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Items: 1 to 50 of 145

1.

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.

PMID:
29358742
2.

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.

PMID:
29046389
3.

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.

PMID:
28978691
4.

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.

5.

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.

6.

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.

PMID:
28242452
7.

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.

8.

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.

9.

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.

10.

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
11.

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.

12.

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.

13.

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
14.

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.

PMID:
26629978
15.

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.

16.
17.

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
18.

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.

19.

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.

20.

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
21.

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.

22.

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.

23.

Proteogenomics.

Pandey A, Pevzner PA.

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

PMID:
25469796
24.

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.

25.

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.

26.

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.

27.

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
28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.

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.

Genome Res. 2013 May;23(5):867-77. doi: 10.1101/gr.150433.112. Epub 2013 Apr 5.

35.

How many signal peptides are there in bacteria?

Ivankov DN, Payne SH, Galperin MY, Bonissone S, Pevzner PA, Frishman D.

Environ Microbiol. 2013 Apr;15(4):983-90. doi: 10.1111/1462-2920.12105.

36.

A new approach to evaluating statistical significance of spectral identifications.

Mohimani H, Kim S, Pevzner PA.

J Proteome Res. 2013 Apr 5;12(4):1560-8. doi: 10.1021/pr300453t. Epub 2013 Mar 8.

37.

Unexpected diversity of signal peptides in prokaryotes.

Payne SH, Bonissone S, Wu S, Brown RN, Ivankov DN, Frishman D, Pasa-Tolić L, Smith RD, Pevzner PA.

MBio. 2012 Nov 20;3(6). pii: e00339-12. doi: 10.1128/mBio.00339-12.

38.

N-terminal protein processing: a comparative proteogenomic analysis.

Bonissone S, Gupta N, Romine M, Bradshaw RA, Pevzner PA.

Mol Cell Proteomics. 2013 Jan;12(1):14-28. doi: 10.1074/mcp.M112.019075. Epub 2012 Sep 23.

39.

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly.

Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA.

J Comput Biol. 2013 Apr;20(4):359-71. doi: 10.1089/cmb.2012.0098. Epub 2012 Jul 17.

40.

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

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.

J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16.

41.

How to apply de Bruijn graphs to genome assembly.

Compeau PE, Pevzner PA, Tesler G.

Nat Biotechnol. 2011 Nov 8;29(11):987-91. doi: 10.1038/nbt.2023. No abstract available.

42.

Multiplex de novo sequencing of peptide antibiotics.

Mohimani H, Liu WT, Yang YL, Gaudêncio SP, Fenical W, Dorrestein PC, Pevzner PA.

J Comput Biol. 2011 Nov;18(11):1371-81. doi: 10.1089/cmb.2011.0158. Epub 2011 Oct 28.

43.

Protein identification using top-down.

Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA.

Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524. Epub 2011 Oct 25.

44.

Target-decoy approach and false discovery rate: when things may go wrong.

Gupta N, Bandeira N, Keich U, Pevzner PA.

J Am Soc Mass Spectrom. 2011 Jul;22(7):1111-20. doi: 10.1007/s13361-011-0139-3. Epub 2011 May 5.

45.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.

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.

Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966.

46.

Cycloquest: identification of cyclopeptides via database search of their mass spectra against genome databases.

Mohimani H, Liu WT, Mylne JS, Poth AG, Colgrave ML, Tran D, Selsted ME, Dorrestein PC, Pevzner PA.

J Proteome Res. 2011 Oct 7;10(10):4505-12. doi: 10.1021/pr200323a. Epub 2011 Sep 7. Erratum in: J Proteome Res. 2011 Dec 2;10(12):5575.

47.

Sequencing cyclic peptides by multistage mass spectrometry.

Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner PA.

Proteomics. 2011 Sep;11(18):3642-50. doi: 10.1002/pmic.201000697. Epub 2011 Aug 9.

48.

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.

Frank AM, Monroe ME, Shah AR, Carver JJ, Bandeira N, Moore RJ, Anderson GA, Smith RD, Pevzner PA.

Nat Methods. 2011 May 15;8(7):587-91. doi: 10.1038/nmeth.1609.

49.

Preface: 2nd Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB-BE 2010).

Pevzner PA, Shamir R.

J Comput Biol. 2011 Jul;18(7):865. doi: 10.1089/cmb.2011.007p. Epub 2011 May 12. No abstract available.

PMID:
21563980
50.

Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera.

Mevers E, Liu WT, Engene N, Mohimani H, Byrum T, Pevzner PA, Dorrestein PC, Spadafora C, Gerwick WH.

J Nat Prod. 2011 May 27;74(5):928-36. doi: 10.1021/np200077f. Epub 2011 Apr 13.

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