Gelio Alves

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi 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

Detail Information

Publications9

  1. ncbi 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
    ..We also address the importance of using spectrum-specific statistics and possible improvement on the current calibration protocol. The spectra used for statistical (E-value) calibration are freely available upon request...
  2. ncbi 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
    ..OPEN PEER REVIEW: Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section...
  3. ncbi 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. ncbi 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. ncbi 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...
  6. ncbi 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...
  7. ncbi 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...
  8. ncbi 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
    ..Other important features of RAId include its potential in de novo sequencing alone and the ease of incorporating post-translational modifications...
  9. ncbi 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...