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Complete sequencing of ape genomes. bioRxiv. 2024 Jul 31.
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. PMID: 39131277; PMCID: PMC11312596.
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PubMed Mentions:
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Synthetic lethality and the minimal genome size problem. mSphere. 2024 Jul 30; 9(7):e0013924.
Rahiminejad S, De Sanctis B, Pevzner P, Mushegian A. PMID: 38904396; PMCID: PMC11288024.
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PubMed Mentions: Fields:
Translation:
Animals
-
UniAligner: a parameter-free framework for fast sequence alignment. Nat Methods. 2023 09; 20(9):1346-1354.
Bzikadze AV, Pevzner PA. PMID: 37580559.
View in:
PubMed Mentions:
3 Fields:
Translation:
Humans
-
Analyzing rare mutations in metagenomes assembled using long and accurate reads. Genome Res. 2022 Nov-Dec; 32(11-12):2119-2133.
Fedarko MW, Kolmogorov M, Pevzner PA. PMID: 36418060; PMCID: PMC9808630.
View in:
PubMed Mentions: Fields:
Translation:
Cells
-
Fast and accurate mapping of long reads to complete genome assemblies with VerityMap. Genome Res. 2022 Nov-Dec; 32(11-12):2107-2118.
Bzikadze AV, Mikheenko A, Pevzner PA. PMID: 36379716; PMCID: PMC9808623.
View in:
PubMed Mentions:
5 Fields:
Translation:
HumansCells
-
Michael Waterman's Contributions to Computational Biology and Bioinformatics. J Comput Biol. 2022 07; 29(7):601-615.
Pevzner P, Vingron M, Reidys C, Sun F, Istrail S. PMID: 35727100.
View in:
PubMed Mentions: Fields:
Translation:
Humans
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New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics. 2022 07; 21(7):100254.
Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. PMID: 35654359; PMCID: PMC9256833.
View in:
PubMed Mentions:
10 Fields:
Translation:
Humans
-
Gene prediction in the immunoglobulin loci. Genome Res. 2022 06; 32(6):1152-1169.
Sirupurapu V, Safonova Y, Pevzner PA. PMID: 35545447; PMCID: PMC9248892.
View in:
PubMed Mentions:
7 Fields:
Translation:
Cells
-
Automated annotation of human centromeres with HORmon. Genome Res. 2022 06; 32(6):1137-1151.
Kunyavskaya O, Dvorkina T, Bzikadze AV, Alexandrov IA, Pevzner PA. PMID: 35545449; PMCID: PMC9248890.
View in:
PubMed Mentions:
10 Fields:
Translation:
HumansCells
-
Complete genomic and epigenetic maps of human centromeres. Science. 2022 04; 376(6588):eabl4178.
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. PMID: 35357911; PMCID: PMC9233505.
View in:
PubMed Mentions:
128 Fields:
Translation:
HumansCells
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Variations in antibody repertoires correlate with vaccine responses. Genome Res. 2022 04; 32(4):791-804.
Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. PMID: 35361626; PMCID: PMC8997358.
View in:
PubMed Mentions:
4 Fields:
Translation:
Animals
-
The complete sequence of a human genome. Science. 2022 04; 376(6588):44-53.
Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sovic I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. PMID: 35357919; PMCID: PMC9186530.
View in:
PubMed Mentions:
770 Fields:
Translation:
HumansCells
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Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads. Nat Biotechnol. 2022 07; 40(7):1075-1081.
Bankevich A, Bzikadze AV, Kolmogorov M, Antipov D, Pevzner PA. PMID: 35228706.
View in:
PubMed Mentions:
29 Fields:
Translation:
Humans
-
viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data. Genome Biol. 2022 02 21; 23(1):57.
Antipov D, Rayko M, Kolmogorov M, Pevzner PA. PMID: 35189932; PMCID: PMC8862349.
View in:
PubMed Mentions:
8 Fields:
Translation:
Cells
-
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nat Biotechnol. 2022 05; 40(5):711-719.
Bickhart DM, Kolmogorov M, Tseng E, Portik DM, Korobeynikov A, Tolstoganov I, Uritskiy G, Liachko I, Sullivan ST, Shin SB, Zorea A, Andreu VP, Panke-Buisse K, Medema MH, Mizrahi I, Pevzner PA, Smith TPL. PMID: 34980911.
View in:
PubMed Mentions:
57 Fields:
Translation:
Animals
-
CentromereArchitect: inference and analysis of the architecture of centromeres. Bioinformatics. 2021 07 12; 37(Suppl_1):i196-i204.
Dvorkina T, Kunyavskaya O, Bzikadze AV, Alexandrov I, Pevzner PA. PMID: 34252949; PMCID: PMC8336445.
View in:
PubMed Mentions:
10 Fields:
Translation:
HumansCells
-
Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun. 2021 Jul 08; 12(1):4318.
Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. PMID: 34238936; PMCID: PMC8266848.
View in:
PubMed Mentions: Fields:
-
ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs. Microbiome. 2021 06 28; 9(1):149.
Dvorkina T, Bankevich A, Sorokin A, Yang F, Adu-Oppong B, Williams R, Turner K, Pevzner PA. PMID: 34183047; PMCID: PMC8240309.
View in:
PubMed Mentions:
3 Fields:
-
Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun. 2021 05 28; 12(1):3225.
Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. PMID: 34050176; PMCID: PMC8163882.
View in:
PubMed Mentions:
20 Fields:
Translation:
HumansCellsPHPublic Health
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Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res. 2021 May; 31(5):934.
Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. PMID: 33941606; PMCID: PMC8092014.
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PubMed Mentions: Fields:
-
Thousands of previously unknown phages discovered in whole-community human gut metagenomes. Microbiome. 2021 03 29; 9(1):78.
Benler S, Yutin N, Antipov D, Rayko M, Shmakov S, Gussow AB, Pevzner P, Koonin EV. PMID: 33781338; PMCID: PMC8008677.
View in:
PubMed Mentions:
70 Fields:
Translation:
HumansCells
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Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nat Commun. 2021 02 16; 12(1):1044.
Yutin N, Benler S, Shmakov SA, Wolf YI, Tolstoy I, Rayko M, Antipov D, Pevzner PA, Koonin EV. PMID: 33594055; PMCID: PMC7886860.
View in:
PubMed Mentions:
51 Fields:
Translation:
HumansCells
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A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria. Mar Drugs. 2021 Jan 06; 19(1).
Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L. PMID: 33418911; PMCID: PMC7825088.
View in:
PubMed Mentions:
14 Fields:
Translation:
Cells
-
Trace Reconstruction Problems in Computational Biology. IEEE Trans Inf Theory. 2021 Jun; 67(6):3295-3314.
Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. PMID: 34176957; PMCID: PMC8224466.
View in:
PubMed Mentions:
1
-
metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods. 2020 11; 17(11):1103-1110.
Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. PMID: 33020656; PMCID: PMC10699202.
View in:
PubMed Mentions:
288 Fields:
Translation:
HumansAnimals
-
V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s. Genome Res. 2020 11; 30(11):1547-1558.
Safonova Y, Pevzner PA. PMID: 32948615; PMCID: PMC7605257.
View in:
PubMed Mentions:
8 Fields:
Translation:
HumansAnimalsCells
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Metaviral SPAdes: assembly of viruses from metagenomic data. Bioinformatics. 2020 08 15; 36(14):4126-4129.
Antipov D, Raiko M, Lapidus A, Pevzner PA. PMID: 32413137.
View in:
PubMed Mentions:
98 Fields:
Translation:
Cells
-
Automated assembly of centromeres from ultra-long error-prone reads. Nat Biotechnol. 2020 11; 38(11):1309-1316.
Bzikadze AV, Pevzner PA. PMID: 32665660; PMCID: PMC10718184.
View in:
PubMed Mentions:
30 Fields:
Translation:
HumansCells
-
Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020 09; 585(7823):79-84.
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM. PMID: 32663838; PMCID: PMC7484160.
View in:
PubMed Mentions:
334 Fields:
Translation:
HumansCells
-
The string decomposition problem and its applications to centromere analysis and assembly. Bioinformatics. 2020 07 01; 36(Suppl_1):i93-i101.
Dvorkina T, Bzikadze AV, Pevzner PA. PMID: 32657390; PMCID: PMC7428072.
View in:
PubMed Mentions:
18 Fields:
Translation:
HumansCells
-
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics. 2020 07 01; 36(Suppl_1):i75-i83.
Mikheenko A, Bzikadze AV, Gurevich A, Miga KH, Pevzner PA. PMID: 32657355; PMCID: PMC7355294.
View in:
PubMed Mentions:
28 Fields:
Translation:
HumansAnimalsCells
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Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information. Genome Res. 2020 06; 30(6):898-909.
Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. PMID: 32540955; PMCID: PMC7370886.
View in:
PubMed Mentions:
49 Fields:
Translation:
Humans
-
Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLoS Comput Biol. 2020 04; 16(4):e1007837.
Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. PMID: 32339161; PMCID: PMC7295240.
View in:
PubMed Mentions:
5 Fields:
Translation:
HumansAnimals
-
De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst. 2020 01 22; 10(1):99-108.e5.
Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA. PMID: 31864964.
View in:
PubMed Mentions:
21 Fields:
Translation:
HumansCells
-
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 2019 10 31; 20(1):226.
Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. PMID: 31672156; PMCID: PMC6822431.
View in:
PubMed Mentions:
30 Fields:
Translation:
HumansAnimals
-
MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst. 2019 12 18; 9(6):600-608.e4.
Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H. PMID: 31629686; PMCID: PMC6952069.
View in:
PubMed Mentions:
31 Fields:
Translation:
HumansCells
-
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs. Bioinformatics. 2019 07 15; 35(14):i61-i70.
Tolstoganov I, Bankevich A, Chen Z, Pevzner PA. PMID: 31510642; PMCID: PMC6612831.
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PubMed Mentions:
14 Fields:
-
BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs. Genome Res. 2019 08; 29(8):1352-1362.
Meleshko D, Mohimani H, Tracanna V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA. PMID: 31160374; PMCID: PMC6673720.
View in:
PubMed Mentions:
28 Fields:
Translation:
HumansCells
-
De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins. Front Immunol. 2019; 10:987.
Safonova Y, Pevzner PA. PMID: 31134072; PMCID: PMC6516046.
View in:
PubMed Mentions:
11 Fields:
Translation:
HumansAnimalsCells
-
Plasmid detection and assembly in genomic and metagenomic data sets. Genome Res. 2019 06; 29(6):961-968.
Antipov D, Raiko M, Lapidus A, Pevzner PA. PMID: 31048319; PMCID: PMC6581055.
View in:
PubMed Mentions:
62 Fields:
Translation:
Humans
-
Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 05; 37(5):540-546.
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. PMID: 30936562.
View in:
PubMed Mentions:
1780 Fields:
Translation:
HumansCells
-
How bioinformatics and open data can boost basic science in countries and universities with limited resources. Nat Biotechnol. 2019 03; 37(3):324-326.
Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E. PMID: 30833765.
View in:
PubMed Mentions:
12 Fields:
Translation:
Humans
-
Dereplication of microbial metabolites through database search of mass spectra. Nat Commun. 2018 10 02; 9(1):4035.
Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA. PMID: 30279420; PMCID: PMC6168521.
View in:
PubMed Mentions:
113 Fields:
Translation:
Cells
-
Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity. Cell Syst. 2018 08 22; 7(2):192-200.e3.
Bankevich A, Pevzner PA. PMID: 30056005.
View in:
PubMed Mentions:
7 Fields:
Translation:
HumansCells
-
American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3).
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut Consortium , Knight R. PMID: 29795809; PMCID: PMC5954204.
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PubMed Mentions:
346 Fields:
-
Detection and analysis of ancient segmental duplications in mammalian genomes. Genome Res. 2018 06; 28(6):901-909.
Pu L, Lin Y, Pevzner PA. PMID: 29735604; PMCID: PMC5991524.
View in:
PubMed Mentions:
18 Fields:
Translation:
HumansAnimalsCells
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A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch. Plant Direct. 2018 Feb; 2(2).
Fisher MF, Zhang J, Taylor NL, Howard MJ, Berkowitz O, Debowski AW, Behsaz B, Whelan J, Pevzner PA, Mylne JS. PMID: 30417166; PMCID: PMC6223261.
View in:
PubMed Mentions:
12
-
Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nat Microbiol. 2018 03; 3(3):319-327.
Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner PA. PMID: 29358742; PMCID: PMC5951390.
View in:
PubMed Mentions:
44 Fields:
Translation:
Cells
-
MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics. 2018 03 30; 176:13-23.
Rozanov DV, Rozanov ND, Chiotti KE, Reddy A, Wilmarth PA, David LL, Cha SW, Woo S, Pevzner P, Bafna V, Burrows GG, Rantala JK, Levin T, Anur P, Johnson-Camacho K, Tabatabaei S, Munson DJ, Bruno TC, Slansky JE, Kappler JW, Hirano N, Boegel S, Fox BA, Egelston C, Simons DL, Jimenez G, Lee PP, Gray JW, Spellman PT. PMID: 29331515; PMCID: PMC5999401.
View in:
PubMed Mentions:
14 Fields:
Translation:
HumansCells
-
The Antibody Repertoire of Colorectal Cancer. Mol Cell Proteomics. 2017 Dec; 16(12):2111-2124.
Cha SW, Bonissone S, Na S, Pevzner PA, Bafna V. PMID: 29046389; PMCID: PMC5724175.
View in:
PubMed Mentions:
4 Fields:
Translation:
HumansCells
-
Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. J Immunol. 2017 11 01; 199(9):3369-3380.
Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. PMID: 28978691; PMCID: PMC5661950.
View in:
PubMed Mentions:
23 Fields:
Translation:
HumansAnimals
-
Single-molecule protein identification by sub-nanopore sensors. PLoS Comput Biol. 2017 05; 13(5):e1005356.
Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA. PMID: 28486472; PMCID: PMC5423552.
View in:
PubMed Mentions:
22 Fields:
-
metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017 05; 27(5):824-834.
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. PMID: 28298430; PMCID: PMC5411777.
View in:
PubMed Mentions:
1531 Fields:
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Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer. J Proteomics. 2017 04 21; 159:67-76.
Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner PA, Makarov A, Beck A, Tsybin YO. PMID: 28242452; PMCID: PMC5478168.
View in:
PubMed Mentions:
23 Fields:
Translation:
Humans
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Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen. mSystems. 2016 Nov-Dec; 1(6).
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, Alexandrov T, Dorrestein PC. PMID: 28028548; PMCID: PMC5183598.
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PubMed Mentions:
20 Fields:
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Assembly of long error-prone reads using de Bruijn graphs. Proc Natl Acad Sci U S A. 2016 12 27; 113(52):E8396-E8405.
Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA. PMID: 27956617; PMCID: PMC5206522.
View in:
PubMed Mentions:
124 Fields:
Translation:
Cells
-
Dereplication of peptidic natural products through database search of mass spectra. Nat Chem Biol. 2017 Jan; 13(1):30-37.
Mohimani H, Gurevich A, Mikheenko A, Garg N, Nothias LF, Ninomiya A, Takada K, Dorrestein PC, Pevzner PA. PMID: 27820803; PMCID: PMC5409158.
View in:
PubMed Mentions:
93 Fields:
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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 08 09; 34(8):828-837.
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. PMID: 27504778; PMCID: PMC5321674.
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PubMed Mentions:
1433 Fields:
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plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics. 2016 11 15; 32(22):3380-3387.
Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA. PMID: 27466620.
View in:
PubMed Mentions:
287 Fields:
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Top-down analysis of protein samples by de novo sequencing techniques. Bioinformatics. 2016 09 15; 32(18):2753-9.
Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolic N, Luider TM, Paša-Tolic L, Pevzner PA. PMID: 27187201; PMCID: PMC6280873.
View in:
PubMed Mentions:
6 Fields:
Translation:
Cells
-
Immunoglobulin Classification Using the Colored Antibody Graph. J Comput Biol. 2016 06; 23(6):483-94.
Bonissone SR, Pevzner PA. PMID: 27149636; PMCID: PMC4904161.
View in:
PubMed Mentions:
4 Fields:
Translation:
HumansAnimalsCells
-
TruSPAdes: barcode assembly of TruSeq synthetic long reads. Nat Methods. 2016 Mar; 13(3):248-50.
Bankevich A, Pevzner PA. PMID: 26828418.
View in:
PubMed Mentions:
18 Fields:
Translation:
Cells
-
Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. Nat Prod Rep. 2016 Jan; 33(1):73-86.
Mohimani H, Pevzner PA. PMID: 26497201; PMCID: PMC5590107.
View in:
PubMed Mentions:
29 Fields:
Translation:
Cells
-
SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra. J Proteome Res. 2016 Jan 04; 15(1):144-51.
Kolmogorov M, Liu X, Pevzner PA. PMID: 26629978; PMCID: PMC6020058.
View in:
PubMed Mentions:
5 Fields:
Translation:
Cells
-
hybridSPAdes: an algorithm for hybrid assembly of short and long reads. Bioinformatics. 2016 04 01; 32(7):1009-15.
Antipov D, Korobeynikov A, McLean JS, Pevzner PA. PMID: 26589280; PMCID: PMC4907386.
View in:
PubMed Mentions:
261 Fields:
Translation:
Cells
-
De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra. J Proteome Res. 2015 Nov 06; 14(11):4450-62.
Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolic N, Dvorkin M, Alexandrova S, Luider TM, Paša-Tolic L, Pevzner PA. PMID: 26412692.
View in:
PubMed Mentions:
14 Fields:
Translation:
HumansAnimalsCells
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Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages. Appl Environ Microbiol. 2015 Dec; 81(24):8265-76.
León-Zayas R, Novotny M, Podell S, Shepard CM, Berkenpas E, Nikolenko S, Pevzner P, Lasken RS, Bartlett DH. PMID: 26386059; PMCID: PMC4644660.
View in:
PubMed Mentions:
19 Fields:
Translation:
CellsPHPublic Health
-
Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. J Proteome Res. 2015 Sep 04; 14(9):3555-67.
Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V. PMID: 26139413; PMCID: PMC4868822.
View in:
PubMed Mentions:
16 Fields:
Translation:
HumansCells
-
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics. 2015 Jun 15; 31(12):i53-61.
Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. PMID: 26072509; PMCID: PMC4542777.
View in:
PubMed Mentions:
20 Fields:
Translation:
Humans
-
Assembling short reads from jumping libraries with large insert sizes. Bioinformatics. 2015 Oct 15; 31(20):3262-8.
Vasilinetc I, Prjibelski AD, Gurevich A, Korobeynikov A, Pevzner PA. PMID: 26040456.
View in:
PubMed Mentions:
25 Fields:
-
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. J Comput Biol. 2015 Jun; 22(6):528-45.
Safonova Y, Bankevich A, Pevzner PA. PMID: 25734602; PMCID: PMC4449708.
View in:
PubMed Mentions:
34 Fields:
-
Proteogenomics. Proteomics. 2014 Dec; 14(23-24):2631-2.
Pandey A, Pevzner PA. PMID: 25469796.
View in:
PubMed Mentions:
6 Fields:
-
MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun. 2014 Oct 31; 5:5277.
Kim S, Pevzner PA. PMID: 25358478; PMCID: PMC5036525.
View in:
PubMed Mentions:
470 Fields:
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What is the difference between the breakpoint graph and the de Bruijn graph? BMC Genomics. 2014; 15 Suppl 6:S6.
Lin Y, Nurk S, Pevzner PA. PMID: 25572416; PMCID: PMC4240671.
View in:
PubMed Mentions:
8 Fields:
Translation:
HumansAnimals
-
NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. J Nat Prod. 2014 Aug 22; 77(8):1902-9.
Mohimani H, Liu WT, Kersten RD, Moore BS, Dorrestein PC, Pevzner PA. PMID: 25116163; PMCID: PMC4143176.
View in:
PubMed Mentions:
46 Fields:
Translation:
Cells
-
De novo protein sequencing by combining top-down and bottom-up tandem mass spectra. J Proteome Res. 2014 Jul 03; 13(7):3241-8.
Liu X, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolic N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-Tolic L, Pevzner PA. PMID: 24874765.
View in:
PubMed Mentions:
24 Fields:
Translation:
AnimalsCells
-
ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics. 2014 Jun 15; 30(12):i293-301.
Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner PA. PMID: 24931996; PMCID: PMC4058921.
View in:
PubMed Mentions:
59 Fields:
Translation:
HumansCells
-
Automated genome mining of ribosomal peptide natural products. ACS Chem Biol. 2014 Jul 18; 9(7):1545-51.
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. PMID: 24802639; PMCID: PMC4215869.
View in:
PubMed Mentions:
69 Fields:
Translation:
Cells
-
Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry. Proteomics. 2014 May; 14(10):1211-22.
Wu S, Brown JN, Tolic N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolic L. PMID: 24591407.
View in:
PubMed Mentions:
25 Fields:
Translation:
HumansCells
-
Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS One. 2014; 9(1):e85140.
Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH. PMID: 24475038; PMCID: PMC3903477.
View in:
PubMed Mentions:
59 Fields:
Translation:
Cells
-
Application of de novo sequencing tools to study abiogenic peptide formations by tandem mass spectrometry. The case of homo-peptides from glutamic acid complicated by substitutions of hydrogen by sodium or potassium atoms. Rapid Commun Mass Spectrom. 2014 Jan 15; 28(1):33-41.
Terterov I, Vyatkina K, Kononikhin AS, Boitsov V, Vyazmin S, Popov IA, Nikolaev EN, Pevzner P, Dubina M. PMID: 24285388.
View in:
PubMed Mentions: Fields:
Translation:
Cells
-
Identification of ultramodified proteins using top-down tandem mass spectra. J Proteome Res. 2013 Dec 06; 12(12):5830-8.
Liu X, Hengel S, Wu S, Tolic N, Pasa-Tolic L, Pevzner PA. PMID: 24188097; PMCID: PMC3905687.
View in:
PubMed Mentions:
25 Fields:
Translation:
HumansCells
-
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013 Oct; 20(10):714-37.
Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. PMID: 24093227; PMCID: PMC3791033.
View in:
PubMed Mentions:
814 Fields:
Translation:
Cells
-
MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms Mol Biol. 2013 Jul 11; 8(1):19.
Castellana NE, Lushnikov A, Rotkiewicz P, Sefcovic N, Pevzner PA, Godzik A, Vyatkina K. PMID: 23844614; PMCID: PMC3738870.
View in:
PubMed Mentions:
3
-
UniNovo: a universal tool for de novo peptide sequencing. Bioinformatics. 2013 Aug 15; 29(16):1953-62.
Jeong K, Kim S, Pevzner PA. PMID: 23766417; PMCID: PMC3722526.
View in:
PubMed Mentions:
30 Fields:
-
Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci U S A. 2013 Jun 25; 110(26):E2390-9.
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, Friedman RM, Nealson KH, Venter JC, Lasken RS. PMID: 23754396; PMCID: PMC3696752.
View in:
PubMed Mentions:
93 Fields:
Translation:
HumansCellsPHPublic Health
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Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions. Proc Natl Acad Sci U S A. 2013 Jun 18; 110(25):10153-8.
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. PMID: 23720318; PMCID: PMC3690903.
View in:
PubMed Mentions:
104 Fields:
Translation:
HumansCells
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Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Res. 2013 May; 23(5):867-77.
McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, Torriani F, Nealson KH, Pevzner PA, Friedman R, Venter JC, Lasken RS. PMID: 23564253; PMCID: PMC3638142.
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PubMed Mentions:
40 Fields:
Translation:
HumansCells
-
How many signal peptides are there in bacteria? Environ Microbiol. 2013 Apr; 15(4):983-90.
Ivankov DN, Payne SH, Galperin MY, Bonissone S, Pevzner PA, Frishman D. PMID: 23556536; PMCID: PMC3621014.
View in:
PubMed Mentions:
12 Fields:
Translation:
Cells
-
A new approach to evaluating statistical significance of spectral identifications. J Proteome Res. 2013 Apr 05; 12(4):1560-8.
Mohimani H, Kim S, Pevzner PA. PMID: 23343606; PMCID: PMC5590104.
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PubMed Mentions:
11 Fields:
Translation:
Cells
-
Unexpected diversity of signal peptides in prokaryotes. mBio. 2012 Nov 20; 3(6).
Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolic L, Smith RD, Pevzner PA. PMID: 23169999; PMCID: PMC3509430.
View in:
PubMed Mentions:
15 Fields:
Translation:
Cells
-
N-terminal protein processing: a comparative proteogenomic analysis. Mol Cell Proteomics. 2013 Jan; 12(1):14-28.
Bonissone S, Gupta N, Romine M, Bradshaw RA, Bradshaw RA, Pevzner PA. PMID: 23001859; PMCID: PMC3536895.
View in:
PubMed Mentions:
35 Fields:
Translation:
Cells
-
Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly. J Comput Biol. 2013 Apr; 20(4):359-71.
Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA. PMID: 22803627; PMCID: PMC3619201.
View in:
PubMed Mentions:
5 Fields:
Translation:
Cells
-
SEQuel: improving the accuracy of genome assemblies. Bioinformatics. 2012 Jun 15; 28(12):i188-96.
Ronen R, Boucher C, Chitsaz H, Pevzner P. PMID: 22689760; PMCID: PMC3371851.
View in:
PubMed Mentions:
34 Fields:
Translation:
Cells
-
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012 May; 19(5):455-77.
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. PMID: 22506599; PMCID: PMC3342519.
View in:
PubMed Mentions:
11879 Fields:
Translation:
Cells
-
Competencies: a cure for pre-med curriculum. Science. 2011 Nov 11; 334(6057):760-1.
Anderson WA, Amasino RM, Ares M, Banerjee U, Bartel B, Corces VG, Drennan CL, Elgin SC, Epstein IR, Fanning E, Guillette LJ, Handelsman J, Hatfull GF, Hoy RR, Kelley D, Leinwand LA, Losick R, Lu Y, Lynn DG, Neuhauser C, O'Dowd DK, Olivera T, Pevzner P, Richards-Kortum RR, Rine J, Sah RL, Strobel SA, Walker GC, Walt DR, Warner IM, Wessler S, Willard HF, Zare RN. PMID: 22076362.
View in:
PubMed Mentions:
1 Fields:
-
How to apply de Bruijn graphs to genome assembly. Nat Biotechnol. 2011 Nov 08; 29(11):987-91.
Compeau PE, Pevzner PA, Tesler G. PMID: 22068540; PMCID: PMC5531759.
View in:
PubMed Mentions:
197 Fields:
Translation:
Cells
-
Multiplex de novo sequencing of peptide antibiotics. J Comput Biol. 2011 Nov; 18(11):1371-81.
Mohimani H, Liu WT, Yang YL, Gaudêncio SP, Fenical W, Dorrestein PC, Pevzner PA. PMID: 22035290; PMCID: PMC3216106.
View in:
PubMed Mentions:
15 Fields:
Translation:
Cells
-
Protein identification using top-down. Mol Cell Proteomics. 2012 Jun; 11(6):M111.008524.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. PMID: 22027200; PMCID: PMC3433905.
View in:
PubMed Mentions:
83 Fields:
Translation:
AnimalsCells
-
Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J Comput Biol. 2011 Nov; 18(11):1625-34.
Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P. PMID: 21999285; PMCID: PMC3216098.
View in:
PubMed Mentions:
21 Fields:
Translation:
HumansCells
-
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol. 2011 Sep 18; 29(10):915-21.
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. PMID: 21926975; PMCID: PMC3558281.
View in:
PubMed Mentions:
106 Fields:
Translation:
Cells
-
Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases. J Proteome Res. 2011 Oct 07; 10(10):4505-12.
Mohimani H, Liu WT, Mylne JS, Poth AG, Colgrave ML, Tran D, Selsted ME, Dorrestein PC, Pevzner PA. PMID: 21851130; PMCID: PMC3242011.
View in:
PubMed Mentions:
18 Fields:
Translation:
AnimalsCells
-
Sequencing cyclic peptides by multistage mass spectrometry. Proteomics. 2011 Sep; 11(18):3642-50.
Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner PA. PMID: 21751357; PMCID: PMC3398611.
View in:
PubMed Mentions:
18 Fields:
Translation:
AnimalsCells
-
Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics. 2011 Jul 01; 27(13):i137-41.
Medvedev P, Scott E, Kakaradov B, Pevzner P. PMID: 21685062; PMCID: PMC3117386.
View in:
PubMed Mentions:
47 Fields:
Translation:
Cells
-
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods. 2011 May 15; 8(7):587-91.
Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA. PMID: 21572408; PMCID: PMC3128193.
View in:
PubMed Mentions:
46 Fields:
-
Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010). J Comput Biol. 2011 Jul; 18(7):865.
Pevzner PA, Shamir R. PMID: 21563980.
View in:
PubMed Mentions: Fields:
Translation:
Humans
-
Target-decoy approach and false discovery rate: when things may go wrong. J Am Soc Mass Spectrom. 2011 Jul; 22(7):1111-20.
Gupta N, Bandeira N, Keich U, Pevzner PA. PMID: 21953092; PMCID: PMC3220955.
View in:
PubMed Mentions:
72 Fields:
Translation:
Humans
-
Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera. J Nat Prod. 2011 May 27; 74(5):928-36.
Mevers E, Liu WT, Engene N, Mohimani H, Byrum T, Pevzner PA, Dorrestein PC, Spadafora C, Gerwick WH. PMID: 21488639; PMCID: PMC3103610.
View in:
PubMed Mentions:
38 Fields:
Translation:
HumansCells
-
Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One. 2011 Apr 12; 6(4):e18565.
Grindberg RV, Ishoey T, Brinza D, Esquenazi E, Coates RC, Liu WT, Gerwick L, Dorrestein PC, Pevzner P, Lasken R, Gerwick WH. PMID: 21533272; PMCID: PMC3075265.
View in:
PubMed Mentions:
48 Fields:
Translation:
Cells
-
Gapped spectral dictionaries and their applications for database searches of tandem mass spectra. Mol Cell Proteomics. 2011 Jun; 10(6):M110.002220.
Jeong K, Kim S, Bandeira N, Pevzner PA. PMID: 21444829; PMCID: PMC3108828.
View in:
PubMed Mentions:
12 Fields:
Translation:
HumansCells
-
Comparative genomics reveals birth and death of fragile regions in mammalian evolution. Genome Biol. 2010; 11(11):R117.
Alekseyev MA, Pevzner PA. PMID: 21118492; PMCID: PMC3156956.
View in:
PubMed Mentions:
11 Fields:
Translation:
HumansAnimals
-
Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing. J Proteome Res. 2010 Oct 01; 9(10):5065-75.
Gupta N, Bark SJ, Lu WD, Taupenot L, O'Connor DT, Pevzner P, Hook V. PMID: 20704348; PMCID: PMC3000314.
View in:
PubMed Mentions:
19 Fields:
Translation:
HumansCells
-
Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics. 2010 Dec; 9(12):2772-82.
Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. PMID: 20855543; PMCID: PMC3101958.
View in:
PubMed Mentions:
80 Fields:
Translation:
Cells
-
The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol Cell Proteomics. 2010 Dec; 9(12):2840-52.
Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA. PMID: 20829449; PMCID: PMC3101864.
View in:
PubMed Mentions:
105 Fields:
Translation:
HumansCells
-
Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis. Proc Natl Acad Sci U S A. 2010 Sep 14; 107(37):16286-90.
Liu WT, Yang YL, Xu Y, Lamsa A, Haste NM, Yang JY, Ng J, Gonzalez D, Ellermeier CD, Straight PD, Pevzner PA, Pogliano J, Nizet V, Pogliano K, Dorrestein PC. PMID: 20805502; PMCID: PMC2941286.
View in:
PubMed Mentions:
98 Fields:
Translation:
Cells
-
Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication. AAPS J. 2010 Dec; 12(4):635-45.
Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O'Connor DT, Pevzner P. PMID: 20734175; PMCID: PMC2976990.
View in:
PubMed Mentions:
15 Fields:
Translation:
HumansCells
-
DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics. 2010 Oct 15; 26(20):2509-16.
Pham SK, Pevzner PA. PMID: 20736338.
View in:
PubMed Mentions:
41 Fields:
Translation:
HumansAnimalsCells
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Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry. Proteomics. 2010 Aug; 10(15):2833-44.
Gupta N, Hixson KK, Culley DE, Smith RD, Pevzner PA. PMID: 20597098; PMCID: PMC3220954.
View in:
PubMed Mentions:
14 Fields:
Translation:
AnimalsCells
-
Synergistic allelochemicals from a freshwater cyanobacterium. Proc Natl Acad Sci U S A. 2010 Jun 22; 107(25):11183-8.
Leão PN, Pereira AR, Liu WT, Ng J, Pevzner PA, Dorrestein PC, König GM, Vasconcelos VM, Gerwick WH. PMID: 20534563; PMCID: PMC2895120.
View in:
PubMed Mentions:
45 Fields:
Translation:
HumansCells
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False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res. 2009 Sep; 8(9):4173-81.
Gupta N, Pevzner PA. PMID: 19627159; PMCID: PMC3398614.
View in:
PubMed Mentions:
85 Fields:
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Computing has changed biology--biology education must catch up. Science. 2009 Jul 31; 325(5940):541-2.
Pevzner P, Shamir R. PMID: 19644094.
View in:
PubMed Mentions:
32 Fields:
-
View in:
PubMed Mentions:
35 Fields:
Translation:
Cells
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Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem. 2009 Jun 01; 81(11):4200-9.
Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC. PMID: 19413302; PMCID: PMC2765223.
View in:
PubMed Mentions:
33 Fields:
Translation:
Cells
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Spectral profiles, a novel representation of tandem mass spectra and their applications for de novo peptide sequencing and identification. Mol Cell Proteomics. 2009 Jun; 8(6):1391-400.
Kim S, Bandeira N, Pevzner PA. PMID: 19254948; PMCID: PMC2690493.
View in:
PubMed Mentions:
12 Fields:
Translation:
Cells
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Breakpoint graphs and ancestral genome reconstructions. Genome Res. 2009 May; 19(5):943-57.
Alekseyev MA, Pevzner PA. PMID: 19218533; PMCID: PMC2675983.
View in:
PubMed Mentions:
53 Fields:
Translation:
Animals
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De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res. 2009 Feb; 19(2):336-46.
Chaisson MJ, Brinza D, Pevzner PA. PMID: 19056694; PMCID: PMC2652199.
View in:
PubMed Mentions:
105 Fields:
Translation:
Cells
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Automated de novo protein sequencing of monoclonal antibodies. Nat Biotechnol. 2008 Dec; 26(12):1336-8.
Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR. PMID: 19060866; PMCID: PMC2891972.
View in:
PubMed Mentions:
49 Fields:
Translation:
Cells
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Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science. 2008 Aug 22; 321(5892):1040; author reply 1040.
Pevzner PA, Kim S, Ng J. PMID: 18719266.
View in:
PubMed Mentions:
20 Fields:
Translation:
Animals
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Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics. 2009 Jan; 8(1):53-69.
Kim S, Gupta N, Bandeira N, Pevzner PA. PMID: 18703573; PMCID: PMC2621003.
View in:
PubMed Mentions:
35 Fields:
Translation:
HumansCells
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Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res. 2008 Aug; 7(8):3354-63.
Kim S, Gupta N, Pevzner PA. PMID: 18597511; PMCID: PMC2689316.
View in:
PubMed Mentions:
230 Fields:
Translation:
Cells
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Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Bioinformatics. 2008 Jul 01; 24(13):i416-23.
Bandeira N, Olsen JV, Mann JV, Mann M, Pevzner PA. PMID: 18785330; PMCID: PMC2718660.
View in:
PubMed Mentions:
12 Fields:
Translation:
Animals
-
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 2008 Jul; 18(7):1133-42.
Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA. PMID: 18426904; PMCID: PMC2493402.
View in:
PubMed Mentions:
46 Fields:
Translation:
Cells
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Interpreting top-down mass spectra using spectral alignment. Anal Chem. 2008 Apr 01; 80(7):2499-505.
Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA. PMID: 18302345.
View in:
PubMed Mentions:
42 Fields:
Translation:
Humans
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Algorithm for identification of fusion proteins via mass spectrometry. J Proteome Res. 2008 Jan; 7(1):89-95.
Ng J, Pevzner PA. PMID: 18173219.
View in:
PubMed Mentions:
2 Fields:
Translation:
HumansCells
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Short read fragment assembly of bacterial genomes. Genome Res. 2008 Feb; 18(2):324-30.
Chaisson MJ, Pevzner PA. PMID: 18083777; PMCID: PMC2203630.
View in:
PubMed Mentions:
172 Fields:
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Clustering millions of tandem mass spectra. J Proteome Res. 2008 Jan; 7(1):113-22.
Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. PMID: 18067247; PMCID: PMC2533155.
View in:
PubMed Mentions:
113 Fields:
Translation:
Cells
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Does trypsin cut before proline? J Proteome Res. 2008 Jan; 7(1):300-5.
Rodriguez J, Gupta N, Smith RD, Pevzner PA. PMID: 18067249.
View in:
PubMed Mentions:
91 Fields:
Translation:
Cells
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Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet. 2007 Nov; 39(11):1361-8.
Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, Eichler EE. PMID: 17922013.
View in:
PubMed Mentions:
120 Fields:
Translation:
HumansAnimalsCells
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Are there rearrangement hotspots in the human genome? PLoS Comput Biol. 2007 Nov; 3(11):e209.
Alekseyev MA, Pevzner PA. PMID: 17997591; PMCID: PMC2065889.
View in:
PubMed Mentions:
18 Fields:
Translation:
HumansCells
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Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007 Sep; 17(9):1362-77.
Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. PMID: 17690205; PMCID: PMC1950905.
View in:
PubMed Mentions:
88 Fields:
Translation:
Cells
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Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing. Proteomics. 2007 Jul; 7(14):2318-29.
Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A. PMID: 17623296.
View in:
PubMed Mentions:
29 Fields:
Translation:
AnimalsCells
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Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS One. 2007 May 30; 2(5):e484.
Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S. PMID: 17534434; PMCID: PMC1871613.
View in:
PubMed Mentions:
46 Fields:
Translation:
HumansAnimals
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Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics. 2007 Jul; 6(7):1123-34.
Bandeira N, Clauser KR, Pevzner PA. PMID: 17446555.
View in:
PubMed Mentions:
24 Fields:
Translation:
AnimalsCells
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Protein identification by spectral networks analysis. Proc Natl Acad Sci U S A. 2007 Apr 10; 104(15):6140-5.
Bandeira N, Tsur D, Frank A, Pevzner PA. PMID: 17404225; PMCID: PMC1851064.
View in:
PubMed Mentions:
76 Fields:
Translation:
Cells
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Correcting base-assignment errors in repeat regions of shotgun assembly. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):54-64.
Zhi D, Keich U, Pevzner P, Heber S, Tang H. PMID: 17277413.
View in:
PubMed Mentions:
3 Fields:
Translation:
Cells
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Colored de Bruijn graphs and the genome halving problem. IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar; 4(1):98-107.
Alekseyev MA, Pevzner PA. PMID: 17277417.
View in:
PubMed Mentions:
8 Fields:
Translation:
HumansAnimalsCells
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De novo peptide sequencing and identification with precision mass spectrometry. J Proteome Res. 2007 Jan; 6(1):114-23.
Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA. PMID: 17203955; PMCID: PMC2538556.
View in:
PubMed Mentions:
61 Fields:
Translation:
HumansCells
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Microinversions in mammalian evolution. Proc Natl Acad Sci U S A. 2006 Dec 26; 103(52):19824-9.
Chaisson MJ, Raphael BJ, Pevzner PA. PMID: 17189424; PMCID: PMC1750909.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansAnimals
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Modeling and characterization of multi-charge mass spectra for peptide sequencing. J Bioinform Comput Biol. 2006 Dec; 4(6):1329-52.
Chong KF, Ning K, Leong HW, Pevzner P. PMID: 17245817.
View in:
PubMed Mentions:
2 Fields:
Translation:
Cells
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Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinformatics. 2006 Oct 20; 7:460.
Zhi D, Krishna SS, Cao H, Pevzner P, Godzik A. PMID: 17052359; PMCID: PMC1626488.
View in:
PubMed Mentions:
4 Fields:
Translation:
Cells
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Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility? J Proteome Res. 2006 Oct; 5(10):2554-66.
Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. PMID: 17022627; PMCID: PMC2536618.
View in:
PubMed Mentions:
145 Fields:
Translation:
HumansCells
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Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches. J Proteome Res. 2006 Sep; 5(9):2448-56.
Wielsch N, Thomas H, Surendranath V, Waridel P, Frank A, Pevzner P, Shevchenko A. PMID: 16944958.
View in:
PubMed Mentions:
12 Fields:
Translation:
AnimalsCells
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Comparative genomics reveals unusually long motifs in mammalian genomes. Bioinformatics. 2006 Jul 15; 22(14):e236-42.
Jones NC, Pevzner PA. PMID: 16873477.
View in:
PubMed Mentions:
2 Fields:
Translation:
HumansAnimalsCells
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The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 2006 Mar; 16(3):311-3.
Bourque G, Tesler G, Pevzner PA. PMID: 16510896; PMCID: PMC1415205.
View in:
PubMed Mentions:
13 Fields:
Translation:
HumansAnimalsCells
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The fragile breakage versus random breakage models of chromosome evolution. PLoS Comput Biol. 2006 Feb; 2(2):e14.
Peng Q, Pevzner PA, Tesler G. PMID: 16501665; PMCID: PMC1378107.
View in:
PubMed Mentions:
41 Fields:
Translation:
HumansAnimalsCells
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Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res. 2006 Mar; 16(3):394-404.
Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C. PMID: 16461635; PMCID: PMC1415204.
View in:
PubMed Mentions:
32 Fields:
Translation:
HumansCells
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Identifying repeat domains in large genomes. Genome Biol. 2006; 7(1):R7.
Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA. PMID: 16507140; PMCID: PMC1431705.
View in:
PubMed Mentions:
17 Fields:
Translation:
HumansAnimalsCells
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Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc. 2006; 1(1):67-72.
Tanner S, Pevzner PA, Bafna V. PMID: 17406213.
View in:
PubMed Mentions:
15 Fields:
Translation:
Cells
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Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol. 2005 Dec; 23(12):1562-7.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. PMID: 16311586.
View in:
PubMed Mentions:
89 Fields:
Translation:
Cells
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Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 2005 Jul 22; 309(5734):613-7.
Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, Beever JE, Chowdhary BP, Galibert F, Gatzke L, Hitte C, Meyers SN, Milan D, Ostrander EA, Pape G, Parker HG, Raudsepp T, Rogatcheva MB, Schook LB, Skow LC, Welge M, Womack JE, O'brien SJ, Pevzner PA, Lewin HA. PMID: 16040707.
View in:
PubMed Mentions:
240 Fields:
Translation:
HumansAnimalsCells
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InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem. 2005 Jul 15; 77(14):4626-39.
Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. PMID: 16013882.
View in:
PubMed Mentions:
244 Fields:
Translation:
Cells
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Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res. 2005 Jul-Aug; 4(4):1287-95.
Frank A, Tanner S, Bafna V, Pevzner P. PMID: 16083278.
View in:
PubMed Mentions:
44 Fields:
Translation:
Cells
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De novo identification of repeat families in large genomes. Bioinformatics. 2005 Jun; 21 Suppl 1:i351-8.
Price AL, Jones NC, Pevzner PA. PMID: 15961478.
View in:
PubMed Mentions:
995 Fields:
Translation:
AnimalsCells
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PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem. 2005 Feb 15; 77(4):964-73.
Frank A, Pevzner P. PMID: 15858974.
View in:
PubMed Mentions:
197 Fields:
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Identification of post-translational modifications via blind search of mass-spectra. Proc IEEE Comput Syst Bioinform Conf. 2005; 157-66.
Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. PMID: 16447973.
View in:
PubMed Mentions:
9 Fields:
Translation:
Cells
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Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem. 2004 Dec 15; 76(24):7221-33.
Bandeira N, Tang H, Bafna V, Pevzner P. PMID: 15595863.
View in:
PubMed Mentions:
16 Fields:
Translation:
Cells
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Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 2005 Jan; 15(1):98-110.
Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G. PMID: 15590940; PMCID: PMC540283.
View in:
PubMed Mentions:
68 Fields:
Translation:
HumansAnimalsCells
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Mammalian phylogenomics comes of age. Trends Genet. 2004 Dec; 20(12):631-9.
Murphy WJ, Pevzner PA, O'Brien SJ. PMID: 15522459.
View in:
PubMed Mentions:
136 Fields:
Translation:
HumansAnimals
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Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 2004 Nov; 14(11):2245-52.
Price AL, Eskin E, Pevzner PA. PMID: 15520288; PMCID: PMC525682.
View in:
PubMed Mentions:
102 Fields:
Translation:
HumansCells
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A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 2004 Nov; 14(11):2336-46.
Raphael B, Zhi D, Tang H, Pevzner P. PMID: 15520295; PMCID: PMC525693.
View in:
PubMed Mentions:
41 Fields:
-
De novo repeat classification and fragment assembly. Genome Res. 2004 Sep; 14(9):1786-96.
Pevzner PA, Pevzner PA, Tang H, Tesler G. PMID: 15342561; PMCID: PMC515325.
View in:
PubMed Mentions:
80 Fields:
Translation:
HumansCells
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Reconstructing tumor amplisomes. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i265-73.
Raphael BJ, Pevzner PA. PMID: 15262808.
View in:
PubMed Mentions:
13 Fields:
Translation:
HumansAnimalsCells
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The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res. 2004; 32(13):3977-83.
Leipzig J, Pevzner P, Heber S. PMID: 15292448; PMCID: PMC506815.
View in:
PubMed Mentions:
29 Fields:
Translation:
HumansCells
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Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements. Genomics. 2004 Jun; 83(6):1053-62.
Andelfinger G, Hitte C, Etter L, Guyon R, Bourque G, Tesler G, Pevzner P, Kirkness E, Galibert F, Benson DW. PMID: 15177558.
View in:
PubMed Mentions:
5 Fields:
Translation:
HumansAnimalsCells
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Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians. Bioinformatics. 2004 Sep 22; 20(14):2159-61.
Pevzner PA. PMID: 15073013.
View in:
PubMed Mentions:
10 Fields:
Translation:
Humans
-
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 04 01; 428(6982):493-521.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F, Rat Genome Sequencing Project Consortium. PMID: 15057822.
View in:
PubMed Mentions:
847 Fields:
Translation:
HumansAnimalsCells
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Fragment assembly with short reads. Bioinformatics. 2004 Sep 01; 20(13):2067-74.
Chaisson M, Pevzner P, Tang H. PMID: 15059830.
View in:
PubMed Mentions:
51 Fields:
Translation:
Cells
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Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 2004 Apr; 14(4):507-16.
Bourque G, Pevzner PA, Tesler G. PMID: 15059991; PMCID: PMC383294.
View in:
PubMed Mentions:
92 Fields:
Translation:
HumansAnimalsCells
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Scalable heuristics for design of DNA probe arrays. J Comput Biol. 2004; 11(2-3):429-47.
Kahng AB, Mandoiu II, Pevzner PA, Reda S, Zelikovsky AZ. PMID: 15285900.
View in:
PubMed Mentions: Fields:
-
Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum Genomics. 2003 Nov; 1(1):30-40.
Murphy WJ, Bourque G, Tesler G, Pevzner P, O'Brien SJ. PMID: 15601531; PMCID: PMC3525001.
View in:
PubMed Mentions:
11 Fields:
Translation:
HumansAnimalsCells
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Finding subtle motifs by branching from sample strings. Bioinformatics. 2003 Oct; 19 Suppl 2:ii149-55.
Price A, Ramabhadran S, Pevzner PA. PMID: 14534184.
View in:
PubMed Mentions:
22 Fields:
Translation:
Cells
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Reconstructing tumor genome architectures. Bioinformatics. 2003 Oct; 19 Suppl 2:ii162-71.
Raphael BJ, Volik S, Collins C, Pevzner PA. PMID: 14534186.
View in:
PubMed Mentions:
32 Fields:
Translation:
HumansCells
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Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A. 2003 Jun 24; 100(13):7672-7.
Pevzner P, Tesler G. PMID: 12810957; PMCID: PMC164646.
View in:
PubMed Mentions:
142 Fields:
Translation:
HumansAnimalsCells
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Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res. 2003 Jan; 13(1):37-45.
Pevzner P, Tesler G. PMID: 12529304; PMCID: PMC430962.
View in:
PubMed Mentions:
118 Fields:
Translation:
HumansAnimalsCells
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Genome-wide analysis of bacterial promoter regions. Pac Symp Biocomput. 2003; 29-40.
Eskin E, Keich U, Gelfand MS, Pevzner PA. PMID: 12603015.
View in:
PubMed Mentions:
11 Fields:
Translation:
Cells
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Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. PMID: 12466850.
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PubMed Mentions:
2842 Fields:
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HumansAnimalsCells
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Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science. 2002 Nov 29; 298(5599):1747-52.
Lunyak VV, Burgess R, Prefontaine GG, Nelson C, Sze SH, Chenoweth J, Schwartz P, Pevzner PA, Glass C, Mandel G, Rosenfeld MG. PMID: 12399542.
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PubMed Mentions:
183 Fields:
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HumansAnimalsCells
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Finding motifs in the twilight zone. Bioinformatics. 2002 Oct; 18(10):1374-81.
Keich U, Pevzner PA. PMID: 12376382.
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PubMed Mentions:
25 Fields:
Translation:
AnimalsCells
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Subtle motifs: defining the limits of motif finding algorithms. Bioinformatics. 2002 Oct; 18(10):1382-90.
Keich U, Pevzner PA. PMID: 12376383.
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PubMed Mentions:
9 Fields:
Translation:
Cells
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Finding composite regulatory patterns in DNA sequences. Bioinformatics. 2002; 18 Suppl 1:S354-63.
Eskin E, Pevzner PA. PMID: 12169566.
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PubMed Mentions:
65 Fields:
Translation:
Cells
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Splicing graphs and EST assembly problem. Bioinformatics. 2002; 18 Suppl 1:S181-8.
Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA. PMID: 12169546.
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PubMed Mentions:
73 Fields:
Translation:
HumansCells
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Combinatorial algorithms for design of DNA arrays. Adv Biochem Eng Biotechnol. 2002; 77:1-19.
Hannenhalli S, Hubell E, Lipshutz R, Pevzner PA. PMID: 12227732.
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PubMed Mentions:
2 Fields:
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Finding weak motifs in DNA sequences. Pac Symp Biocomput. 2002; 235-46.
Sze SH, Gelfand MS, Pevzner PA. PMID: 11928479.
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PubMed Mentions:
4 Fields:
Translation:
Cells
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EULER-PCR: finishing experiments for repeat resolution. Pac Symp Biocomput. 2002; 199-210.
Mulyukov Z, Pevzner PA. PMID: 11928476.
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PubMed Mentions:
8 Fields:
Translation:
Cells
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Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 2002 Jan; 12(1):26-36.
Bourque G, Pevzner PA. PMID: 11779828; PMCID: PMC155248.
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PubMed Mentions:
127 Fields:
Translation:
HumansAnimalsCells
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Assembling puzzles from preassembled blocks. Genome Res. 2001 Sep; 11(9):1461-2.
Pevzner PA. PMID: 11544188.
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HumansAnimals
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An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A. 2001 Aug 14; 98(17):9748-53.
Pevzner PA, Tang H, Waterman MS. PMID: 11504945; PMCID: PMC55524.
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PubMed Mentions:
382 Fields:
Translation:
Cells
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A new approach to sequence comparison: normalized sequence alignment. Bioinformatics. 2001 Apr; 17(4):327-37.
Arslan AN, Egecioglu O, Pevzner PA. PMID: 11301301.
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PubMed Mentions:
10 Fields:
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Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res. 2001 Feb; 11(2):290-9.
Pevzner PA, Mulyukov Z, Dancik V, Tang CL. PMID: 11157792; PMCID: PMC544186.
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PubMed Mentions:
25 Fields:
Translation:
Cells
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Fragment assembly with double-barreled data. Bioinformatics. 2001; 17 Suppl 1:S225-33.
Pevzner PA, Tang H. PMID: 11473013.
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PubMed Mentions:
36 Fields:
Translation:
Cells
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Combinatorial approaches to finding subtle signals in DNA sequences. Proc Int Conf Intell Syst Mol Biol. 2000; 8:269-78.
Pevzner PA, Sze SH. PMID: 10977088.
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PubMed Mentions:
85 Fields:
Translation:
HumansAnimals
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Mutation-tolerant protein identification by mass spectrometry. J Comput Biol. 2000; 7(6):777-87.
Pevzner PA, Dancík V, Tang CL. PMID: 11382361.
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PubMed Mentions:
37 Fields:
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De novo peptide sequencing via tandem mass spectrometry. J Comput Biol. 1999 Fall-Winter; 6(3-4):327-42.
Dancík V, Addona TA, Clauser KR, Vath JE, Pevzner PA. PMID: 10582570.
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PubMed Mentions:
125 Fields:
Translation:
Cells
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SST versus EST in gene recognition. Microb Comp Genomics. 1999; 4(3):167-72.
Mironov AA, Pevzner PA. PMID: 10587944.
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Humans
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Fidelity probes for DNA arrays. Proc Int Conf Intell Syst Mol Biol. 1999; 113-7.
Hubbell E, Pevzner PA. PMID: 10786293.
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PubMed Mentions:
1 Fields:
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Performance-guarantee gene predictions via spliced alignment. Genomics. 1998 Aug 01; 51(3):332-9.
Mironov AA, Roytberg MA, Pevzner PA, Gelfand MS. PMID: 9721203.
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PubMed Mentions:
5 Fields:
Translation:
HumansCells
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Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs. Genomics. 1998 Jan 15; 47(2):171-9.
Xu G, Sze SH, Liu CP, Pevzner PA, Arnheim N. PMID: 9479489.
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PubMed Mentions:
1 Fields:
Translation:
HumansAnimals
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Algorithms and software for support of gene identification experiments. Bioinformatics. 1998; 14(1):14-9.
Sze SH, Roytberg MA, Gelfand MS, Mironov AA, Astakhova TV, Pevzner PA. PMID: 9520497.
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PubMed Mentions:
1 Fields:
Translation:
HumansAnimals
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Software for DNA sequencing by hybridization. Comput Appl Biosci. 1997 Apr; 13(2):205-10.
Belyi I, Pevzner PA. PMID: 9146969.
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Cells
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Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment. J Comput Biol. 1997; 4(3):297-309.
Sze SH, Pevzner PA. PMID: 9278061.
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PubMed Mentions:
4 Fields:
Translation:
HumansAnimalsCells
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Gene recognition via spliced sequence alignment. Proc Natl Acad Sci U S A. 1996 Aug 20; 93(17):9061-6.
Gelfand MS, Mironov AA, Pevzner PA. PMID: 8799154; PMCID: PMC38595.
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PubMed Mentions:
51 Fields:
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HumansAnimalsCells
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Positional sequencing by hybridization. Comput Appl Biosci. 1996 Feb; 12(1):19-24.
Hannenhalli S, Feldman W, Lewis HF, Skiena SS, Pevzner PA. PMID: 8670615.
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PubMed Mentions:
3 Fields:
Translation:
Cells
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Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics. 1995 Nov 20; 30(2):299-311.
Hannenhalli S, Chappey C, Koonin EV, Pevzner PA. PMID: 8586431.
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PubMed Mentions:
23 Fields:
Translation:
Cells
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DNASUN: a package of computer programs for the biotechnology laboratory. Comput Appl Biosci. 1995 Jun; 11(3):331-5.
Mironov AA, Alexandrov NN, Grigorjev A, Lebedev VF, Lunovskaya LV, Truchan ME, Pevzner PA. PMID: 7583703.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Combinatorial methods for DNA mapping and sequencing. J Comput Biol. 1995; 2(2):153-8.
Pevzner PA. PMID: 7497124.
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Cells
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Gray code masks for sequencing by hybridization. Genomics. 1994 Sep 01; 23(1):233-5.
Feldman W, Pevzner P. PMID: 7829077.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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Rearrangements of DNA sequences and SBH. Comput Chem. 1994 Sep; 18(3):221-3.
Pevzner PA. PMID: 7952892.
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Cells
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Extendable words in nucleotide sequences. Comput Appl Biosci. 1992 Apr; 8(2):129-35.
Gelfand MS, Kozhukhin CG, Pevzner PA. PMID: 1375526.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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Statistical distance between texts and filtration methods in sequence comparison. Comput Appl Biosci. 1992 Apr; 8(2):121-7.
Pevzner PA. PMID: 1591607.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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Improved chips for sequencing by hybridization. J Biomol Struct Dyn. 1991 Oct; 9(2):399-410.
Pevzner PA, Khrapko KR, Belyavsky AV, Florentiev VL, Mirzabekov AD. PMID: 1741970.
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PubMed Mentions:
4 Fields:
Translation:
Cells
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[Optimal chips for megabase DNA sequencing]. Mol Biol (Mosk). 1991 Mar-Apr; 25(2):552-62.
Pevzner PA, Lysov IuP, Khrapko KR, Beliavskii AV, Florent'ev VL, Mirzabekov AD. PMID: 1881398.
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Cells
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Genome inhomogeneity is determined mainly by WW and SS dinucleotides. Comput Appl Biosci. 1991 Jan; 7(1):39-49.
Kozhukhin CG, Pevzner PA. PMID: 2004273.
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PubMed Mentions:
8 Fields:
Translation:
HumansAnimalsCells
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1-Tuple DNA sequencing: computer analysis. J Biomol Struct Dyn. 1989 Aug; 7(1):63-73.
Pevzner PA. PMID: 2684223.
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PubMed Mentions:
35 Fields:
Translation:
Cells
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[Paths in graphs and selection of oligonucleotide linkers]. Mol Biol (Mosk). 1989 Jul-Aug; 23(4):1075-9.
Pevzner PA, Veiko VP. PMID: 2555681.
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Cells
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Linguistics of nucleotide sequences. II: Stationary words in genetic texts and the zonal structure of DNA. J Biomol Struct Dyn. 1989 Apr; 6(5):1027-38.
Pevzner PA, Mironov AA. PMID: 2531597.
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PubMed Mentions:
8 Fields:
Translation:
Cells
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Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurrence of words. J Biomol Struct Dyn. 1989 Apr; 6(5):1013-26.
Pevzner PA, Mironov AA. PMID: 2531596.
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PubMed Mentions:
21 Fields:
Translation:
Cells
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[Effective method for physical mapping the DNA molecule]. Mol Biol (Mosk). 1987 May-Jun; 21(3):788-96.
Pevzner PA, Mironov AA. PMID: 3657777.
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