Lewis Y Geer

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes
    Viswanadham Sridhara
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD, USA
    Database (Oxford) 2011:bar019. 2011
  2. pmc Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge
    Viswanadham Sridhara
    National Library of Medicine, NIH, Bethesda, Maryland, USA
    Proteome Sci 10:8. 2012
  3. pmc Automated annotation of chemical names in the literature with tunable accuracy
    Jun D Zhang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Cheminform 3:52. 2011
  4. pmc The NCBI BioSystems database
    Lewis Y Geer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D492-6. 2010
  5. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:D5-12. 2007
  6. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D5-15. 2009
  7. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
  8. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:D13-21. 2008
  9. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
  10. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D13-25. 2012

Collaborators

Detail Information

Publications26

  1. pmc Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes
    Viswanadham Sridhara
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD, USA
    Database (Oxford) 2011:bar019. 2011
    ..sapiens, M. musculus and D. melanogaster. The method scales automatically, so as the amount of experimental phosphoproteomics data increases, more conserved phosphorylation sites may be revealed...
  2. pmc Increasing peptide identifications and decreasing search times for ETD spectra by pre-processing and calculation of parent precursor charge
    Viswanadham Sridhara
    National Library of Medicine, NIH, Bethesda, Maryland, USA
    Proteome Sci 10:8. 2012
    ..abstract:..
  3. pmc Automated annotation of chemical names in the literature with tunable accuracy
    Jun D Zhang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Cheminform 3:52. 2011
    ..abstract:..
  4. pmc The NCBI BioSystems database
    Lewis Y Geer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D492-6. 2010
    ....
  5. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:D5-12. 2007
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  6. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D5-15. 2009
    ..Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  7. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
    ..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  8. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 36:D13-21. 2008
    ..Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  9. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  10. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D13-25. 2012
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  11. pmc MMDB: Entrez's 3D-structure database
    Jie Chen
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 31:474-7. 2003
    ..MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html...
  12. pmc CDD: a Conserved Domain Database for protein classification
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:D192-6. 2005
    ..Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system...
  13. pmc CDD: conserved domains and protein three-dimensional structure
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:D348-52. 2013
    ..To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts...
  14. pmc MMDB: annotating protein sequences with Entrez's 3D-structure database
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:D298-300. 2007
    ..The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure)...
  15. pmc CDD: specific functional annotation with the Conserved Domain Database
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:D205-10. 2009
    ....
  16. pmc CDD: a database of conserved domain alignments with links to domain three-dimensional structure
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:281-3. 2002
    ..CD-Search runs reverse-position-specific BLAST (RPS-BLAST), a variant of the widely used PSI-BLAST algorithm. CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST service at http://www.ncbi.nlm.nih.gov/BLAST...
  17. pmc CDD: a Conserved Domain Database for the functional annotation of proteins
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D225-9. 2011
    ..CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml...
  18. ncbi request reprint DBParser: web-based software for shotgun proteomic data analyses
    Xiaoyu Yang
    National Institutes of Health, 10 Center Drive, Room 3D42, Bethesda, Maryland 20892 1262, USA
    J Proteome Res 3:1002-8. 2004
    ..DBParser actively links to the primary mass spectral data and to public online databases such as NCBI, GO, and Swiss-Prot in order to structure contextually specific reports for biologists and biochemists...
  19. pmc MMDB: 3D structures and macromolecular interactions
    Thomas Madej
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D461-4. 2012
    ..MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure...
  20. pmc CDD: a curated Entrez database of conserved domain alignments
    Aron Marchler-Bauer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 31:383-7. 2003
    ..This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members...
  21. pmc Database resources of the National Center for Biotechnology Information
    David L Wheeler
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:D173-80. 2006
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov...
  22. pmc CDART: protein homology by domain architecture
    Lewis Y Geer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 12:1619-23. 2002
    ..Searches can be further refined by taxonomy and by selecting domains of interest. CDART is available at http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi...
  23. ncbi request reprint Open mass spectrometry search algorithm
    Lewis Y Geer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Proteome Res 3:958-64. 2004
    ..At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets...
  24. pmc MMDB: Entrez's 3D-structure database
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:249-52. 2002
    ..MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure...
  25. ncbi request reprint Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry
    Ming Xu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Proteome Res 4:300-5. 2005
    ..Many spectra examined that do not have significant matches are assessed to have good spectral quality, indicating that advances in search methods may yield substantial improvements in results...
  26. pmc Modeling the evolution of protein domain architectures using maximum parsimony
    Jessica H Fong
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    J Mol Biol 366:307-15. 2007
    ..Domain architecture "neighbors" identified in this way may lead to new insights about the evolution of protein function...