Christine Vogel Assistant Professor of Biology Ph.D. (Computational and Structural Biology), University of Cambridge; M.S. (Mathematical Biology), University College London; Masters (Biochemistry/Molecular Biology), Jena, Germany. Office Address: New York University Department of Biology Center for Genomics and Systems Biology 12 Waverly Place, Room 403 New York, NY 10003 Email: Phone: 212-998-3976 List of Publications from Pubmed List of citations from Google Scholar Lab Homepage

Research

My research revolves around proteins, their properties, evolution, and expression patterns. I am a systems biologist who uses statistical and computational tools, large-scale quantitative mass spectrometry, and molecular biology techniques to study the dynamics of the cellular proteome.

Quantitative shotgun proteomics

Until recently, it was impossible to accurately estimate the absolute and relative concentrations of thousands of proteins in complex biological samples. Our quantitative proteomics technology called APEX (Absolute Protein Expression Index, Nature Biotech, 2007 25(1)) allows us to do so – for everything from bacteria to yeast and human. Mass spectrometry data is highly complex, and we continuously improve our data mining methods with respect to the identification and quantification of proteins. For example, in MSpresso and MSnet (Bioinformatics 2009a, b), we use mRNA expression data and protein functional network information, respectively, to increase the number of proteins that were identified by mass spectrometry analysis.

The dynamics of protein expression The expression levels of proteins are determined by transcription, translation, mRNA and protein stability, and these processes are regulated by a plethora of mechanisms. Thus, the relationship between protein and mRNA expression levels varies across organisms and sets of proteins (Mol BioSystems, 2009 5(12)). Using yeast and human cell lines, we characterize the proteome and transcriptome under normal conditions and in response to stimuli. Time course data allows us to describe cellular processes as dynamical systems and will enable us to better understand protein expression regulation – both mathematically and biologically.

Proteomics characterization of translation regulators The human genome encodes ~600 proteins with RNA-binding domains, and many of these proteins are putative translation regulators. Using quantitative proteomics approaches and complementary molecular biology techniques, we characterize the impact of RNA-binding proteins on the 'translation regulatory network'. One example is Musashi-1 which is a key regulator involved in brain tumor formation, and we analyze its impact on the human proteome and transcriptome. This project is carried out in collaboration with Luiz Penalva (UTexas San Antonio).

Areas of Research/Interest

mass spectrometry, quantitative proteomics, dynamical systems, translation regulation, stress response, protein evolution

Fellowships/Honors

Human Frontier Science Program (2005-2008); Boehringer Ingelheim Fonds Pre-doctoral Fellowship (2001-2004); German National Merit Foundation (1998-2000)

Publications

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet   (2012 Apr) Vogel C, Marcotte EM

Protein expression regulation under oxidative stress. Mol Cell Proteomics   (2011 Dec) Vogel C, Silva GM, Marcotte EM

Translation's coming of age. Mol Syst Biol   (2011 May 24) Vogel C

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. J Proteome Res   (2011 Jul 1) Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM

Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics   (2010 Dec) Laurent JM, Vogel C, Kwon T, Craig SA, Boutz DR, Huse HK, Nozue K, Walia H, Whiteley M, Ronald PC, Marcotte EM

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol   (2010 Aug 24) Vogel C, Abreu Rde S, Ko D, Le SY, Shapiro BA, Burns SC, Sandhu D, Boutz DR, Marcotte EM, Penalva LO

Global signatures of protein and mRNA expression levels. Mol Biosyst   (2009 Dec) de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C

Absolute abundance for the masses. Nat Biotechnol   (2009 Sep) Vogel C, Marcotte EM

Mining gene functional networks to improve mass-spectrometry-based protein identification. Bioinformatics   (2009 Nov 15) Ramakrishnan SR, Vogel C, Kwon T, Penalva LO, Marcotte EM, Miranker DP

A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation. RNA Biol   (2009 Sep-Oct) Galante PA, Sandhu D, de Sousa Abreu R, Gradassi M, Slager N, Vogel C, de Souza SJ, Penalva LO

Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics   (2009 Jun 1) Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R

Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes. J Biol Chem   (2009 May 1) 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

Buffering by gene duplicates: an analysis of molecular correlates and evolutionary conservation. BMC Genomics   (2008) Hannay K, Marcotte EM, Vogel C

The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics   (2008) Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res   (2009 Jan) Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J

Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat Protoc   (2008) Vogel C, Marcotte EM

The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol   (2007 Mar 2) Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol   (2007 Jan) Lu P, Vogel C, Wang R, Yao X, Marcotte EM

The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res   (2007 Jan) Wilson D, Madera M, Vogel C, Chothia C, Gough J

Duplication, divergence and formation of novel protein topologies. Bioessays   (2006 Oct) Vogel C, Morea V

Protein family expansions and biological complexity. PLoS Comput Biol   (2006 May) Vogel C, Chothia C

The relationship between domain duplication and recombination. J Mol Biol   (2005 Feb 11) Vogel C, Teichmann SA, Pereira-Leal J

Glucosinolate biosynthesis: demonstration and characterization of the condensing enzyme of the chain elongation cycle in Eruca sativa. Phytochemistry   (2004 Apr) Falk KL, Vogel C, Textor S, Bartram S, Hick A, Pickett JA, Gershenzon J

Supra-domains: evolutionary units larger than single protein domains. J Mol Biol   (2004 Feb 20) Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA

Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol   (2004 Apr) Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA

The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res   (2004 Jan 1) Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J

The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development   (2003 Dec) Vogel C, Teichmann SA, Chothia C

Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res   (2003 Aug) Bankier AT, Spriggs HF, Fartmann B, Konfortov BA, Madera M, Vogel C, Teichmann SA, Ivens A, Dear PH

Evolution of the protein repertoire. Science   (2003 Jun 13) Chothia C, Gough J, Vogel C, Teichmann SA