Projects, Papers, Presentations - Christine Vogel

You can hear and see a brief description of one of our research areas at this free online webinar on Genes to Proteins which was part of the AAAS Science Webinar series (Oct 28, 2009). Answers to some of the (many) questions that were asked can be found at the DNA2.0 Forum.

Links (databases)

• Publications in PubMed
  
• APEX Protocol - Perl scripts for APEX calculations
• APEX Quantitative Proteomics Tool - Java based software
• Mass Spectrometry Data Repository - Proteomics RAW data
• MSpresso - Supplementary information
• SUPERFAMILY - protein domain database

Publications

• Vogel C, Marcotte EM. Absolute abundance for the masses. (News and Views article) Nature Biotechnology. 2009 27(9):825-6
• Abreu SR, Penalva LOF, Marcotte EM, Vogel C. Global signatures of protein and mRNA expression levels. Molecular BioSystems. 2009 (in press / Raw data
• Ramakrishnan SR, Vogel C, Kwon T, Penalva LOF, Marcotte EM, Miranker DP. Protein Identification by Integrative Analysis of Shotgun Proteomics and Functional Networks. Bioinformatics. 2009 (E-pub Jul 24) / Raw data
• Galante PAF, Sandhu D, Abreu SA, Gradassi M, Slager N, Vogel C, Souza SJ, Penalva LOF. A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue; identification of potential players in tumor formation. RNA Biology. 2009 6(4) / Raw data
• Ramakrishnan SR*, Vogel C*, Prince J, Li Z, Wang R, Penalva LOF, Myers M, Marcotte EM, Miranker DP. Integrating Shotgun Proteomics and mRNA expression data to Improve Protein Identification. Bioinformatics. 2009 (E-pub Mar 24) MSpresso Supplementary Website / Raw data
• de Sousa Abreu R*, Sanchez-Diaz PC*, Vogel C, Burns SC, Ko D, Burton TL, Vo DT, Chennasamudaram S, Le SY, Shapiro BA, Penalva LO. Genomic Analyses of Musashi1 Downstream Targets Show a Strong Association with Cancer-related Processes. J Biol Chem. 2009 284(18):12125-35 / Raw data
• Hannay K, Marcotte EM, Vogel C. Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics. 2008 Dec 16;9:609.
• Braisted JP*, Kuntumalla S*, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huan ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R. The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics. 2008 Dec 9;9:529 Website
• Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J. SUPERFAMILY - sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res. 2009 Jan;37(Database issue):D380-6
• Vogel C, Marcotte EM. Calculating absolute and relative protein expression from mass spectrometry based data. Nature Protocols, Aug 21, 2008 Pre-print / Supplementary Website
• Rangan Latha*, Vogel C*, Srivastava A. Analysis of context sequence surrounding translation initiation sites from complete genome model plants. Molecular Biotechnology, Humana Press, 2008, vol. 39, no. 3, pp. 207-213 Pre-print
• Lu P*, Vogel C*, Wang R*, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnology, 2007;25(1):117-24. Pre-print. Recommended as News and Views in Nature Biotechnology and Nature Methods.
• Talavera D*, Vogel C*, Orozco M, Teichmann SA, de la Cruz X. The (in)dependence alternative splicing and gene duplication. PLoS Computational Biology, 2007;3(3):e33 Pre-print
• Wilson D, Madera M, Vogel C, Chothia C, Gough J. The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Research Database Issue. 2007;35(Database issue):D308-13. Pre-print/ SUPERFAMILY database
  
• Vogel C, Morea V. Duplication, divergence and the formation of novel protein topologies. BioEssays. 2006;28(10):973-8. Pre-print
  
• Vogel C, Chothia C. Protein family expansions and biology complexity. PLoS Computational Biology 2006; Vol. 2, No. 5, e48; Pre-print/ Supplementary Website
  
• Vogel C. Review of Anna Tramontano's book on "Protein Structure Prediction", Wiley-VCH. Quarterly Reviews of Biology. 2006
  
• Vogel C, Teichmann SA, Pereira-Leal J. The relationship between domain duplication and recombination. J Mol Biology 2005;346(1):355-65. Pre-print
  
• Vogel C, Gough J, Bashton M, Berzuini C, Teichmann SA. Supra-Domains. Evolutionary units larger than protein domains. J Mol Biology 2004; 336, 809-823 Pre-print/ Supplementary Website Recommended as Must-Read in Faculty1000
  
• Vogel C, Bashton M, Kerrison N, Chothia C, Teichmann SA. Structure, function and evolution of multi-domain proteins. Curr Opinion Struc Bio. 2004;14(2):208-16; Pre-print
  
• Kummerfeld SK, Vogel C, Madera M, Pacold M, Teichmann SA. Gene fusion and Fission rates across genomes. ISMB 2004 short paper.
  
• Falk, K, Vogel C, Textor S, Bartram S, Hick A, Pickett JA, Gershenzon J. Glucosinolate biosynthesis: demonstration and characterization of the condensing enzyme of the chain elongation cycle in Eryca sativa. Phytochemistry. 2004 Apr;65(8):1073-84. Pre-print
  
• Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J. The SUPERFAMILY database in 2004: additions and improvements. Nucl. Acids Res. 2004;32(1):D235-9. Pre-print/ SUPERFAMILY website
  
• Vogel C, Chothia C, Teichmann SA. The Immunoglobulin Superfamily Repertoire in Drosophila melanogaster as Compared to Caenorhabditis elegans . Development. 2003 Dec; 130(25):6317-28. Pre-print/ Supplementary Website
Response to Correspondence by Hobert et al. : Vogel C, Chothia C, Teichmann SA. Looking at the bigger picture. Development. 2004; 131(10):2237-8; reply: 2238-40. Pre-print

• Bankier AT, Spriggs HF, Fartmann B, Konfortov BA, Madera M, Vogel C, Teichmann SA, Ivens A, Dear PH. Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res. 2003;13(8):1787-99. Pre-print
• Chothia C, Gough J, Vogel C, Teichmann SA. Evolution of the protein repertoire. Science. 2003;300(5626):1701-3. Pre-print

Book Chapter

• Vogel C, Sasidharan R, Hill EE. The evolution of the protein repertoire. Chapter in "Encyclopedia of Molecular Cell Biology and Molecular Medicine", Wiley-VCH. R.A. Meyers. 2005
  

Presentations (selected)

• Meeting of the RNA Society, Madison WI. 2009
• RECOMB Satellite Meeting on Systems Biology. 2008.
• Barbados Systems Biology Meeting, Barbados, Carribean.2008. Invited participant/speaker
• RECOMB Satellite Meeting on Systems Biology. San Diego, USA, 2007.
• Cambridge Symposium in Honour of Cyrus Chothia. Cambridge, UK 2007
• Human Frontier Science Program - Intergovernmental Conference. Ottawa, Canada, 2007
• RECOMB Satellite Meeting on Systems Biology. Workshop in Algorithmic Biology. San Diego, USA, 2006. Video archive.
• Symposium on Comparative and Functional Genomics, Penn State University, USA, 2005
• STRAPP Workshop on Systems and Genomics, Dresden, Germany, 2004
• British-Hungarian Workshop Human genomics, Budapest, Hungary, 2004
• COPE Workshop on Comparative Analysis of Protein Evolution. Muenster, Germany, 2002
• Cambridge Computational Biology Meeting. Cambridge, UK, 2002
• Genome-to-Life Summer School, Cargese, France, 2002

Theses

• PhD Thesis 2005: 'A domain perspective on protein evolution' with Cyrus Chothia and Sarah Teichmann, University of Cambridge, Cambridge, UK.
• MRes Thesis 2001: 'The Immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans' with Sarah Teichmann at University College London, UK.
• Diploma Thesis 2000: 'Glucosinolate Biosynthesis in Eruca sativa' (summary) with Kim Falk and Jonathan Gershenzon at Max-Planck-Institute for Chemical Ecology, Jena, Germany.