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2017

Mulvey, CM, Breckels, LM, Geladaki, A, Kočevar Britovšek, N, Nightingale, DJH. Christoforou, C, Elzek, M, Deery MJ, Gatto L, Lilley KS  (2017) Using HyperLOPIT to perform high resolution mapping of the spatial proteome. Nature Protocols 12(6):1110-1135. doi: 10.1038/nprot.2017.026.

Thul PJ et al, Lilley KS, Uhlen, M and Lundberg E. (2017) A subcellular map of the human proteome. Science 356(6340). pii: eaal3321. doi: 10.1126/science.aal3321

Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A. (2017) Tracking the embryonic stem cell transition from ground state pluripotency. Development.  Feb 7. pii: dev.142711. doi: 10.1242/dev.142711.

Minde DP, Dunker AK, Lilley KS. (2017)Time, space and disorder in the expanding proteome universe. Proteomics. Feb 1. doi: 10.1002/pmic.201600399.

Mata CI, Fabre B, Hertog ML, Parsons HT, Deery MJ, Lilley KS, Nicolaï BM. (2017) In-depth characterization of the tomato fruit pericarp proteome.Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600406.

Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP.(2017) Selective Proteomic Proximity Labeling Assay Using Tyramide (SPPLAT): A Quantitative Method for the Proteomic Analysis of Localized Membrane-Bound Protein Clusters. Curr Protoc Protein Sci. Apr 3;88:19.27.1-19.27.18. doi: 10.1002/cpps.27.

El-Sharnouby S, Fischer B, Magbanua JP, Umans B, Flower R, Choo SW, Russell S, White R. (2017) Regions of very low H3K27me3 partition the Drosophila genome into topological domains. PLoS One. Mar 10;12(3):e0172725. doi: 10.1371/journal.pone.0172725.

Pacini C, Ajioka JW, Micklem G. (2017) Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure. BMC Bioinformatics. Apr 12;18(1):213. doi: 10.1186/s12859-017-1623-y.

Modrell MS, Lyne M, Carr AR, Zakon HH, Buckley D, Campbell AS, Davis MC, Micklem G, Baker CV (2017) Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome. Elife. 2017 Mar 27;6. pii: e24197. doi: 10.7554/eLife.24197.

Gracia T, Wang X, Su Y, Norgett EE, Williams TL, Moreno P, Micklem G, Karet Frankl FE.(2017) Urinary Exosomes Contain MicroRNAs Capable of Paracrine Modulation of Tubular Transporters in Kidney. Sci Rep. 2017 Jan 17;7:40601. doi: 10.1038/srep40601.

Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, Miller JR, Vaughn MW, Micklem G, Town CD, Chan AP (2017) ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.Plant Cell Physiol. 2017 Jan 1;58(1):e4. doi: 10.1093/pcp/pcw200.

Cankorur-Cetinkaya A, Dikicioglu D, Oliver SG. (2017) Metabolic modelling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. Biotechnol Bioeng. 2017 Jul 10. doi: 10.1002/bit.26380.

Cankorur-Cetinkaya A, Dias JML, Kludas J, Slater NKH, Rousu J, Oliver SG, Dikicioglu D. (2017) CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology. Microbiology. 2017 Jun;163(6):829-839. doi: 10.1099/mic.0.000477.

McKeever PM, Kim T, Hesketh AR, MacNair L, Miletic D, Favrin G, Oliver SG, Zhang Z, St George-Hyslop P, Robertson J. (2017) Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease Neurobiol Aging. 2017 May 25;57:104-119. doi: 10.1016/j.neurobiolaging.2017.05.014.

Ciryam P, Lambert-Smith IA, Bean DM, Freer R, Cid F, Tartaglia GG, Saunders DN, Wilson MR, Oliver SG, Morimoto RI, Dobson CM, Vendruscolo M, Favrin G, Yerbury JJ. (2017) Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS. Proc Natl Acad Sci U S A. May 16;114(20):E3935-E3943. doi: 10.1073/pnas.1613854114.

Vlastaridis P, Kyriakidou P, Chaliotis A, Van de Peer Y, Oliver SG, Amoutzias GD. (2017) Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes. Gigascience. 2017 Feb 1;6(2):1-11. doi: 10.1093/gigascience/giw015.

Vlastaridis P, Papakyriakou A, Chaliotis A, Stratikos E, Oliver SG, Amoutzias GD. (2017) The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism. G3 (Bethesda). Apr 3;7(4):1239-1249. doi: 10.1534/g3.116.037218.

Charidemou E, Ashmore T, Griffin JL (2017) The use of stable isotopes in the study of human pathophysiology. Int J Biochem Cell Biol. 2017 Jul 20. pii: S1357-2725(17)30176-0. doi: 10.1016/j.biocel.2017.07.012

Stanley EG, Jenkins BJ, Walker CG, Koulman A, West AL, Calder PC, Jebb SA, Griffin JL. (2017) Lipidomic profiling of human adipose tissue identifies a pattern of lipids associated with fish oil supplementation. J Proteome Res. 2017 Jun 6. doi: 10.1021/acs.jproteome.7b00161.

Horscroft JA, et al (2017)  Metabolic basis to Sherpa altitude adaptation. Proc Natl Acad Sci U S A. 2017 Jun 13;114(24):6382-6387. doi: 10.1073/pnas.1700527114.

Mansor LS, Sousa Fialho MDL, Yea G, Coumans WA, West JA, Kerr M, Carr CA, Luiken JJFP, Glatz JFC, Evans RD, Griffin JL, Tyler DJ, Clarke K, Heather LC. (2017) Inhibition of sarcolemmal FAT/CD36 by sulfo-N-succinimidyl oleate rapidly corrects metabolism and restores function in the diabetic heart following hypoxia/reoxygenation. Cardiovasc Res. Jun 1;113(7):737-748. doi: 10.1093/cvr/cvx045.

Lecommandeur E, Baker D, Cox TM, Nicholls AW, Griffin JL. (2017) Alterations in endo-lysosomal function induce similar hepatic lipid profiles in rodent models of drug-induced phospholipidosis and Sandhoff disease. J Lipid Res. Jul;58(7):1306-1314. doi: 10.1194/jlr.M073395..

Hall Z, Chu Y, Griffin JL. (2017) Liquid Extraction Surface Analysis Mass Spectrometry Method for Identifying the Presence and Severity of Nonalcoholic Fatty Liver Disease. Anal Chem. May 2;89(9):5161-5170. doi: 10.1021/acs.analchem.7b01097.

Jenkins BJ, et al (2017) Odd Chain Fatty Acids; New Insights of the Relationship Between the Gut Microbiota, Dietary Intake, Biosynthesis and Glucose Intolerance. Sci Rep. 2017 Mar 23;7:44845. doi: 10.1038/srep44845.

Acharjee A, Prentice P, Acerini C, Smith J, Hughes IA, Ong K, Griffin JL, Dunger D, Koulman A. (2017) The translation of lipid profiles to nutritional biomarkers in the study of infant metabolism. Metabolomics. 2017;13(3):25. doi: 10.1007/s11306-017-1166-2. Epub 2017 Jan 28.

Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR. (2017) Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.Metabolomics. 13(2):12. doi: 10.1007/s11306-016-1147-x.

Roberts LD, Ashmore T, McNally BD, Murfitt SA, Fernandez BO, Feelisch M, Lindsay R, Siervo M, Williams EA, Murray AJ, Griffin JL.(2017)  Inorganic Nitrate Mimics Exercise-Stimulated Muscular Fiber-Type Switching and Myokine and γ-Aminobutyric Acid Release. Diabetes. 2017 Mar;66(3):674-688. doi: 10.2337/db16-0843.

Siskos AP, Jain P, Römisch-Margl W, Bennett M, Achaintre D, Asad Y, Marney L, Richardson L, Koulman A, Griffin JL, Raynaud F, Scalbert A, Adamski J, Prehn C, Keun HC. (2017)Interlaboratory Reproducibility of a Targeted Metabolomics Platform for Analysis of Human Serum and Plasma. Anal Chem. Jan 3;89(1):656-665. doi: 10.1021/acs.analchem.6b02930.

Hall Z, Bond NJ, Ashmore T, Sanders F, Ament Z, Wang X, Murray AJ, Bellafante E, Virtue S, Vidal-Puig A, Allison M, Davies SE, Koulman A, Vacca M, Griffin JL.(2017) Lipid zonation and phospholipid remodeling in nonalcoholic fatty liver disease. Hepatology. Apr;65(4):1165-1180. doi: 10.1002/hep.28953.

Ferrazza R, Griffin JL, Guella G, Franceschi P. (2017) IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes. Bioinformatics. Jan 15;33(2):300-302. doi: 10.1093/bioinformatics/btw588.