Christine Vogel

Associate Professor of Biology

Education

Ph.D. (Computational and Structural Biology), University of Cambridge

M.S. (Mathematical Biology), University College London

Masters (Biochemistry/Molecular Biology), Jena, Germany

Areas of Research/Interest

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

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).

Fellowships/Honors

Publications

Quantifying protein (dis)order.
Science (2017 Feb 24) PMID: 28232536
Vogel C

Quantifying gene expression: the importance of being subtle.
Mol Syst Biol (2016 Oct 20) PMC5081482 free full-text archive
Silva GM, Vogel C

Time-course proteomics dataset monitoring HeLa cells subjected to DTT induced endoplasmic reticulum stress.
Data Brief (2016 Sep) PMC4978201 free full-text archive
Cheng Z, Rendleman J, Vogel C

A synopsis on aging-Theories, mechanisms and future prospects.
Ageing Res Rev (2016 Aug) PMID: 27353257
da Costa JP, Vitorino R, Silva GM, Vogel C, Duarte AC, Rocha-Santos T

Systems Approaches to the Eukaryotic Stress Response.
PLoS Comput Biol (2016 Mar) PMC4786331 free full-text archive
Vogel C

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
Mol Syst Biol (2016 Jan 20) PMC4731011 free full-text archive
Cheng Z, Teo G, Krueger S, Rock TM, Koh HW, Choi H, Vogel C

High-throughput analyses of hnRNP H1 dissects its multi-functional aspect.
RNA Biol (2016) PMC4841607 free full-text archive
Uren PJ, Bahrami-Samani E, de Araujo PR, Vogel C, Qiao M, Burns SC, Smith AD, Penalva LO

Next-generation analysis of gene expression regulation--comparing the roles of synthesis and degradation.
Mol Biosyst (2015 Oct) PMC4573910 free full-text archive
McManus J, Cheng Z, Vogel C

Mass spectrometry analysis of K63-ubiquitinated targets in response to oxidative stress.
Data Brief (2015 Sep) PMC4510443 free full-text archive
Silva GM, Vogel C

BONLAC: A combinatorial proteomic technique to measure stimulus-induced translational profiles in brain slices.
Neuropharmacology (2016 Jan) PMC4584208 free full-text archive
Bowling H, Bhattacharya A, Zhang G, Lebowitz JZ, Alam D, Smith PT, Kirshenbaum K, Neubert TA, Vogel C, Chao MV, Klann E

Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins.
Biomolecules (2015 Jul 15) PMC4598758 free full-text archive
Bish R, Cuevas-Polo N, Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C

K63 polyubiquitination is a new modulator of the oxidative stress response.
Nat Struct Mol Biol (2015 Feb) PMC4318705 free full-text archive
Silva GM, Finley D, Vogel C

Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput.
Wiley Interdiscip Rev RNA (2015 May-Jun) PMC4397117 free full-text archive
Bahrami-Samani E, Vo DT, de Araujo PR, Vogel C, Smith AD, Penalva LO, Uren PJ

One third of dynamic protein expression profiles can be predicted by a simple rate equation.
Mol Biosyst (2014 Nov) PMC4183714 free full-text archive
Tchourine K, Poultney CS, Wang L, Silva GM, Manohar S, Mueller CL, Bonneau R, Vogel C

Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains.
J Proteome Res (2014 May 02) PMC4012837 free full-text archive
Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM

RNA binding protein-mediated post-transcriptional gene regulation in medulloblastoma.
Mol Cells (2014 May) PMC4044306 free full-text archive
Bish R, Vogel C

Evolution. Protein expression under pressure.
Science (2013 Nov 29) PMID: 24288321
Vogel C

Statistical approach to protein quantification.
Mol Cell Proteomics (2014 Feb) PMC3916661 free full-text archive
Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Buhlmann P

PECA: a novel statistical tool for deconvoluting time-dependent gene expression regulation.
J Proteome Res (2014 Jan 03) PMID: 24229407
Teo G, Vogel C, Ghosh D, Kim S, Choi H

Translation regulation gets its 'omics' moment.
Wiley Interdiscip Rev RNA (2013 Nov-Dec) PMC3797170 free full-text archive
Kuersten S, Radek A, Vogel C, Penalva LO

The proteomic response to mutants of the Escherichia coli RNA degradosome.
Mol Biosyst (2013 Apr 05) PMC3709862 free full-text archive
Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C

The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis.
Am J Pathol (2012 Nov) PMC3761132 free full-text archive
Vo DT, Subramaniam D, Remke M, Burton TL, Uren PJ, Gelfond JA, de Sousa Abreu R, 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 LO

Label-free protein quantitation using weighted spectral counting.
Methods Mol Biol (2012) PMC3654649 free full-text archive
Vogel C, Marcotte EM

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses.
Nat Rev Genet (2012 Mar 13) PMC3654667 free full-text archive
Vogel C, Marcotte EM

Protein expression regulation under oxidative stress.
Mol Cell Proteomics (2011 Dec) PMC3237073 free full-text archive
Vogel C, Silva GM, Marcotte EM

Translation's coming of age.
Mol Syst Biol (2011 May 24) PMC3130562 free full-text archive
Vogel C

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.
J Proteome Res (2011 Jul 01) PMC3128686 free full-text archive
Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM

Protein abundances are more conserved than mRNA abundances across diverse taxa.
Proteomics (2010 Dec) PMC3113407 free full-text archive
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) PMC2947365 free full-text archive
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) PMC4089977 free full-text archive
de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C

Absolute abundance for the masses.
Nat Biotechnol (2009 Sep) PMC4979316 free full-text archive
Vogel C, Marcotte EM

Mining gene functional networks to improve mass-spectrometry-based protein identification.
Bioinformatics (2009 Nov 15) PMC2773251 free full-text archive
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) PMC2935330 free full-text archive
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 01) PMC2682515 free full-text archive
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 01) PMC2673281 free full-text archive
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 Dec 16) PMC2627895 free full-text archive
Hannay K, Marcotte EM, Vogel C

The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.
BMC Bioinformatics (2008 Dec 09) PMC2639435 free full-text archive
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) PMC2686452 free full-text archive
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) PMID: 18772871
Vogel C, Marcotte EM

The (in)dependence of alternative splicing and gene duplication.
PLoS Comput Biol (2007 Mar 02) PMC1808492 free full-text archive
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) PMID: 17187058
Lu P, Vogel C, Wang R, Yao X, Marcotte EM

The SUPERFAMILY database in 2007: families and functions.
Nucleic Acids Res (2007 Jan) PMC1669749 free full-text archive
Wilson D, Madera M, Vogel C, Chothia C, Gough J

Duplication, divergence and formation of novel protein topologies.
Bioessays (2006 Oct) PMID: 16998824
Vogel C, Morea V

Protein family expansions and biological complexity.
PLoS Comput Biol (2006 May) PMC1464810 free full-text archive
Vogel C, Chothia C

The relationship between domain duplication and recombination.
J Mol Biol (2005 Feb 11) PMID: 15663950
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) PMID: 15110687
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) PMID: 15095989
Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA

Structure, function and evolution of multidomain proteins.
Curr Opin Struct Biol (2004 Apr) PMID: 15093836
Vogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA

The SUPERFAMILY database in 2004: additions and improvements.
Nucleic Acids Res (2004 Jan 01) PMC308851 free full-text archive
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) PMID: 14623821
Vogel C, Teichmann SA, Chothia C

Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum.
Genome Res (2003 Aug) PMC403770 free full-text archive
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) PMID: 12805536
Chothia C, Gough J, Vogel C, Teichmann SA