Publications

Papers

Publications in PubMed

Publications in Google Scholar

* = joint first or last authors with equal contribution

BioRxiv / Other
  • Patient Subtyping Analysis of Baseline Multi-omic Data Reveals Distinct Pre-immune States Predictive of Vaccination Responses. Bayrak CS, Forst C, Jones DR, Gresham D, Pushalkar S, Wu S, Vogel C, Mahal L, Ghedin E, Ross T, García-Sastre A, Zhang B. bioRxiv [Preprint]. 2024 Jan 22:2024.01.18.576213. doi: 10.1101/2024.01.18.576213.
  • Koussa J, Vitrinel B, Whitney P, Kasper B, Mahal L, Vogel C, lustigman S, Salehi-Ashtiani S, Ghedin E. Sex-specific glycosylation of secreted immunomodulatory proteins in the filarial nematode Brugia malayi. https://www.biorxiv.org/content/10.1101/2021.02.24.432741v1
  • Rendleman J, Haizel S, Liu J, Mohammad M, Pressler M, Maity S, Hronová V, Gao Z, Herrmannová A, Lei A, Allgoewer K, Sultanov D, Hinckley W, Szkop K, Topisirovic I, Larsson O, Hatzoglou M, Valášek L, Vogel C. Regulatory start-stop elements in 5’ untranslated regions pervasively modulate translation. https://www.biorxiv.org/content/10.1101/2021.07.26.453809v3
  • Wiechecki K, Manohar S, Silva G, Tchourine G, Jacob J, Valleriani V, Vogel C. Integrative meta-analysis reveals that most yeast proteins are very stable. https://doi.org/10.1101/16529
  • Yao X, Gandhi S, Bish R, Vogel C. iSUMO – integrative prediction of functionally relevant SUMOylated proteins.  http://biorxiv.org/content/early/2016/12/21/056564
2024
  • Stem-loop-induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control. Smirnova AM, Hronová V, Mohammad MP, Herrmannová A, Gunišová S, Petráčková D, Halada P, Coufal Š, Świrski M, Rendleman J, Jendruchová K, Hatzoglou M, Beznosková P, Vogel C, Valášek LS. Cell Rep. 2024 Mar 19;43(4):113976. doi: 10.1016/j.celrep.2024.113976. Online ahead of print. PMID: 38507410
  • Identification of molecular signatures defines the differential proteostasis response in induced spinal and cranial motor neurons. Fiore APZP, Maity S, Jeffery L, An D, Rendleman J, Iannitelli D, Choi H, Mazzoni E, Vogel C. Cell Rep. 2024 Mar 26;43(3):113885. doi: 10.1016/j.celrep.2024.113885. Epub 2024 Mar 7. PMID: 38457337
  • Complex changes in serum protein levels in COVID-19 convalescents. Pushalkar S, Wu S, Maity S, Pressler M, Rendleman J, Vitrinel B, Jeffery L, Abdelhadi R, Chen M, Ross T, Carlock M, Choi H, Vogel C. Sci Rep. 2024 Feb 23;14(1):4479. doi: 10.1038/s41598-024-54534-7.
2023
  • Allgoewer K, Choi H, Vogel C. Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection. Mol Omics. 2023 Feb. doi: 10.1039/D2MO00258B.
  • Fractionation of Native Protein Complexes from Mammalian Cells to Determine the Differential Proteasome Activity and Abundance. Fiore APZP, Vogel C. Bio Protoc. 2023 Sep 20;13(18):e4822. doi: 10.21769/BioProtoc.4822. eCollection 2023 Sep 20. PMID: 37753477 
  • Ring Finger 149-Related Is an FGF/MAPK-Independent Regulator of Pharyngeal Muscle Fate Specification. Vitrinel B, Vogel C, Christiaen L. Int J Mol Sci. 2023 May 16;24(10):8865. doi: 10.3390/ijms24108865. PMID: 37240211
2022
  • Fiore A, Silva A, Filho H, Manucci A, Ribeiro P, Botelho M, Vogel C, Oliveira P, Pagano M, Bruni-Cardoso A. Extracellular matrix stiffness regulates degradation of MST2 via SCFβTrCP. BBA – General Subjects. 2022 Dec. doi: 10.1016/j.bbagen.2022.130238.
  • Wu S, Pushalkar S, Maity S, Pressler M, Rendleman J, Vitrinel B, Carlock M,  Ross T, Choi H, Vogel C. Proteomic Signatures of the Serological Response to Influenza Vaccination in a Large Human Cohort Study. Viruses. 2022 Nov 9. doi: 10.3390/v14112479.
  • Kar F, Vogel C, Hochwagen A. Meiotic DNA breaks activate a streamlined phospho-signaling response that largely avoids protein level changes. Life Sci Alliance. 2022 Sep 1. doi: 10.26508/lsa.202201454.
  • Qin R, Meng G, Pushalkar S, Carlock M, Ross T, Vogel C, Mahal L. Prevaccination Glycan Markers of Response to an Influenza Vaccine Implicate the Complement Pathway. J Proteome Res. 2022 Aug 5. doi: 10.1021/acs.jproteome.2c00251.
  • Johnson K, Conrads T, Drake R, Herr A, Iyengar R, Kelly R, Lundberg E, MacCoss M, Naba A, Nolan G, Pevzner P, Rodland K, Sechi S, Slavov N, Spraggins J, Eyk J, Vidal M, Vogel C, Walt D, Kelleher N. New views of old proteins: clarifying the enigmatic proteome. Mol Cell Proteomics. 2022 Jul. doi: 10.1016/j.mcpro.2022.100254.
  • Wu S, Ross T, Carlock M, Ghedin E, Choi H, Vogel C. Evaluation of determinants of the serological response to the split-inactivated influenza vaccine. Mol Syst Biol. 2022 May. doi: 10.15252/msb.202110724.
  • Vogel C, Balázsi G, Löwer A, Jiang C, Schmid A, Sommer M, Yang L, Münch C, Wang A, Israni-Winger K, Mühlhaus T, Des Marais D, Oster H, Socolovsky M. What differentiates a stress response from responsiveness in general? Cell Syst. 2022 Mar 16. doi: 10.1016/j.cels.2022.02.002.
  • Jackson C, Vogel C. New horizons in the stormy sea of multimodal single-cell data integration. Mol Cell. 2022 Jan 20. doi: 10.1016/j.molcel.2021.12.012.
2021
  • Rajasekaran S, Siddiqui J, Rakijas J, Nicolay B, Lin C, Khan E, Patel R, Morris R, Wyler E, Boukhali M, Balasubramanyam J, Kumar R, Rechem C, Vogel C, Elchuri S, Landthaler M, Obermayer B, Haas W, Dyson N, Miles W. Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses. Commun Biol 2021 Aug 17. doi: 10.1038/s42003-021-02495-2.
  • Levy E, Vogel C. “Structuromics”: another step toward a holistic view of the cell. Cell 2021 Jan 21. doi: 10.1016/j.cell.2020.12.030.
  • Allgoewer K*, Maity S*, Zhao A, Lashua L, Ramgopal M, Balkaran BN, Liu L, Purushwani S, Arévalo MT, Ross TM, Choi H, Ghedin E, Vogel C. New proteomic signatures to distinguish between Zika and dengue infections. Mol Cell Proteomics. 2021 Feb 11:100052. doi: 10.1016/j.mcpro.2021.100052. Epub ahead of print. PMID: 33582300.
2020
  • Zhou Y, Kastritis PL, Dougherty SE, Bouvette J, Hsu AL, Burbaum L, Mosalaganti S, Pfeffer S, Hagen WJH, Förster F, Borgnia MJ, Vogel C, Beck M, Bartesaghi A, Silva GM. Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress. Proc Natl Acad Sci USA. 2020 Aug 27:202005301. doi: 10.1073/pnas.2005301117. Online ahead of print.
  • Vitrinel B, Iannitelli DE, Mazzoni EO, Christiaen L, Vogel C. Simple Method to Quantify Protein Abundances from 1000 Cells. ACS Omega. 2020;5(25):15537-15546. Published 2020 Jun 19. doi:10.1021/acsomega.0c01191
  • Li GX, Munro D, Fermin D, Vogel C, Choi H. Gene-to-Protein-to-Disease: a segmentation-based approach to identify new cancer prognostic signatures of exome sequence variants. Human Mutation in press
2019
  • Bhatt D, Stan RC, Pinhata R, Machado M, Maity S, Cunningham-Rundles C, Vogel C, de Camargo MM. Chemical chaperones reverse early suppression of regulatory circuits during Unfolded Protein Response in B cells from Common Variable Immunodeficiency patients. Clin Exp Immunol. 2019 Dec 20. doi: 10.1111/cei.13410. PubMed PMID: 31859362.
  • Manohar S, Jacob S, Wang JC, Wiechecki KA, Koh HW, Simões V, Choi H, Vogel C*, Silva GM*. Polyubiquitin chains linked by lysine residue 48 (K48) selectively target oxidized proteins in vivo. Antioxid Redox Signal. 2019 Sep 4. doi: 10.1089/ars.2019.7826. PubMed PMID: 31482721.
  • Vitrinel B, Koh HW, Kar FM, Maity S, Rendleman J, Choi H, Vogel C. Exploiting interdata relationships in next-generation proteomics analysis. Mol Cell Proteomics. 2019 August 9. pii: mcp.MR118.001246. doi: 10.1074/mcp.MR118.001246. PubMed PMID: 31126983.
  • Koh HWL, Fermin D, Vogel C, Choi KP, Ewing RM, Choi H. iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery. NPJ Syst Biol Appl. 2019 Jul 9;5:22. doi: 10.1038/s41540-019-0099-y. PubMed PMID: 31312515.
  • 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. Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons. Elife. 2019 Jun 3;8. pii: e44423. doi: 10.7554/eLife.44423. PubMed PMID: 31157617.
  • Leung AK, Ramesh N, Vogel C, Unniappan S. Nucleobindins and encoded peptides: From cell signaling to physiology. Adv Protein Chem Struct Biol. 2019;116:91-133. doi: 10.1016/bs.apcsb.2019.02.001. Review. PubMed PMID: 31036300.
  • Koh HWL, Zhang Y, Vogel C*, Choi H*. EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data. J Proteome Res. 2019 Feb 1;18(2):748-752. doi: 10.1021/acs.jproteome.8b00483. PubMed PMID: 30411623.
  • Back S, Gorman AW, Vogel C*, Silva GM*. Site-Specific K63 Ubiquitinomics Provides Insights into Translation Regulation under Stress. J Proteome Res. 2019 Jan 4;18(1):309-318. doi: 10.1021/acs.jproteome.8b00623. PubMed PMID: 30489083.
2018
  • 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. New insights into the cellular temporal response to proteostatic stress. Elife. 2018 Oct 1;7. pii: e39054. doi: 10.7554/eLife.39054. PubMed PMID: 30272558. https://elifesciences.org/articles/39054
  • Rendleman JR, Choi HW, Vogel C. Integration of large-scale multi-omic datasets: a protein-centric view. Current Opinion Systems Biology 2018 Review https://doi.org/10.1016/j.coisb.2018.09.001
  • Li GX, Vogel C, Choi HW. PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes. Molecular Omics 2018 Jun 12;14(3):197-209. doi: 10.1039/c8mo00027a. PubMed PMID: 29876573.
  • Tchourine K, Vogel C, Bonneau R. Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.  Cell Reports. 2018 Apr 10;23(2):376-388. doi: 10.1016/j.celrep.2018.03.048. PubMed PMID: 29641998.
  • Lin YC, Sekedat MD, Cornell WC, Silva GM, Okegbe C, Price-Whelan A, Vogel C, Dietrich LEP. Phenazines regulate Nap-dependent denitrification in Pseudomonas aeruginosa biofilms. J Bacteriology. 2018 Apr 9;200(9). pii: e00031-18. doi: 10.1128/JB.00031-18. PubMed PMID: 29463605.
2017
  • Teo G, Bin Zhang Y, Vogel C*, Choi H*. PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments. NPJ Systems Biology & Appl. 2017 Dec 19;4:3 
  • Vogel C. Quantifying protein (dis)order. Science. 2017 Feb 24;355(6327):794-795. doi: 10.1126/science.aam8036. Perspective
2016
  • Silva GM, Vogel C. Quantifying gene expression: the importance of being subtle. Molecular Systems Biology. 2016 News & Views
  • da Costa JP, Vitorino R, Silva GM, Vogel C, Duarte AC, Rocha-Santos T. A synopsis on aging-Theories, mechanisms and future prospects. Ageing Res Rev. 2016 Aug;29:90-112. doi: 10.1016/j.arr.2016.06.005. Epub 2016 Jun 25. Review. PubMed PMID: 27353257.
  • Cheng Z, Rendleman J, Vogel C. Time-course proteomics dataset monitoring HeLa cells subjected to DTT induced endoplasmic reticulum stress. Data Brief. 2016 Juy 26;8:1168-72. doi: 10.1016/j.dib.2016.07.038. eCollection 2016 Sep. PubMed PMID: 27547793; PubMed Central PMCID: PMC4978201.
  • Cheng Z, Teo G, Krueger S, Rock TM, Koh HWL, Choi H, Vogel C. Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress. Molecular Systems Biology. Jan 20;12(1):855. doi: 10.15252/msb.20156423. PubMed PMID: 26792871; PubMed Central PMCID: PMC4731011.
  • Vogel C. Systems Approaches to the Eukaryotic Stress Response. PLoS Comp Biology. Perspective Article as part of the “About my Lab” series. 2016. In Press
  • Uren PJ, Bahrami-Samani E, de Araujo PR, Vogel C, Qiao M, Burns SC, Smith AD, Penalva LO. High-throughput analyses of hnRNP H1 dissects its multi-functional aspect. RNA Biol. 2016 Jan 13:0.
2015
  • McManus JM, Cheng Z, Vogel C. Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation. Molecular BioSystems. Review. 2015 Oct;11(10):2680-9. doi: 10.1039/c5mb00310e.
  • Bish R, Cuevas Polo N,  Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C. Comprehensive protein interactome analysis of a key RNA helicase:detection of novel stress granule proteins. Biomolecules. 2015 Jul 15;5(3):1441-66. doi: 10.3390/biom5031441. PubMed PMID: 26184334.
  • Silva GM, Wei W, Manohar C, Vogel C. Identification and quantification of K63-ubiquitinated proteins in neuronal cells by high-resolution mass spectrometry. Methods in Molecular Biology – Analysis of Post-Translational Modifications and Proteolysis in Neuroscience. Book chapter. Wiley 2015
  • Silva GM, Vogel C. Mass spectrometry analysis of K63-ubiquitinated targets in response to oxidative stress. Data in Brief 2015, Volume 4, Pages 130-134, ISSN 2352-3409, http://dx.doi.org/10.1016/j.dib.2015.05.002.
  • Bowling H, Bhattacharya A, Zhang G, Lebowitz JZ, Alam D, Smith PT, Kirshenbaum K, Neubert TA, Vogel C, Chao MV, Klann E. BONLAC: A Combinatorial Proteomic Technique to Measure Stimulus-induced Translational Profiles in Brain Slices. Neuropharmacology. 2015 Jul 20. pii: S0028-3908(15)30023-X. doi: 10.1016/j.neuropharm.2015.07.017. [Epub ahead of print] Review. PubMed PMID: 26205778.
  • Silva GM, Finley D, Vogel C. K63 polyubiquitination as a new modulator of the oxidative stress response. Nature Structural & Molecular Biology 2015 Feb;22(2):116-23. doi: 10.1038/nsmb.2955. Epub 2015 Jan 26.
2014
  • Bahrami-Samani E1, Vo DT, de Araujo PR, Vogel C, Smith AD, Penalva LO, Uren PJ. Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. Wiley Interdiscip Rev RNA. 2014 Dec 16. doi: 10.1002/wrna.1274. 
  • 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. 2014 10(11):2850-62
  • 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
  • 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. 2014 Jan 3;13(1):29-37. doi: 10.1021/pr400855q. Epub 2013 Nov 26.
2013
  • Vogel C. Protein expression under pressure. Science. 2013 Nov 29;342(6162):1052-3. doi: 10.1126/science.1247833.
  • Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Buhlmann P. Statistical approach to protein quantification. Mol Cell Proteomics. 2014 Feb;13(2):666-77. doi: 10.1074/mcp.M112.025445. Epub 2013 Nov 19.
  • Kuersten S, Radek A, Vogel C*, Penalva LOF*. Translation regulation gets its ‘omics’ moment. Wiley Interdisciplinary Reviews RNA. 2013 Nov-Dec;4(6):617-30. doi: 10.1002/wrna.1173. Epub 2013 May 15.
  • 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 prognosis. The 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 article) Molecular 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-print. 
    • News: 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 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-print/ SUPERFAMILY 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-print/ Supplementary 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-print/ Supplementary 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 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/ Supplementary 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