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Items: 1 to 50 of 192

1.

BiosyntheticSPAdes: Reconstructing Biosynthetic Gene Clusters From Assembly Graphs.

Meleshko D, Mohimani H, Traccana V, Hajirasouliha I, Medema MH, Korobeynikov A, Pevzner PA.

Genome Res. 2019 Jun 3. pii: gr.243477.118. doi: 10.1101/gr.243477.118. [Epub ahead of print]

PMID:
31160374
2.

De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins.

Safonova Y, Pevzner PA.

Front Immunol. 2019 May 3;10:987. doi: 10.3389/fimmu.2019.00987. eCollection 2019.

3.

Plasmid detection and assembly in genomic and metagenomic data sets.

Antipov D, Raiko M, Lapidus A, Pevzner PA.

Genome Res. 2019 Jun;29(6):961-968. doi: 10.1101/gr.241299.118. Epub 2019 May 2.

PMID:
31048319
4.

Assembly of long, error-prone reads using repeat graphs.

Kolmogorov M, Yuan J, Lin Y, Pevzner PA.

Nat Biotechnol. 2019 May;37(5):540-546. doi: 10.1038/s41587-019-0072-8. Epub 2019 Apr 1.

PMID:
30936562
5.

How bioinformatics and open data can boost basic science in countries and universities with limited resources.

Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E.

Nat Biotechnol. 2019 Mar;37(3):324-326. doi: 10.1038/s41587-019-0053-y. No abstract available.

PMID:
30833765
6.

A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch.

Fisher MF, Zhang J, Taylor NL, Howard MJ, Berkowitz O, Debowski AW, Behsaz B, Whelan J, Pevzner PA, Mylne JS.

Plant Direct. 2018 Feb;2(2). pii: e00042. doi: 10.1002/pld3.42. Epub 2018 Feb 28.

7.

Dereplication of microbial metabolites through database search of mass spectra.

Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA.

Nat Commun. 2018 Oct 2;9(1):4035. doi: 10.1038/s41467-018-06082-8.

8.

Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity.

Bankevich A, Pevzner PA.

Cell Syst. 2018 Aug 22;7(2):192-200.e3. doi: 10.1016/j.cels.2018.06.009. Epub 2018 Jul 25.

PMID:
30056005
9.

American Gut: an Open Platform for Citizen Science Microbiome Research.

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.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

10.

Detection and analysis of ancient segmental duplications in mammalian genomes.

Pu L, Lin Y, Pevzner PA.

Genome Res. 2018 Jun;28(6):901-909. doi: 10.1101/gr.228718.117. Epub 2018 May 7.

11.

Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra.

Gurevich A, Mikheenko A, Shlemov A, Korobeynikov A, Mohimani H, Pevzner PA.

Nat Microbiol. 2018 Mar;3(3):319-327. doi: 10.1038/s41564-017-0094-2. Epub 2018 Jan 22.

12.

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection.

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.

J Proteomics. 2018 Mar 30;176:13-23. doi: 10.1016/j.jprot.2018.01.004. Epub 2018 Jan 10.

13.

The Antibody Repertoire of Colorectal Cancer.

Cha SW, Bonissone S, Na S, Pevzner PA, Bafna V.

Mol Cell Proteomics. 2017 Dec;16(12):2111-2124. doi: 10.1074/mcp.RA117.000397. Epub 2017 Oct 18.

14.

Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.

Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA.

J Immunol. 2017 Nov 1;199(9):3369-3380. doi: 10.4049/jimmunol.1700485. Epub 2017 Oct 4.

15.

Single-molecule protein identification by sub-nanopore sensors.

Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA.

PLoS Comput Biol. 2017 May 9;13(5):e1005356. doi: 10.1371/journal.pcbi.1005356. eCollection 2017 May.

16.

metaSPAdes: a new versatile metagenomic assembler.

Nurk S, Meleshko D, Korobeynikov A, Pevzner PA.

Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15.

17.

Top-down analysis of immunoglobulin G isotypes 1 and 2 with electron transfer dissociation on a high-field Orbitrap mass spectrometer.

Fornelli L, Ayoub D, Aizikov K, Liu X, Damoc E, Pevzner PA, Makarov A, Beck A, Tsybin YO.

J Proteomics. 2017 Apr 21;159:67-76. doi: 10.1016/j.jprot.2017.02.013. Epub 2017 Feb 27.

18.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen.

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.

mSystems. 2016 Dec 20;1(6). pii: e00139-16. doi: 10.1128/mSystems.00139-16. eCollection 2016 Nov-Dec.

19.

Assembly of long error-prone reads using de Bruijn graphs.

Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):E8396-E8405. doi: 10.1073/pnas.1604560113. Epub 2016 Dec 12.

20.

Dereplication of peptidic natural products through database search of mass spectra.

Mohimani H, Gurevich A, Mikheenko A, Garg N, Nothias LF, Ninomiya A, Takada K, Dorrestein PC, Pevzner PA.

Nat Chem Biol. 2017 Jan;13(1):30-37. doi: 10.1038/nchembio.2219. Epub 2016 Oct 31.

21.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

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.

Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597.

22.

plasmidSPAdes: assembling plasmids from whole genome sequencing data.

Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA.

Bioinformatics. 2016 Nov 15;32(22):3380-3387. Epub 2016 Jul 27.

PMID:
27466620
23.

Top-down analysis of protein samples by de novo sequencing techniques.

Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolić N, Luider TM, Paša-Tolić L, Pevzner PA.

Bioinformatics. 2016 Sep 15;32(18):2753-9. doi: 10.1093/bioinformatics/btw307. Epub 2016 May 14.

24.

Immunoglobulin Classification Using the Colored Antibody Graph.

Bonissone SR, Pevzner PA.

J Comput Biol. 2016 Jun;23(6):483-94. doi: 10.1089/cmb.2016.0010. Epub 2016 May 5.

25.

TruSPAdes: barcode assembly of TruSeq synthetic long reads.

Bankevich A, Pevzner PA.

Nat Methods. 2016 Mar;13(3):248-50. doi: 10.1038/nmeth.3737. Epub 2016 Feb 1.

PMID:
26828418
26.

SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.

Kolmogorov M, Liu X, Pevzner PA.

J Proteome Res. 2016 Jan 4;15(1):144-51. doi: 10.1021/acs.jproteome.5b00610. Epub 2015 Dec 17.

27.

hybridSPAdes: an algorithm for hybrid assembly of short and long reads.

Antipov D, Korobeynikov A, McLean JS, Pevzner PA.

Bioinformatics. 2016 Apr 1;32(7):1009-15. doi: 10.1093/bioinformatics/btv688. Epub 2015 Nov 20.

28.
29.

De Novo Sequencing of Peptides from Top-Down Tandem Mass Spectra.

Vyatkina K, Wu S, Dekker LJ, VanDuijn MM, Liu X, Tolić N, Dvorkin M, Alexandrova S, Luider TM, Paša-Tolić L, Pevzner PA.

J Proteome Res. 2015 Nov 6;14(11):4450-62. doi: 10.1021/pr501244v. Epub 2015 Oct 13.

PMID:
26412692
30.

Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages.

León-Zayas R, Novotny M, Podell S, Shepard CM, Berkenpas E, Nikolenko S, Pevzner P, Lasken RS, Bartlett DH.

Appl Environ Microbiol. 2015 Dec;81(24):8265-76. doi: 10.1128/AEM.01659-15. Epub 2015 Sep 18.

31.

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.

Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V.

J Proteome Res. 2015 Sep 4;14(9):3555-67. doi: 10.1021/acs.jproteome.5b00264. Epub 2015 Jul 21.

32.

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA.

Bioinformatics. 2015 Jun 15;31(12):i53-61. doi: 10.1093/bioinformatics/btv238.

33.

Assembling short reads from jumping libraries with large insert sizes.

Vasilinetc I, Prjibelski AD, Gurevich A, Korobeynikov A, Pevzner PA.

Bioinformatics. 2015 Oct 15;31(20):3262-8. doi: 10.1093/bioinformatics/btv337. Epub 2015 Jun 3.

PMID:
26040456
34.

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.

Safonova Y, Bankevich A, Pevzner PA.

J Comput Biol. 2015 Jun;22(6):528-45. doi: 10.1089/cmb.2014.0153. Epub 2015 Mar 3.

35.

What is the difference between the breakpoint graph and the de Bruijn graph?

Lin Y, Nurk S, Pevzner PA.

BMC Genomics. 2014;15 Suppl 6:S6. doi: 10.1186/1471-2164-15-S6-S6. Epub 2014 Oct 17.

36.

Proteogenomics.

Pandey A, Pevzner PA.

Proteomics. 2014 Dec;14(23-24):2631-2. doi: 10.1002/pmic.201470173. No abstract available.

PMID:
25469796
37.

MS-GF+ makes progress towards a universal database search tool for proteomics.

Kim S, Pevzner PA.

Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.

38.

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery.

Mohimani H, Liu WT, Kersten RD, Moore BS, Dorrestein PC, Pevzner PA.

J Nat Prod. 2014 Aug 22;77(8):1902-9. doi: 10.1021/np500370c. Epub 2014 Aug 12.

39.

ExSPAnder: a universal repeat resolver for DNA fragment assembly.

Prjibelski AD, Vasilinetc I, Bankevich A, Gurevich A, Krivosheeva T, Nurk S, Pham S, Korobeynikov A, Lapidus A, Pevzner PA.

Bioinformatics. 2014 Jun 15;30(12):i293-301. doi: 10.1093/bioinformatics/btu266.

40.

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

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.

J Proteome Res. 2014 Jul 3;13(7):3241-8. doi: 10.1021/pr401300m. Epub 2014 Jun 18.

PMID:
24874765
41.

Automated genome mining of ribosomal peptide natural products.

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.

ACS Chem Biol. 2014 Jul 18;9(7):1545-51. doi: 10.1021/cb500199h. Epub 2014 May 23.

42.

Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry.

Wu S, Brown JN, Tolić N, Meng D, Liu X, Zhang H, Zhao R, Moore RJ, Pevzner P, Smith RD, Paša-Tolić L.

Proteomics. 2014 May;14(10):1211-22. doi: 10.1002/pmic.201300378. Epub 2014 Apr 13.

PMID:
24591407
43.

Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways.

Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH, Allen EE, Gerwick L, Gerwick WH.

PLoS One. 2014 Jan 27;9(1):e85140. doi: 10.1371/journal.pone.0085140. eCollection 2014.

44.

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.

Terterov I, Vyatkina K, Kononikhin AS, Boitsov V, Vyazmin S, Popov IA, Nikolaev EN, Pevzner P, Dubina M.

Rapid Commun Mass Spectrom. 2014 Jan 15;28(1):33-41. doi: 10.1002/rcm.6757.

PMID:
24285388
45.

Identification of ultramodified proteins using top-down tandem mass spectra.

Liu X, Hengel S, Wu S, Tolić N, Pasa-Tolić L, Pevzner PA.

J Proteome Res. 2013 Dec 6;12(12):5830-8. doi: 10.1021/pr400849y. Epub 2013 Nov 15.

46.

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.

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.

J Comput Biol. 2013 Oct;20(10):714-37. doi: 10.1089/cmb.2013.0084.

47.

MORPH-PRO: a novel algorithm and web server for protein morphing.

Castellana NE, Lushnikov A, Rotkiewicz P, Sefcovic N, Pevzner PA, Godzik A, Vyatkina K.

Algorithms Mol Biol. 2013 Jul 11;8(1):19. doi: 10.1186/1748-7188-8-19.

48.

UniNovo: a universal tool for de novo peptide sequencing.

Jeong K, Kim S, Pevzner PA.

Bioinformatics. 2013 Aug 15;29(16):1953-62. doi: 10.1093/bioinformatics/btt338. Epub 2013 Jun 12.

49.

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.

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.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10.

50.

Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.

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.

Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10153-8. doi: 10.1073/pnas.1221210110. Epub 2013 May 29.

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