Christine Vogel

Associate Professor of Biology; Director, Biology PhD Program

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

Integrative systems biology, quantitative proteomics, dynamic systems, translation regulation, stress response, protein evolution

Research

Our research revolves around proteins, their properties and expression regulation in response to environmental stress. Our lab integrates statistical and computational tools, sequencing, large-scale quantitative mass spectrometry, and molecular biology techniques to study the dynamics of the cellular proteome.

Fellowships/Honors

  • 2017 Biognosys Research Challenge Award (1st prize)
  • 2017 Robert J. Cotter New Investigator Award by the US Human Proteome Organization
  • 2013 NYU Whitehead Fellowship
  • 2011-2012 Vivian G. Prins Fellowship by New York University
  • 2005-2008 Human Frontier Science Program
  • 2001-2004 Boehringer Ingelheim Fonds Pre-doctoral Fellowship
  • 1998-2000 German National Merit Foundation

Publications

Date of these PubMed search results: March 24 2020
Get the current Pubmed search results

  1. A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes.
    Hum Mutat (2020 Jan 12) PMID: 31930623
    Li GXH, Munro D, Fermin D, Vogel C, Choi H
  2. Polyubiquitin Chains Linked by Lysine Residue 48 (K48) Selectively Target Oxidized Proteins In Vivo.
    Antioxid Redox Signal (2019 Nov 20) PMC6798811 free full-text archive
    Manohar S, Jacob S, Wang J, Wiechecki KA, Koh HWL, Simoes V, Choi H, Vogel C, Silva GM
  3. iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery.
    NPJ Syst Biol Appl (2019) PMC6616462 free full-text archive
    Koh HWL, Fermin D, Vogel C, Choi KP, Ewing RM, Choi H
  4. Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons.
    Elife (2019 Jun 3) PMC6594754 free full-text archive
    An D, Fujiki R, Iannitelli DE, Smerdon JW, Maity S, Rose MF, Gelber A, Wanaselja EK, Yagudayeva I, Lee JY, Vogel C, Wichterle H, Engle EC, Mazzoni EO
  5. Exploiting Interdata Relationships in Next-generation Proteomics Analysis.
    Mol Cell Proteomics (2019 Aug 9) PMC6692783 free full-text archive
    Vitrinel B, Koh HWL, Mujgan Kar F, Maity S, Rendleman J, Choi H, Vogel C
  6. Nucleobindins and encoded peptides: From cell signaling to physiology.
    Adv Protein Chem Struct Biol (2019) PMID: 31036300
    Leung AK, Ramesh N, Vogel C, Unniappan S
  7. Integration of large-scale multi-omic datasets: a protein-centric view.
    Curr Opin Syst Biol (2018 Oct) PMC6426335 free full-text archive
    Rendleman J, Choi H, Vogel C
  8. Site-Specific K63 Ubiquitinomics Provides Insights into Translation Regulation under Stress.
    J Proteome Res (2019 Jan 4) PMC6465141 free full-text archive
    Back S, Gorman AW, Vogel C, Silva GM
  9. EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data.
    J Proteome Res (2019 Feb 1) PMC6433620 free full-text archive
    Koh HWL, Zhang Y, Vogel C, Choi H
  10. New insights into the cellular temporal response to proteostatic stress.
    Elife (2018 Oct 12) PMC6185107 free full-text archive
    Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YBM, Lei A, Parker B, Landthaler M, Freeberg L, Kuersten S, Choi H, Vogel C
  11. PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes.
    Mol Omics (2018 Jun 12) PMC6115748 free full-text archive
    Li GXH, Vogel C, Choi H
  12. Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.
    Cell Rep (2018 Apr 10) PMC5987223 free full-text archive
    Tchourine K, Vogel C, Bonneau R
  13. Phenazines Regulate Nap-Dependent Denitrification in Pseudomonas aeruginosa Biofilms.
    J Bacteriol (2018 May 1) PMC5892114 free full-text archive
    Lin YC, Sekedat MD, Cornell WC, Silva GM, Okegbe C, Price‑Whelan A, Vogel C, Dietrich LEP
  14. PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments.
    NPJ Syst Biol Appl (2018) PMC5736550 free full-text archive
    Teo G, Bin Zhang Y, Vogel C, Choi H
  15. Quantifying protein (dis)order.
    Science (2017 Feb 24) PMID: 28232536
    Vogel C
  16. Quantifying gene expression: the importance of being subtle.
    Mol Syst Biol (2016 Oct 20) PMC5081482 free full-text archive
    Silva GM, Vogel C
  17. 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
  18. A synopsis on aging-Theories, mechanisms and future prospects.
    Ageing Res Rev (2016 Aug) PMC5991498 free full-text archive
    da Costa JP, Vitorino R, Silva GM, Vogel C, Duarte AC, Rocha‑Santos T
  19. Systems Approaches to the Eukaryotic Stress Response.
    PLoS Comput Biol (2016 Mar) PMC4786331 free full-text archive
    Vogel C
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains.
    J Proteome Res (2014 May 2) PMC4012837 free full-text archive
    Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM
  30. RNA binding protein-mediated post-transcriptional gene regulation in medulloblastoma.
    Mol Cells (2014 May) PMC4044306 free full-text archive
    Bish R, Vogel C
  31. Evolution. Protein expression under pressure.
    Science (2013 Nov 29) PMID: 24288321
    Vogel C
  32. 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
  33. PECA: a novel statistical tool for deconvoluting time-dependent gene expression regulation.
    J Proteome Res (2014 Jan 3) PMID: 24229407
    Teo G, Vogel C, Ghosh D, Kim S, Choi H
  34. 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
  35. The proteomic response to mutants of the Escherichia coli RNA degradosome.
    Mol Biosyst (2013 Apr 5) PMC3709862 free full-text archive
    Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C
  36. 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
  37. Label-free protein quantitation using weighted spectral counting.
    Methods Mol Biol (2012) PMC3654649 free full-text archive
    Vogel C, Marcotte EM
  38. 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
  39. Protein expression regulation under oxidative stress.
    Mol Cell Proteomics (2011 Dec) PMC3237073 free full-text archive
    Vogel C, Silva GM, Marcotte EM
  40. Translation's coming of age.
    Mol Syst Biol (2011 May 24) PMC3130562 free full-text archive
    Vogel C
  41. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.
    J Proteome Res (2011 Jul 1) PMC3128686 free full-text archive
    Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM
  42. 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
  43. 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
  44. 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
  45. Absolute abundance for the masses.
    Nat Biotechnol (2009 Sep) PMC4979316 free full-text archive
    Vogel C, Marcotte EM
  46. 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
  47. 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
  48. Integrating shotgun proteomics and mRNA expression data to improve protein identification.
    Bioinformatics (2009 Jun 1) PMC2682515 free full-text archive
    Ramakrishnan SR, Vogel C, Prince JT, Li Z, Penalva LO, Myers M, Marcotte EM, Miranker DP, Wang R
  49. Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes.
    J Biol Chem (2009 May 1) 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
  50. 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
  51. The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.
    BMC Bioinformatics (2008 Dec 9) 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
  52. 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
  53. Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
    Nat Protoc (2008) PMID: 18772871
    Vogel C, Marcotte EM
  54. The (in)dependence of alternative splicing and gene duplication.
    PLoS Comput Biol (2007 Mar 2) PMC1808492 free full-text archive
    Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X
  55. 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
  56. 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
  57. Duplication, divergence and formation of novel protein topologies.
    Bioessays (2006 Oct) PMID: 16998824
    Vogel C, Morea V
  58. Protein family expansions and biological complexity.
    PLoS Comput Biol (2006 May) PMC1464810 free full-text archive
    Vogel C, Chothia C
  59. The relationship between domain duplication and recombination.
    J Mol Biol (2005 Feb 11) PMID: 15663950
    Vogel C, Teichmann SA, Pereira‑Leal J
  60. 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
  61. 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
  62. 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
  63. The SUPERFAMILY database in 2004: additions and improvements.
    Nucleic Acids Res (2004 Jan 1) PMC308851 free full-text archive
    Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J
  64. 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
  65. 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
  66. Evolution of the protein repertoire.
    Science (2003 Jun 13) PMID: 12805536
    Chothia C, Gough J, Vogel C, Teichmann SA