PatternLab for proteomics
pattern recognition software
 
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Links & Acknowledgements

This project is under development by joint efforts from the Systems Engineering and Computer Science Program at the Federal University of Rio de Janreiro (Brazil) and the Biological Mass Spectrometry Laboratory (Yates Lab) from the Scripps Research institute (La Jolla, California).

Publications related to PatternLab:

  • Moresco JJ, Carvalho PC, Yates JR III, Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry, Journal of Proteomics, to appear.

  • Carvalho PC, Yates, JR III, Barbosa VC, Analyzing shotgun proteomic data with PatternLab for proteomics, Current Protocols in Bioinformatics, 13.13.1-13.13.15, 2010.

  • Carvalho PC, Han X, Xu T, Cociorva D, Carvalho MGC, Barbosa VC, Yates, JR III, XDIA: Improving on the label-free data-independent analysis, Bioinformatics., 26: pp. 847-848, 2010

  • Fischer JSG, Lujian Liau, Carvalho PC, Barbosa VC, Domont GB, Carvalho MGC, Yates JR, III. Dynamic proteomic analysis of the membrane enriched fraction of glioblastoma cells (A172) exposed to perillyl alcohol. Journal of Proteomics, 73 (2010), 1018–1027.
  • Carvalho PC, Xu T, Han X, Cociorva D, Barbosa VC, Yates JR, III. YADA: A tool for taking the most out of high resolution mass spectra. Bioinformatics, 25: 2734-2736, 2009.

  • Carvalho PC, Cociorva D, Wong C, Carvalho MGC, Barbosa VC, Yates JR, III. Charge Prediction Machine: A tool for inferring precursor charge states of Electron Transfer Dissociation tandem mass spectra, Anal. Chem., 81 (5), pp 1996–2003, 2009.

  • Carvalho PC, Fischer JSG, Chen EI, Domont GB, Carvalho MGC, Degrave WM, Yates JR III, Barbosa VC. GO Explorer: A gene-ontology tool to aid in the interpretation of spectral counting data in shotgun proteomics, Proteome Science 2009, 7:6., Flagged as highly accessed.

  • Carvalho PC, Fischer JSG, Chen E, Yates JR III, Barbosa VC. PatternLab for proteomics: a tool for differential shotgun proteomics, BMC Bioinformatics 9:316, 2008 - Flagged as highly accessed.

  • Carvalho PC, Hewel J, Barbosa VC, Yates JR III. Identifying differences in protein expression levels by by spectral counts and feature selection, Genetics and Molecular Research 7 (2): 342-356, 2008

Weifeng Gu, et al., Molecular Cell, Volume 36, Supplemental Data, , Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline, 2009.

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea, Zivanovic et al., Genome Biology, 2009.

PatternLab for differential shotgun proteomics, Journal of Proteome Research, 2008; highlights

[Link to PatternLab poster presented at the LaJolla Proteomics meeting in UCSD, 2008]

 

Acknowledgments

** PatternLab uses SVMLight to perform any SVM calculation.

** PatternLab also makes use of ALGLIB