Christine Vogel

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. pmc Integrating shotgun proteomics and mRNA expression data to improve protein identification
    Smriti R Ramakrishnan
    Department of Computer Sciences, The University of Texas at Austin, Austin, TX 78712, USA
    Bioinformatics 25:1397-403. 2009
  2. pmc The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results
    John C Braisted
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Bioinformatics 9:529. 2008
  3. doi request reprint Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
    Christine Vogel
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, MBB 3 210, Austin, Texas 78712, USA
    Nat Protoc 3:1444-51. 2008
  4. ncbi request reprint Duplication, divergence and formation of novel protein topologies
    Christine Vogel
    Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
    Bioessays 28:973-8. 2006
  5. pmc Protein family expansions and biological complexity
    Christine Vogel
    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
    PLoS Comput Biol 2:e48. 2006
  6. pmc Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line
    Christine Vogel
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78229 3900, USA
    Mol Syst Biol 6:400. 2010
  7. pmc MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines
    Taejoon Kwon
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
    J Proteome Res 10:2949-58. 2011
  8. pmc Mining gene functional networks to improve mass-spectrometry-based protein identification
    Smriti R Ramakrishnan
    Department of Computer Sciences, 1 University Station C0500, The University of Texas at Austin, Austin, TX 78712, USA
    Bioinformatics 25:2955-61. 2009
  9. pmc The proteomic response to mutants of the Escherichia coli RNA degradosome
    Li Zhou
    University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX, USA
    Mol Biosyst 9:750-7. 2013
  10. doi request reprint Global signatures of protein and mRNA expression levels
    Raquel de Sousa Abreu
    Children s Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX, USA
    Mol Biosyst 5:1512-26. 2009

Collaborators

Detail Information

Publications21

  1. pmc Integrating shotgun proteomics and mRNA expression data to improve protein identification
    Smriti R Ramakrishnan
    Department of Computer Sciences, The University of Texas at Austin, Austin, TX 78712, USA
    Bioinformatics 25:1397-403. 2009
    ..However, there is often other information available, e.g. the probability of a protein's presence is likely to correlate with its mRNA concentration...
  2. pmc The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results
    John C Braisted
    Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Rockville, MD 20850, USA
    BMC Bioinformatics 9:529. 2008
    ..This predicted spectral count is compared to the protein's observed MS total spectral count during APEX computation of protein abundances...
  3. doi request reprint Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data
    Christine Vogel
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, MBB 3 210, Austin, Texas 78712, USA
    Nat Protoc 3:1444-51. 2008
    ..e., measuring relative protein abundances. APEX-based protein abundances span 3-4 orders of magnitude and are applicable to mixtures of 100s to 1,000s of proteins...
  4. ncbi request reprint Duplication, divergence and formation of novel protein topologies
    Christine Vogel
    Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
    Bioessays 28:973-8. 2006
    ..In spite of this, circular permutations are relatively rare and we discuss possible reasons for their existence...
  5. pmc Protein family expansions and biological complexity
    Christine Vogel
    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
    PLoS Comput Biol 2:e48. 2006
    ..Our work identifies important protein families and provides one explanation of the discrepancy between the total number of genes and the apparent physiological complexity of eukaryotic organisms...
  6. pmc Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line
    Christine Vogel
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78229 3900, USA
    Mol Syst Biol 6:400. 2010
    ....
  7. pmc MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines
    Taejoon Kwon
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
    J Proteome Res 10:2949-58. 2011
    ..We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses...
  8. pmc Mining gene functional networks to improve mass-spectrometry-based protein identification
    Smriti R Ramakrishnan
    Department of Computer Sciences, 1 University Station C0500, The University of Texas at Austin, Austin, TX 78712, USA
    Bioinformatics 25:2955-61. 2009
    ..However, there is often other evidence to suggest that a protein is present and confidence in individual protein identification can be updated accordingly...
  9. pmc The proteomic response to mutants of the Escherichia coli RNA degradosome
    Li Zhou
    University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX, USA
    Mol Biosyst 9:750-7. 2013
    ....
  10. doi request reprint Global signatures of protein and mRNA expression levels
    Raquel de Sousa Abreu
    Children s Cancer Research Institute, University of Texas Health Science Center at San Antonio, TX, USA
    Mol Biosyst 5:1512-26. 2009
    ..We summarize the information that can be derived from comparison of protein and mRNA expression levels and discuss how corresponding sequence characteristics suggest modes of regulation...
  11. pmc Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation
    Kevin Hannay
    Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, University of Texas at Austin, 2500 Speedway, MBB 3 210, Austin, TX 78712, USA
    BMC Genomics 9:609. 2008
    ....
  12. pmc Protein abundances are more conserved than mRNA abundances across diverse taxa
    Jon M Laurent
    Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, TX, USA
    Proteomics 10:4209-12. 2010
    ..0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge...
  13. ncbi request reprint Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    Peng Lu
    Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 2500 Speedway, University of Texas, Austin, Texas 78712, USA
    Nat Biotechnol 25:117-24. 2007
    ..Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms...
  14. pmc The (in)dependence of alternative splicing and gene duplication
    David Talavera
    Molecular Modeling and Bioinformatics Unit, Parc Cientific de Barcelona, Barcelona, Spain
    PLoS Comput Biol 3:e33. 2007
    ..We discuss possible explanations that relate to the order of appearance of AS and GD in a gene family, and to the selection pressure imposed by the environment...
  15. ncbi request reprint The relationship between domain duplication and recombination
    Christine Vogel
    MRC Laboratory of Molecular Biology, Hills Rd, Cambridge CB2 2QH, UK
    J Mol Biol 346:355-65. 2005
    ..Some of the pair-wise domain combinations that are highly duplicated also recur frequently with other partner domains, and thus represent evolutionary units larger than single protein domains, which we term "supra-domains"...
  16. pmc The SUPERFAMILY database in 2004: additions and improvements
    Martin Madera
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 32:D235-9. 2004
    ..In addition, the webserver provides the following standard services: sequence search; keyword search for genomes, superfamilies and sequence identifiers; and multiple alignment of genomic, PDB and custom sequences...
  17. ncbi request reprint Evolution of the protein repertoire
    Cyrus Chothia
    Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 300:1701-3. 2003
    ..Proteins of known structure can be matched to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins of these processes...
  18. pmc The SUPERFAMILY database in 2007: families and functions
    Derek Wilson
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 35:D308-13. 2007
    ..The SUPERFAMILY database can be used for general protein evolution and superfamily-specific studies, genomic annotation, and structural genomics target suggestion and assessment...
  19. ncbi request reprint Supra-domains: evolutionary units larger than single protein domains
    Christine Vogel
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
    J Mol Biol 336:809-23. 2004
    ..Since this is the case for only a quarter of the supra-domains, we provide a list of the most important unknown supra-domains as potential targets for structural genomics projects...
  20. ncbi request reprint Structure, function and evolution of multidomain proteins
    Christine Vogel
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Curr Opin Struct Biol 14:208-16. 2004
    ..Future work will require a domain-centric functional classification scheme and efforts to determine structures of domain combinations...
  21. ncbi request reprint The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity
    Christine Vogel
    MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
    Development 130:6317-28. 2003
    ..These results suggest that the expansion of this protein superfamily is one of the factors that have contributed to the formation of the more complex physiological features that are found in Drosophila...