3 Publications

Papers

Publications in PubMed

Publications in Google Scholar

/* = joint first (or last) authors

2014

  • Tchourine KM*, Poultney CS*, Wang L*, Silva GM, Manohar S, Mueller CL, Bonneau R, Vogel C. One third of dynamic gene expression profiles can be predicted by simple rate equations. Molecular BioSystems (in press)
  • Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM. Mechanisms of post-transcriptional regulation are highly-conserved between Pseudomonas aeruginosa reference strains. J Proteomics Research 2014 Apr 17
  • Bish R, Vogel C. RNA Binding Protein-Mediated Post-Transcriptional Gene Regulation in Medulloblastoma. Mol Cells 2014 Mar 6. doi: 10.14348/molcells.2014.0008

2013

  • Vogel C. Protein expression under pressure. Science. 2013 (Perspective, in press)
  • Teo G*, Vogel C*, Ghosh D, Kim S, Choi H. Statistical analysis of significant RNA and protein concentration changes in time course data. J Proteome Research. 2013 (in press)
  • Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Buhlmann P. Statistical approach to protein quantification. Mol Cell Proteomics. 2013 (in press)
  • Kuersten S, Radek A, Vogel C*, Penalva LOF*. Translation regulation gets its 'omics' moment. Wiley Interdisciplinary Reviews RNA. 2013 (in press)
  • Zhou L*, Zhang AB*, Wang R, Marcotte EM, Vogel C. The proteomic response to mutants of the Escherichia coli RNA degradosome. Molecular BioSystems. 2013, 9(4):750-7

2012

  • Vo DT, Subramaniam D, Remke M, Burton TL, Uren PJ, Gelfond JA, Abreu RdS, Burns SC, Qiao M, Suresh U, Korshunov A, Dubuc AM, Northcott PA, Smith AD, Pfister SM, Taylor MD, Janga SC, Anant S, Vogel C, Penalva LPO. The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosisThe American Journal of Pathology. 2012, 181(5):1762-72.
  • Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analysis. Nature Reviews Genetics. 2012, 13(4):227-32
  • Vogel C, Marcotte EM. Label-free protein quantitation using weighted spectral counting Methods in Molecular Biology (Humana Press, book chapter). 2012, 893:321-41

2011

  • Vogel C, Silva GM, Marcotte EM.. Protein Expression Regulation under Oxidative Stress. Mol Cell Proteomics. 2011 Dec;10(12):M111.009217. Epub 2011 Sep 20.
  • Vogel C. Translation's coming of age. (News and Views articleMolecular Systems Biology. 2011 May 24;7:498.
  • Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res. 2011 Jul 1;10(7):2949-58. Epub 2011 Apr 29.

2010

  • Vogel C*, de Sousa Abreu R*, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR,Marcotte EM, Penalva LO. Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Molecular Systems Biology. 2010 (6) 400 
    The work for this paper was presented in a free online webinar about 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
    The paper was also featured in a News and Views article by Joshua Plotkin (UPenn), in the same issue of Molecular Systems Biology
  • Laurent J, Vogel C*, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics. 2010, 10(23):4209-12.

2009

  • 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

2008

  • 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

2007

  • 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-printRecommended 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-printSUPERFAMILY database

2006

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

2005

  • Vogel C, Teichmann SA, Pereira-Leal J. The relationship between domain duplication and recombination. J Mol Biology 2005;346(1):355-65. Pre-print 

2004

  • 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-printSupplementary 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 sativaPhytochemistry. 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-printSUPERFAMILY 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-printSupplementary 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 

2003

  • 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 
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