Some recent papers from the group

Costello JL, Kershaw CJ, Castelli LM, Talavera D, Rowe W, Sims PFG, Ashe MP,
Grant CM, Hubbard SJ, Pavitt GD. Dynamic changes in eIF4F-mRNA interactions
revealed by global analyses of environmental stress responses. Genome Biol. 2017
Oct 27;18(1):201. doi: 10.1186/s13059-017-1338-4. PubMed PMID: 29078784; PubMed
Central PMCID: PMC5660459.

Miller MAE, O’Cualain R, Selley J, Knight D, Karim MF, Hubbard SJ, Johnson GN.
Dynamic Acclimation to High Light in Arabidopsis thaliana Involves Widespread
Reengineering of the Leaf Proteome. Front Plant Sci. 2017 Jul 20;8:1239. doi:
10.3389/fpls.2017.01239. eCollection 2017. PubMed PMID: 28775726; PubMed Central
PMCID: PMC5517461.

Jarnuczak AF, Lee DC, Lawless C, Holman SW, Eyers CE, Hubbard SJ. Analysis of
Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute
Quantitative Proteomics. J Proteome Res. 2016 Sep 2;15(9):2945-59. doi:
10.1021/acs.jproteome.6b00048. Epub 2016 Aug 8. PubMed PMID: 27454336.

Mackenzie RJ, Lawless C, Holman SW, Lanthaler K, Beynon RJ, Grant CM, Hubbard
SJ, Eyers CE. Absolute protein quantification of the yeast chaperome under
conditions of heat shock. Proteomics. 2016 Aug;16(15-16):2128-40. doi:
10.1002/pmic.201500503. Epub 2016 Jul 22. PubMed PMID: 27252046; PubMed Central
PMCID: PMC4996341.

Lawless C, Holman SW, Brownridge P, Lanthaler K, Harman VM, Watkins R, Hammond DE, Miller RL, Sims PF, Grant CM, Eyers CE, Beynon RJ, Hubbard SJ. Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring. Mol Cell Proteomics. 2016 Jan 10. pii: mcp.M115.054288. [Epub ahead of print] PubMed PMID: 26750110

Buckley M, Fariña RA, Lawless C, Tambusso PS, Varela L, Carlini AA, Powell JE, Martinez JG. Collagen Sequence Analysis of the Extinct Giant Ground Sloths Lestodon and Megatherium. PLoS One. 2015 Nov 5;10(11):e0139611. doi:10.1371/journal.pone.0139611. eCollection 2015. Erratum in: PLoS One.2015;10(12):e0144793. PubMed PMID: 26540101; PubMed Central PMCID: PMC4634953.

Kershaw CJ, Costello JL, Talavera D, Rowe W, Castelli LM, Sims PF, Grant CM, Ashe MP, Hubbard SJ, Pavitt GD. Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p. Sci Rep. 2015 Oct 23;5:15518. doi: 10.1038/srep15518. PubMed PMID: 26493364; PubMed Central PMCID: PMC4616039.

Qi D, Zhang H, Fan J, Perkins S, Pisconti A, Simpson DM, Bessant C, Hubbard S, Jones AR. The mzqLibrary–An open source Java library supporting the HUPO-PSI quantitative proteomics standard. Proteomics. 2015 Sep;15(18):3152-62. doi:10.1002/pmic.201400535. Epub 2015 Jul 14. PubMed PMID: 26037908.

Lilley KS, Beynon RJ, Eyers CE, Hubbard SJ. Focus on Quantitative Proteomics. Proteomics. 2015 Sep;15(18):3101-3. doi: 10.1002/pmic.201570163. PubMed PMID: 26372724.

Castelli LM, Talavera D, Kershaw CJ, Mohammad-Qureshi SS, Costello JL, Rowe W, Sims PF, Grant CM, Hubbard SJ, Ashe MP, Pavitt GD. The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation. PLoS Genet. 2015 May 14;11(5):e1005233. doi: 10.1371/journal.pgen.1005233. eCollection 2015 May. PubMed PMID: 25973932; PubMed Central PMCID: PMC4431810.

Jarnuczak AF, Eyers CE, Schwartz JM, Grant CM, Hubbard SJ. Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae. Proteomics. 2015 Sep;15(18):3126-39. doi: 10.1002/pmic.201400527. Epub 2015 Apr 10. PubMed PMID: 25689132.

Qi D, Lawless C, Teleman J, Levander F, Holman SW, Hubbard S, Jones AR. Representation of selected-reaction monitoring data in the mzQuantML data standard. Proteomics. 2015 Aug;15(15):2592-6. doi: 10.1002/pmic.201400281. Epub 2015 Jun 5. PubMed PMID: 25884107.

Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM. The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response. PLoS Genet. 2015 Jan;11(1) e1004903. doi:10.1371/journal.pgen.1004903. PubMed PMID: 25569619; PubMed Central PMCID: PMC4287443.

Costello J, Castelli LM, Rowe W, Kershaw CJ, Talavera D, Mohammad-Qureshi SS, Sims PFG, Grant CM, Pavitt GD, Hubbard SJ, Ashe MP. Global mRNA selection mechanisms for translation initiation. Genome Biol. 2015;16(1) . PubMed Central PMCID: PMC4302535.

Lee DC, Jones AR, Hubbard SJ. Computional phosphoproteomics: From identification to localisation. Proteomics. 2014 Dec . PubMed PMID: 25475148.

Alberio T, McMahon K, Cuccurullo M, Gethings LA, Lawless C, Zibetti M, Lopiano L, Vissers JP, Fasano M. Verification of a Parkinson’s disease protein signature in T-lymphocytes by multiple reaction monitoring. J Proteome Res. 2014 Aug 1;13(8):3554-61. doi: 10.1021/pr401142p. Epub 2014 Jul 1. PubMed PMID:24946097.

Rowe W, Kershaw CJ, Castelli LM, Costello JL, Ashe MP, Grant CM, Sims PF, Pavitt GD, Hubbard SJ. Puf3p induces translational repression of genes linked to oxidative stress. Nucleic Acids Res. 2014 Jan;42(2) 1026-1041. doi:10.1093/nar/gkt948. PubMed PMID: 24163252; PubMed Central PMCID: PMC3902938.

Brownridge P, Lawless C, Payapilly AB, Lanthaler K, Holman SW, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. Quantitative analysis of chaperone network throughput in budding yeast. Proteomics. 2013 Apr;13(8) 1276-1291. doi:10.1002/pmic.201200412. PubMed PMID: 23420633; PubMed Central PMCID: PMC3791555.

Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR. A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS. 2012 Sep;16(9) 431-442. doi:10.1089/omi.2012.0022. PubMed PMID: 22804616; PubMed Central PMCID: PMC3437040.

Lawless C, Hubbard SJ. Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics. OMICS. 2012 Sep;16(9) 449-456. doi:10.1089/omi.2011.0156. PubMed PMID: 22804685; PubMed Central PMCID: PMC3437044.

Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D. The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics. 2012 Jul;11(7) M111.014381. doi:10.1074/mcp.m111.014381. PubMed PMID: 22375074; PubMed Central PMCID: PMC3394945.

Blakeley P, Overton IM, Hubbard SJ. Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J Proteome Res. 2012 Nov;11(11) 5221-5234. doi:10.1021/pr300411q. PubMed PMID: 23025403; PubMed Central PMCID: PMC3703792.

Eyers CE, Lawless C, Wedge DC, Lau KW, Gaskell SJ, Hubbard SJ. CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches. Mol Cell Proteomics. 2011 Nov;10(11) M110.003384. doi:10.1074/mcp.m110.003384. PubMed PMID: 21813416; PubMed Central PMCID: PMC3226394.

Brownridge P, Holman SW, Gaskell SJ, Grant CM, Harman VM, Hubbard SJ, Lanthaler K, Lawless C, O’Cualain R, Sims P, Watkins R, Beynon RJ. Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy. Proteomics. 2011 Aug;11(15) 2957-2970. doi:10.1002/pmic.201100039. PubMed PMID: 21710569.


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