New Papers

• Castellana CE, Payne SH, Zhen Z, Stanke M, Bafna V, Briggs SP
  Proteogenomic discovery, correction and confirmation of Arabidopsis gene models
  
  
• Bandeira N, Ng J, Melluzi D, Linington RG, Dorrestein P, Pevzner PA
  De Novo Sequencing of Nonribosomal Peptides
  
  
• Bandeira N, Olson J, Mann M, Pevzner PA
  De Novo Peptide Sequencing via Multi-Stage Mass Spectrometry
  
  
• Frank AM, Pesavento JJ, Mizzen CA, Kelleher NL, Pevzner PA
  Interpreting Top-Down Mass Spectra Using Spectral Alignment
  
  
• Gupta N, Benhamida J. Bhargava V, Goodman D, Kain E, Kerman J, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Romine M, Bafna V, Smith RD, Pevzner PA.
  Comparative Proteogenomics: Combining Mass Spectrometry and Comparative Genomics to Analyze Multiple Genomes
  
  
• Kim S, Gupta N, Pevzner P.A.
  The Partition Function of Tandem Mass Spectra:a New Approach to Peptide Identifications
  
  
• Kim S, Gupta N, Pevzner P.A.
  Spectral Dictionaries: Integrating De Novo Peptide Sequencing with Database Search of Tandem Mass Spectra
  
  
• Ng J, Pevzner PA
  Algorithm for Identification of Fusion Proteins via Mass Spectrometry
  
  
• Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V.
  Phosphorylation specific MS/MS scoring for rapid and accurate phospho-proteome analysis.
  
  
• Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H.
  High-Coverage Phosphoproteome Analysis Using HILIC based Multi-Dimensional Chromatography
  
  
  

2007

• Rodriguez J, Gupta N, Pevzner PA.
  Does trypsin cut before proline?
  J. Proteome Research (in press)
  
  
• Frank AM, Bandeira N, Tanner S, Briggs, SP, Smith RD, Pevzner PA
  Clustering Millions of Tandem Mass Spectra
  J. Proteome Res. (in press)
  
  
• Tanner S, Payne SH,, Dasari S, Shen Z, Wilmarth P, David L, Loomis WF, Briggs SP, Bafna V.
  Accurate Annotation of Peptide Modifications through Unrestrictive Database Search.
  J. Proteome Res. (in press)
  
  
• Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA.
  Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.
  Genome Res. 2007 Sep;17(9):1362-77.
  
  
• Waridel P, Frank A, Thomas H, Surendranath V, Sunyaev S, Pevzner P, Shevchenko A.
  Sequence similarity-driven proteomics in organisms with unknown genomes by LC-MS/MS and automated de novo sequencing.
  Proteomics. 2007 Jul;7(14):2318-29.
  
  
• Bandeira N, Clauser KR, Pevzner PA.
  Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.
  Mol Cell Proteomics. 2007 Jul;6(7):1123-34. Epub 2007 Apr 19.
  
  
• Bandeira N, Tsur D, Frank A, Pevzner PA.
  Protein identification by spectral networks analysis.
  Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6140-5. Epub 2007 Apr 2.
  
  
• Tanner S, Shen Z, Ng J, Florea L, Guigo R, Briggs SP, Bafna V.
  Improving gene annotation using peptide mass spectrometry.
  Genome Res. 2007 Feb;17(2):231-9. Epub 2006 Dec 22.
  
  
• Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA.
  De novo peptide sequencing and identification with precision mass spectrometry.
  J Proteome Res. 2007 Jan;6(1):114-23.
  

2006

• Tanner S, Pevzner PA, Bafna V.
  Unrestrictive identification of post-translational modifications through peptide mass spectrometry.
  Nat Protoc. 2006;1(1):67-72.
  
  
• Chong KF, Ning K, Leong HW, Pevzner P.
  Modeling and characterization of multi-charge mass spectra for peptide sequencing.
  J Bioinform Comput Biol. 2006 Dec;4(6):1329-52.
  
  
• Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL.
  Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?
  J Proteome Res. 2006 Oct;5(10):2554-66.
  
  
• Wielsch N, Thomas H, Surendranath V, Waridel P, Frank A, Pevzner P, Shevchenko A.
  Rapid validation of protein identifications with the borderline statistical confidence via de novo sequencing and MS BLAST searches.
  J Proteome Res. 2006 Sep;5(9):2448-56.
  
  

2005

• Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA.
  Identification of post-translational modifications by blind search of mass spectra.
  Nat Biotechnol. 2005 Dec;23(12):1562-7. Epub 2005 Nov 27.
  
  
• Frank A, Tanner S, Bafna V, Pevzner P.
  Peptide sequence tags for fast database search in mass-spectrometry.
  J Proteome Res. 2005 Jul-Aug;4(4):1287-95.
  
  
• Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V.
  InsPecT: identification of posttranslationally modified peptides from tandem mass spectra.
  Anal Chem. 2005 Jul 15;77(14):4626-39.
  
  
• Frank A, Pevzner P.
  PepNovo: de novo peptide sequencing via probabilistic network modeling.
  Anal Chem. 2005 Feb 15;77(4):964-73.
  
  
  

2003

• Vineet Bafna, Nathan Edwards
  On de novo interpretation of tandem mass spectra for peptide identification.
  RECOMB 2003: 9-18
  
  

2001

• Pevzner PA, Mulyukov Z, Dancik V, Tang CL.
  Efficiency of database search for identification of mutated and modified proteins via mass spectrometry.
  Genome Res. 2001 Feb;11(2):290-9.
  
  
• Bafna V, Edwards N.
  SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database.
  Bioinformatics. 2001;17 Suppl 1:S13-21.
  
  

2000

• Pevzner PA, Dancik V, Tang CL.
  Mutation-tolerant protein identification by mass spectrometry.
  J Comput Biol. 2000;7(6):777-87.
  
  

1999

• Dancik V, Addona TA, Clauser KR, Vath JE, Pevzner PA.
  De novo peptide sequencing via tandem mass spectrometry.
  J Comput Biol. 1999 Fall-Winter;6(3-4):327-42.