Gelio Alves

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Calibrating E-values for MS2 database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:26. 2007
  2. pmc Detection of co-eluted peptides using database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
    Biol Direct 3:27. 2008
  3. pmc RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    BMC Genomics 9:505. 2008
  4. pmc RAId_DbS: peptide identification using database searches with realistic statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:25. 2007
  5. pmc RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 5:e15438. 2010
  6. pmc Enhancing peptide identification confidence by combining search methods
    Gelio Alves
    National Center for Biotechnology Information, Library of Medicine, NIH, Bethesda, MD 20894, USA
    J Proteome Res 7:3102-13. 2008
  7. ncbi request reprint Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:3726-32. 2005
  8. pmc Assigning statistical significance to proteotypic peptides via database searches
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Proteomics 74:199-211. 2011
  9. pmc Improving peptide identification sensitivity in shotgun proteomics by stratification of search space
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
    J Proteome Res 12:2571-81. 2013
  10. pmc Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
    J Am Soc Mass Spectrom 25:57-70. 2014

Detail Information

Publications12

  1. pmc Calibrating E-values for MS2 database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:26. 2007
    ..Although each search engine has its strength, combining the strengths of various search engines is not yet realizable largely due to the lack of a unified statistical framework that is applicable to any method...
  2. pmc Detection of co-eluted peptides using database search methods
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
    Biol Direct 3:27. 2008
    ....
  3. pmc RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    BMC Genomics 9:505. 2008
    ..Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies...
  4. pmc RAId_DbS: peptide identification using database searches with realistic statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Biol Direct 2:25. 2007
    ..The peptide identification performance and statistical accuracy of RAId_DbS are assessed and compared with several other search tools. The executables and data related to RAId_DbS are freely available upon request...
  5. pmc RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 5:e15438. 2010
    ..The web link is http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html. Relevant binaries for Linux, Windows, and Mac OS X are available from the same page...
  6. pmc Enhancing peptide identification confidence by combining search methods
    Gelio Alves
    National Center for Biotechnology Information, Library of Medicine, NIH, Bethesda, MD 20894, USA
    J Proteome Res 7:3102-13. 2008
    ..The data related to this study are freely available upon request...
  7. ncbi request reprint Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 21:3726-32. 2005
    ..The characteristics of the noise can only be uncovered once a spectrum is given. We wish to overcome such issues...
  8. pmc Assigning statistical significance to proteotypic peptides via database searches
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Proteomics 74:199-211. 2011
    ..The advantage of including proteotypic information is evidenced by its superior retrieval performance when compared to regular database searches...
  9. pmc Improving peptide identification sensitivity in shotgun proteomics by stratification of search space
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
    J Proteome Res 12:2571-81. 2013
    ..Our results show that this scheme can significantly improve retrieval performance compared to those of search strategies that assign equal Bonferroni correction factors to all qualified peptides...
  10. pmc Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
    J Am Soc Mass Spectrom 25:57-70. 2014
    ..MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html. ..
  11. pmc Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e22647. 2011
    ..ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/CoinedPValues.html...
  12. pmc Accuracy evaluation of the unified P-value from combining correlated P-values
    Gelio Alves
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 9:e91225. 2014
    ..However, when the correlation information is available, the weighting-capable statistical method, first introduced by Brown and recently modified by Hou, seems to perform the best amongst the methods investigated...