. PMID 7952892 DOI: 10.1016/0097-8485(94)85016-X  1
1993 Pevzner PA, Waterman MS. Generalized Sequence Alignment and Duality Advances in Applied Mathematics. 14: 139-171. DOI: 10.1006/Aama.1993.1008  1
1993 Pevzner PA, Gelfand MS. Foreword Biosystems. 30: vii-ix.  1
1992 Pevzner PA. Statistical distance between texts and filtration methods in sequence comparison. Computer Applications in the Biosciences : Cabios. 8: 121-7. PMID 1591607 DOI: 10.1093/Bioinformatics/8.2.121  1
1992 Gelfand MS, Kozhukhin CG, Pevzner PA. Extendable words in nucleotide sequences. Computer Applications in the Biosciences : Cabios. 8: 129-35. PMID 1375526 DOI: 10.1093/Bioinformatics/8.2.129  1
1992 Pevzner PA. Nucleotide sequences versus Markov models Computers and Chemistry. 16: 103-106. DOI: 10.1016/0097-8485(92)80036-Y  1
1991 Kozhukhin CG, Pevzner PA. Genome inhomogeneity is determined mainly by WW and SS dinucleotides. Computer Applications in the Biosciences : Cabios. 7: 39-49. PMID 2004273 DOI: 10.1093/Bioinformatics/7.1.39  1
1991 Pevzner PA, Lysov IuP, Khrapko KR, BeliavskiÄ­ AV, Florent'ev VL, Mirzabekov AD. [Optimal chips for megabase DNA sequencing]. Molekuliarnaia Biologiia. 25: 552-62. PMID 1881398  1
1991 Pevzner PA, Lysov YuP, Khrapko KR, Belyavsky AV, Florentiev VL, Mirzabekov AD. Improved chips for sequencing by hybridization. Journal of Biomolecular Structure & Dynamics. 9: 399-410. PMID 1741970 DOI: 10.1080/07391102.1991.10507920  1
1989 Pevzner PA. 1-Tuple DNA sequencing: computer analysis. Journal of Biomolecular Structure & Dynamics. 7: 63-73. PMID 2684223 DOI: 10.1080/07391102.1989.10507752  1
1989 Pevzner PA, VeÄ­ko VP. [Paths in graphs and selection of oligonucleotide linkers]. Molekuliarnaia Biologiia. 23: 1075-9. PMID 2555681  1
1989 Pevzner PA, Borodovsky MYu, Mironov AA. Linguistics of nucleotide sequences. II: Stationary words in genetic texts and the zonal structure of DNA. Journal of Biomolecular Structure & Dynamics. 6: 1027-38. PMID 2531597 DOI: 10.1080/07391102.1989.10506529  1
1989 Pevzner PA, Borodovsky MYu, Mironov AA. Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words. Journal of Biomolecular Structure & Dynamics. 6: 1013-26. PMID 2531596 DOI: 10.1080/07391102.1989.10506528  1
1987 Pevzner PA, Mironov AA. [Effective method for physical mapping the DNA molecule]. Molekuliarnaia Biologiia. 21: 788-96. PMID 3657777  1
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