Publications

Research

• Vogel C, Marcotte EM. Calculating absolute and relative protein expression from mass spectrometry based data. Nature Protocols, 2008 in press. pre-print (to come) / accompanying website


• Rangan Latha*, Vogel C*, Srivastava A. Analysis of context sequence surrounding translation initiation sites from complete genome model plants. Molecular Biotechnology, 2008 in press pre-print


• Lu P*, Vogel C*, Wang R*, Yao X, Marcotte EM. An estimate of relative contributions of transcriptional and translational regulation by absolute protein expression profiling. 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 PDF


• 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, Chothia C. Protein family expansions and biology complexity. PLoS Computational Biology 2006; Vol. 2, No. 5, e48; PDF/ Supplementary Website
  


• 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
  


• 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/ Supplements
  

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
  

Invited / Reviews / Book Chapters

• Vogel C. Review of Anna Tramontano's book on "Protein Structure Prediction", Wiley-VCH. Quarterly Reviews of Biology. 2006
  


• Vogel C, Morea V. Duplication, divergence and the formation of novel protein topologies. BioEssays. 2006;28(10):973-8. pre-print
  


• 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
  


• 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
  


• Chothia C, Gough J, Vogel C, Teichmann SA. Evolution of the protein repertoire. Science. 2003;300(5626):1701-3. pre-print
  

Projects

Presentations (selected)

• 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.