Journal papers N. Gupta*, S. Bark*, W.D. Lu*, L. Taupenot, D. O'Connor, P.A. Pevzner, V. Hook. Mass Spectrometry-Based Neuropeptidomics of Human Secretory Vesicles Reveals Novel Properties of Post-Translational Processing for Neuropeptide Biosynthesis. Submitted. L. Wich and N. Gupta. MS-Operon: Using tandem mass spectrometry for operon prediction and validation. Submitted. S. Bonissone, N. Gupta, M. Romine and P.A. Pevzner. Comparative proteogenomics reveals a possible functional role of N-terminal Methionine Excision. Submitted. N. Gupta, K. K. Hixson, D. E. Culley, R. D. Smith and P. A. Pevzner. Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass-spectrometry. Submitted. N. Gupta, N. Bandeira and P.A. Pevzner. Target-decoy approach in proteomics: when things may go wrong. Submitted. N. Gupta and P.A. Pevzner (2009). False discovery rates of protein identifications: a strike against the two-peptide rule. Journal of Proteome Research. 8(9):4173-81. [Pubmed] * Commentary on this article by Katie Cottingham * Noted as one of the 10 most accessed articles of the journal in third quarter of 2009 S. Kim, N. Gupta, N. Bandeira and P.A. Pevzner (2009). Spectral Dictionaries: Integrating De Novo Peptide Sequencing with Database Search of Tandem Mass Spectra. Molecular and Cellular Proteomics. 8(1):53-69. [Pubmed] B. Dost, T. Shlomi, N. Gupta, E. Ruppin, V. Bafna, and R. Sharan (2008). QNet: a tool for querying protein interaction networks. Journal of Computational Biology. 15(7):913-25. [Pubmed] N. Gupta, J. Benhamida, V. Bhargava, D. Goodman, E. Kain, I. Kerman, N. Nguyen, N. Ollikainen, J. Rodriguez, J. Wang, M.S. Lipton, M. Romine, V. Bafna, R.D. Smith and P.A. Pevzner (2008). Comparative Proteogenomics: Combining Mass Spectrometry and Comparative Genomics to Analyze Multiple Genomes. Genome Research. 18:1133-1142 [Pubmed] * Included
in Research Highlights of Nature
Reviews Genetics, 6:418, 2008 [link] * Presented (talk) by Nitin Gupta at the conference ASMS 2008 * Press releases on undergraduate-involvement: UCSD | HHMI S. Kim, N. Gupta and P.A. Pevzner (2008). Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. Journal of Proteome Research. 7(8): 3354 - 3363. [Pubmed] J. Rodriguez, N. Gupta, R.D. Smith and P.A. Pevzner (2008). Does trypsin cut before Proline? Journal of Proteome Research. 7(1):300-5. [Full Text] [Pubmed] * Noted as one
of the 10 most accessed articles of the journal in the first quarter of 2008. N. Gupta, S. Tanner, N. Jaitly, J.N. Adkins, M. Lipton, R. Edwards, M. Romine, A. Osterman, V. Bafna, R.D. Smith and P.A. Pevzner (2007). Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Research. 17(9):1362-77. [Full Text] [Pubmed] K. Gaurav, N. Gupta and R. Sowdhamini (2005). FASSM: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs. In Silico Biology. 5:0040. [Pubmed] N. Gupta, N. Mangal and S. Biswas (2005). Evolution and similarity evaluation of protein structures in contact map space. Proteins: Structure, Function and Bioinformatics. 59(2):196-204. [Pubmed] A. Bhaduri, G. Pugalenthi, N. Gupta and R. Sowdhamini (2004). iMOT: an interactive package for the selection of spatially interacting motifs. Nucleic Acids Research. 32:W602-W605. [PubMed] N. Gupta and A. Irback (2004). Coupled folding-binding versus docking: A lattice model study. Journal of Chemical Physics. 120:3983-3989. [PDF] [Pubmed] Conference papers B. Dost, T. Shlomi, N. Gupta, V. Bafna, and R. Sharan. QNet: A tool for querying biological networks. RECOMB 2007. [PDF] * Also
published in Lecture
Notes in Bioinformatics, 4453,
p. 1 ff. N. Gupta, N. Mangal, K. Tiwari and P. Mitra. Mining quantitative association rules in protein sequences. Proceedings of the third Australasian Data Mining Conference 2004 (AusDM'04), Cairns, Australia. [PDF] * Also
published in
Lecture Notes in Computer Science, Volume 3755 / 2006,
pp. 273 - 281. N. Gupta and V. K. Agrawal. Two Criterion Optimization in state assignment for synchronous finite state machines using NSGA-II. Proceedings of the International Conference on Adaptive and Natural Computing Algorithms, 2005 (ICANNGA'05), Coimbra, Portugal. [PDF] Patent S. Kim, N. Gupta and P.A. Pevzner. Method for identifying peptides using tandem mass spectra by dynamically determining the number of peptide reconstructions required. Patent Pending. US provisional application Number: 60/941,276. PCT International application No: PCT/US2008/065548. |