| Year |
Citation |
Score |
| 2023 |
Bzikadze AV, Pevzner PA. UniAligner: a parameter-free framework for fast sequence alignment. Nature Methods. 20: 1346-1354. PMID 37580559 DOI: 10.1038/s41592-023-01970-4 |
0.307 |
|
| 2022 |
Pevzner P, Vingron M, Reidys C, Sun F, Istrail S. Michael Waterman's Contributions to Computational Biology and Bioinformatics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35727100 DOI: 10.1089/cmb.2022.29066.pp |
0.662 |
|
| 2022 |
Istrail S, Pevzner P, Sun F, Vingron M. Special Issue: Professor Michael Waterman's 80th Birthday, Part 1. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35704861 DOI: 10.1089/cmb.2022.29065.si |
0.576 |
|
| 2022 |
Sirupurapu V, Safonova Y, Pevzner PA. Gene prediction in the immunoglobulin loci. Genome Research. 32: 1152-1169. PMID 35545447 DOI: 10.1101/gr.276676.122 |
0.711 |
|
| 2022 |
Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Research. PMID 35361626 DOI: 10.1101/gr.276027.121 |
0.752 |
|
| 2021 |
Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Trace Reconstruction Problems in Computational Biology. Ieee Transactions On Information Theory. 67: 3295-3314. PMID 34176957 DOI: 10.1109/tit.2020.3030569 |
0.7 |
|
| 2021 |
Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, et al. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nature Communications. 12: 3225. PMID 34050176 DOI: 10.1038/s41467-021-23502-4 |
0.326 |
|
| 2021 |
Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, ... Pevzner P, et al. Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Research. 31: 934. PMID 33941606 DOI: 10.1101/gr.275614.121 |
0.442 |
|
| 2021 |
Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, ... Pevzner P, et al. A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Marine Drugs. 19. PMID 33418911 DOI: 10.3390/md19010020 |
0.61 |
|
| 2020 |
Safonova Y, Pevzner PA. V(DD)J recombination is an important and evolutionary conserved mechanism for generating antibodies with unusually long CDR3s. Genome Research. PMID 32948615 DOI: 10.1101/Gr.259598.119 |
0.752 |
|
| 2020 |
Bzikadze AV, Pevzner PA. Automated assembly of centromeres from ultra-long error-prone reads. Nature Biotechnology. PMID 32665660 DOI: 10.1038/S41587-020-0582-4 |
0.33 |
|
| 2020 |
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, ... ... Pevzner PA, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. PMID 32663838 DOI: 10.1038/S41586-020-2547-7 |
0.357 |
|
| 2020 |
Dvorkina T, Bzikadze AV, Pevzner PA. The string decomposition problem and its applications to centromere analysis and assembly. Bioinformatics (Oxford, England). 36: i93-i101. PMID 32657390 DOI: 10.1093/Bioinformatics/Btaa454 |
0.32 |
|
| 2020 |
Mikheenko A, Bzikadze AV, Gurevich A, Miga KH, Pevzner PA. TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics (Oxford, England). 36: i75-i83. PMID 32657355 DOI: 10.1093/Bioinformatics/Btaa440 |
0.314 |
|
| 2020 |
Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, ... Pevzner P, et al. Ultra-low input single tube linked-read library method enables short-read second-generation sequencing systems to generate highly accurate and economical long-range sequencing information routinely. Genome Research. PMID 32540955 DOI: 10.1101/Gr.260380.119 |
0.53 |
|
| 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 |
0.377 |
|
| 2020 |
Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. Plos Computational Biology. 16: e1007837. PMID 32339161 DOI: 10.1371/Journal.Pcbi.1007837 |
0.73 |
|
| 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 |
0.41 |
|
| 2019 |
Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, ... ... Pevzner PA, et al. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biology. 20: 226. PMID 31672156 DOI: 10.1186/S13059-019-1834-9 |
0.349 |
|
| 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 |
0.397 |
|
| 2019 |
Tolstoganov I, Bankevich A, Chen Z, Pevzner PA. cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. Bioinformatics (Oxford, England). 35: i61-i70. PMID 31510642 DOI: 10.1093/Bioinformatics/Btz349 |
0.318 |
|
| 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 |
0.388 |
|
| 2019 |
Safonova Y, Pevzner PA. Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins. Frontiers in Immunology. 10: 987. PMID 31134072 DOI: 10.3389/Fimmu.2019.00987 |
0.726 |
|
| 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 |
0.372 |
|
| 2019 |
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology. PMID 30936562 DOI: 10.1038/S41587-019-0072-8 |
0.376 |
|
| 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 |
0.353 |
|
| 2018 |
Bankevich A, Pevzner PA. Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity. Cell Systems. PMID 30056005 DOI: 10.1016/J.Cels.2018.06.009 |
0.379 |
|
| 2018 |
Pu L, Lin Y, Pevzner P. Detection and analysis of ancient segmental duplications in mammalian genomes. Genome Research. PMID 29735604 DOI: 10.1101/Gr.228718.117 |
0.408 |
|
| 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 |
0.38 |
|
| 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 |
0.557 |
|
| 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 |
0.634 |
|
| 2017 |
Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. Journal of Immunology (Baltimore, Md. : 1950). PMID 28978691 DOI: 10.4049/Jimmunol.1700485 |
0.734 |
|
| 2017 |
Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA. Single-molecule protein identification by sub-nanopore sensors. Plos Computational Biology. 13: e1005356. PMID 28486472 DOI: 10.1371/Journal.Pcbi.1005356 |
0.343 |
|
| 2017 |
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Research. PMID 28298430 DOI: 10.1101/Gr.213959.116 |
0.322 |
|
| 2017 |
Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner PA, 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. Journal of Proteomics. PMID 28242452 DOI: 10.1016/J.Jprot.2017.02.013 |
0.328 |
|
| 2016 |
Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA. Assembly of long error-prone reads using de Bruijn graphs. Proceedings of the National Academy of Sciences of the United States of America. PMID 27956617 DOI: 10.1073/Pnas.1604560113 |
0.329 |
|
| 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 |
0.411 |
|
| 2016 |
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, ... ... Pevzner P, et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology. 34: 828-837. PMID 27504778 DOI: 10.1038/Nbt.3597 |
0.633 |
|
| 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 |
0.365 |
|
| 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 |
0.366 |
|
| 2016 |
Bankevich A, Pevzner PA. TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nature Methods. PMID 26828418 DOI: 10.1038/Nmeth.3737 |
0.35 |
|
| 2016 |
Safonova Y, Shlemov A, Bzikadze A, Bankevich S, Pevzner P. A novel toolkit for analysis of adaptive immune repertoires using sequencing and mass spectra data F1000research. 5. DOI: 10.7490/F1000Research.1113448.1 |
0.349 |
|
| 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 |
0.457 |
|
| 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 |
0.321 |
|
| 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 |
0.452 |
|
| 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 |
0.491 |
|
| 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 |
0.592 |
|
| 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 |
0.757 |
|
| 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 |
0.331 |
|
| 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 |
0.764 |
|
| 2014 |
Lin Y, Nurk S, Pevzner PA. What is the difference between the breakpoint graph and the de Bruijn graph? Bmc Genomics. 15: S6. PMID 25572416 DOI: 10.1186/1471-2164-15-S6-S6 |
0.319 |
|
| 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 |
0.625 |
|
| 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 |
0.457 |
|
| 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 |
0.384 |
|
| 2014 |
Liu X, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolić N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-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 |
0.463 |
|
| 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 |
0.72 |
|
| 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 |
0.359 |
|
| 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 |
0.358 |
|
| 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 |
0.4 |
|
| 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 |
0.702 |
|
| 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 |
0.702 |
|
| 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 |
0.712 |
|
| 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 |
0.409 |
|
| 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 |
0.31 |
|
| 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 |
0.365 |
|
| 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 |
0.622 |
|
| 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 |
0.588 |
|
| 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 |
0.502 |
|
| 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 |
0.682 |
|
| 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 |
0.662 |
|
| 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 |
0.603 |
|
| 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 |
0.352 |
|
| 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 |
0.706 |
|
| 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 |
0.622 |
|
| 2012 |
Monroe E, Choi H, Lesin V, Sirotkin A, Dvorkin M, Pevzner P, Gerwick W, Gerwick L. Genomic insights into secondary metabolism of the natural product-rich cyanobacterium Moorea bouillonii Planta Medica. 78. DOI: 10.1055/S-0032-1320287 |
0.31 |
|
| 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 |
0.387 |
|
| 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 |
0.421 |
|
| 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 |
0.347 |
|
| 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 |
0.712 |
|
| 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 |
0.395 |
|
| 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 |
0.451 |
|
| 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 |
0.422 |
|
| 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 |
0.766 |
|
| 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 |
0.375 |
|
| 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 |
0.801 |
|
| 2011 |
Mohimani H, Liu W, 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 (vol 10, pg 4505, 2010) Journal of Proteome Research. 10: 5575-5575. DOI: 10.1021/Pr201019Q |
0.414 |
|
| 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 |
0.474 |
|
| 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 |
0.665 |
|
| 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 |
0.651 |
|
| 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 |
0.755 |
|
| 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 |
0.576 |
|
| 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 |
0.413 |
|
| 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 |
0.716 |
|
| 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 |
0.56 |
|
| 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 |
0.578 |
|
| 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 |
0.527 |
|
| 2010 |
Alekseyev MA, Peng Q, Pevzner PA, Tesler G. Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-scale Duplications Communications in Information and Systems. 10: 1-22. DOI: 10.4310/Cis.2010.V10.N1.A1 |
0.71 |
|
| 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 |
0.623 |
|
| 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 |
0.342 |
|
| 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 |
0.549 |
|
| 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 |
0.759 |
|
| 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 |
0.754 |
|
| 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 |
0.747 |
|
| 2009 |
Alekseyev MA, Pevzner PA. Breakpoint graphs and ancestral genome reconstructions. Genome Research. 19: 943-57. PMID 19218533 DOI: 10.1101/Gr.082784.108 |
0.705 |
|
| 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 |
0.325 |
|
| 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 |
0.806 |
|
| 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 |
0.676 |
|
| 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 |
0.644 |
|
| 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 |
0.676 |
|
| 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 |
0.692 |
|
| 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 |
0.698 |
|
| 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 |
0.805 |
|
| 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 |
0.654 |
|
| 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 |
0.663 |
|
| 2008 |
Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Research. 18: 324-30. PMID 18083777 DOI: 10.1101/Gr.7088808 |
0.372 |
|
| 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 |
0.581 |
|
| 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 |
0.8 |
|
| 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 |
0.683 |
|
| 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 |
0.562 |
|
| 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 |
0.687 |
|
| 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 |
0.405 |
|
| 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 |
0.832 |
|
| 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 |
0.722 |
|
| 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 |
0.402 |
|
| 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 |
0.7 |
|
| 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 |
0.782 |
|
| 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 |
0.679 |
|
| 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 |
0.773 |
|
| 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 |
0.705 |
|
| 2007 |
Alekseyev MA, Pevzner PA. Whole genome duplications and contracted breakpoint graphs Siam Journal On Computing. 36: 1748-1763. DOI: 10.1137/05064727X |
0.705 |
|
| 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 |
0.806 |
|
| 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 |
0.372 |
|
| 2006 |
Chaisson MJ, Raphael BJ, Pevzner PA. Microinversions in mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America. 103: 19824-9. PMID 17189424 DOI: 10.1073/Pnas.0603984103 |
0.369 |
|
| 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 |
0.497 |
|
| 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 |
0.767 |
|
| 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 |
0.7 |
|
| 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 |
0.606 |
|
| 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 |
0.346 |
|
| 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 |
0.539 |
|
| 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 |
0.482 |
|
| 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 |
0.385 |
|
| 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 |
0.567 |
|
| 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 |
0.802 |
|
| 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 |
0.808 |
|
| 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 |
0.832 |
|
| 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 |
0.814 |
|
| 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 |
0.631 |
|
| 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 |
0.68 |
|
| 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 |
0.411 |
|
| 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 |
0.766 |
|
| 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 |
0.391 |
|
| 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 |
0.588 |
|
| 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 |
0.362 |
|
| 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 |
0.421 |
|
| 2004 |
Leipzig J, Pevzner P, Heber S. The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Research. 32: 3977-83. PMID 15292448 DOI: 10.1093/Nar/Gkh731 |
0.788 |
|
| 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 |
0.367 |
|
| 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 |
0.326 |
|
| 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 |
0.401 |
|
| 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. |
0.65 |
|
| 2003 |
Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Human Genomics. 1: 30-40. PMID 15601531 DOI: 10.1186/1479-7364-1-1-30 |
0.377 |
|
| 2003 |
Pevzner P, Tesler G. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America. 100: 7672-7. PMID 12810957 DOI: 10.1073/Pnas.1330369100 |
0.368 |
|
| 2003 |
Pevzner P, Tesler G. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Research. 13: 37-45. PMID 12529304 DOI: 10.1101/Gr.757503 |
0.396 |
|
| 2002 |
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Pevzner P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262 |
0.424 |
|
| 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 |
0.358 |
|
| 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 |
0.355 |
|
| 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 |
0.778 |
|
| 2002 |
Mulyukov Z, Pevzner PA. EULER-PCR: finishing experiments for repeat resolution. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 199-210. PMID 11928476 |
0.303 |
|
| 2002 |
Bourque G, Pevzner PA. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Research. 12: 26-36. PMID 11779828 |
0.306 |
|
| 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 |
0.612 |
|
| 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 |
0.431 |
|
| 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 |
0.382 |
|
| 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 |
0.458 |
|
| 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 |
0.324 |
|
| 2000 |
Pevzner PA, DancÃk 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 |
0.403 |
|
| 1999 |
DancÃk 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 |
0.501 |
|
| 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 |
0.359 |
|
| 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 |
0.332 |
|
| 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 |
0.342 |
|
| 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 |
0.384 |
|
| 1998 |
Bafna V, Pevzner PA. Sorting by transpositions Siam Journal On Discrete Mathematics. 11: 224-240. DOI: 10.1137/S089548019528280X |
0.617 |
|
| 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 |
0.358 |
|
| 1997 |
Waterman MS, Istrail S, Pevzner PA. Preface: Special RECOMB'97 Issues Journal of Computational Biology. 4: 215-215. DOI: 10.1089/Cmb.1997.4.215 |
0.513 |
|
| 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 |
0.546 |
|
| 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 |
0.371 |
|
| 1996 |
Bafna V, Pevzner PA. Genome rearrangements and sorting by reversals Siam Journal On Computing. 25: 272-289. DOI: 10.1137/S0097539793250627 |
0.608 |
|
| 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 |
0.422 |
|
| 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 |
0.318 |
|
| 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 |
0.625 |
|
| 1995 |
Pevzner PA, Waterman MS. Multiple filtration and approximate pattern matching Algorithmica. 13: 135-154. DOI: 10.1007/Bf01188584 |
0.58 |
|
| 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 |
0.575 |
|
| 1994 |
Pevzner PA. Rearrangements of DNA sequences and SBH. Computers & Chemistry. 18: 221-3. PMID 7952892 DOI: 10.1016/0097-8485(94)85016-X |
0.353 |
|
| 1993 |
Pevzner PA, Waterman MS. Generalized Sequence Alignment and Duality Advances in Applied Mathematics. 14: 139-171. DOI: 10.1006/Aama.1993.1008 |
0.598 |
|
| 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 |
0.333 |
|
| 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 |
0.301 |
|
| 1992 |
Pevzner PA. Nucleotide sequences versus Markov models Computers and Chemistry. 16: 103-106. DOI: 10.1016/0097-8485(92)80036-Y |
0.32 |
|
| 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 |
0.356 |
|
| 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 |
0.33 |
|
| 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 |
0.313 |
|
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