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2016

Bilsland E, Bean DM, Devaney E, Oliver SG (2016) Yeast-Based High-Throughput Screens to Identify Novel Compounds Active against Brugia malayi. PLoS Negl Trop Dis. 2016 Jan 26;10(1):e0004401. doi: 10.1371/journal.pntd.0004401. eCollection 2016.

FidanerIB, Cankorur-CetinkayaA, DikiciogluD, KirdarB, Ali AT, Oliver SG (2016) CLUSTERnGO: A user-defined non-linear modelling platform for two-stage clustering of time-series data. Bioinformatics 32, 388-397.

Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS. (2016) A draft map of the mouse pluripotent stem cell spatial proteome. Nature Commun. Jan 12;7:8992. doi: 10.1038/ncomms9992

Breckels LM, Holden SB, Wojnar D, Mulvey CM, Christoforou A, Groen A, Trotter MW, Kohlbacher O, Lilley KS, Gatto L. (2016) Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PLoS Comput Biol. May 13;12(5):e1004920. doi: 10.1371/journal.pcbi.1004920. eCollection 2016 May.

Fabre B, Korona D, Groen A, Vowinckel J, Gatto L, Deery MJ, Ralser M, Russell S, Lilley KS. (2016) Analysis of the Drosophila melanogaster proteome dynamics during the embryo early development by a combination of label-free proteomics approaches. Proteomics. 2016 Mar 31. doi: 10.1002/pmic.201500482.

Swatton JE, Davenport PW, Maunders EA, Griffin JL, Lilley KS, Welch M. (2016) Impact of Azithromycin on the Quorum Sensing-Controlled Proteome of Pseudomonas aeruginosa. PLoS One. 2016 Jan 25;11(1):e0147698. doi: 10.1371/journal.pone.0147698.

Syed YA, Zhao C, Mahad D, Möbius W, Altmann F, Foss F, Sentürk A, Acker-Palmer A, Lubec G, Lilley K, Franklin RJ, Nave KA, Kotter MR. (2016) Antibody-mediated neutralization of myelin-associated EphrinB3 accelerates CNS remyelination. Acta Neuropathol. Feb;131(2):281-98. doi: 10.1007/s00401-015-1521-1. Epub 2015 Dec 19.

Marondedze C, Groen AJ, Thomas L, Lilley KS, Gehring C. (2016) A Quantitative Phosphoproteome Analysis of cGMP-Dependent Cellular Responses in Arabidopsis thaliana.  Mol Plant. 2016 Apr 4;9(4):621-3. doi: 10.1016/j.molp.2015.11.007.

Marondedze C, Thomas L, Serano,N, Lilley KS, Gehring C (2016) The RNA-binding protein repertoire of Arabidopsis thaliana Scientific reports 6:29766. doi: 10.1038/srep29766

Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmaneshfar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. (2016) The metabolic background is a global player in Saccharomyces gene expression epistasis. Nature Microbiol. 1;1:15030. doi: 10.1038/nmicrobiol.2015.30.

Muleya V, Marondedze C, Wheeler JI, Thomas L, Mok YF, Griffin MD, Manallack DT, Kwezi L, Lilley KS, Gehring C, Irving HR. (2016) Phosphorylation of the dimeric cytoplasmic domain of the phytosulfokine receptor, PSKR1.  Biochem J. 2016 Oct 1;473(19):3081-98. doi: 10.1042/BCJ20160593.

Lee H, Cho DY, Whitworth C, Eisman R, Phelps M, Roote J, Kaufman T, Cook K, Russell S, Przytycka T, Oliver B. (2016) Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PLoS Genet. Sep 6;12(9):e1006295. doi: 10.1371/journal.pgen.1006295.

Niwa H, Nakamura A, Urata M, Shirae-Kurabayashi M, Kuraku S, Russell S, Ohtsuka S. (2016) The evolutionally-conserved function of group B1 Sox family members confers the unique role of Sox2 in mouse ES cells. BMC Evol Biol. 2016 Aug 31;16:173. doi: 10.1186/s12862-016-0755-4.

Beh CY, El-Sharnouby S, Chatzipli A, Russell S, Choo SW, White R. (2016) Roles of cofactors and chromatin accessibility in Hox protein target specificity. Epigenetics Chromatin. Jan 8;9:1. doi: 10.1186/s13072-015-0049-x..

Hammond A, Galizi R, Kyrou K, Simoni A, Siniscalchi C, Katsanos D, Gribble M, Baker D, Marois E, Russell S, Burt A, Windbichler N, Crisanti A, Nolan T. (2016) A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nat Biotechnol. Jan;34(1):78-83. doi: 10.1038/nbt.3439. Epub 2015 Dec 7.

Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, Piel J, Ashoor H, Bougouffa S, Bajic VB, Ryu T, Ravasi T, Bayer T, Micklem G, Kim H, Bhak J, LaJeunesse TC, Voolstra CR. (2016) Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci Rep. Dec 22;6:39734. doi: 10.1038/srep39734.

Cao L, Tang Y, Quan Z, Zhang Z, Oliver SG, Zhang N. (2016) Chronological Lifespan in Yeast Is Dependent on the Accumulation of Storage Carbohydrates Mediated by Yak1, Mck1 and Rim15 Kinases. PLoS Genet. 2016 Dec 6;12(12):e1006458. doi: 10.1371/journal.pgen.1006458. eCollection 2016 Dec.

Kell DB, Oliver SG. (2016) The metabolome 18 years on: a concept comes of age. Metabolomics. 12(9):148. Epub 2016 Sep 2. Review.

Oliver SG, Lock A, Harris MA, Nurse P, Wood V. (2016) Model organism databases: essential resources that need the support of both funders and users. BMC Biol. 2016 Jun 22;14:49. doi: 10.1186/s12915-016-0276-z.

Mendes P, Oliver SG, Kell DB. Response to 'The Need for Speed', by Matsson et al. (2016)Trends Pharmacol Sci. 2016 Apr;37(4):245-6. doi: 10.1016/j.tips.2016.02.004. Feb 26. No abstract available.

Aubrey W, Riley MC, Young M, King RD, Oliver SG, Clare A. A (2016) Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation. PLoS One. 2015 Dec 2;10(12):e0142494. doi: 10.1371/journal.pone.0142494. eCollection 2015.

Dikicioglu D, Kırdar B, Oliver SG. (2016) Biomass composition: the "elephant in the room" of metabolic modelling. Metabolomics. 2015;11(6):1690-1701. Epub 2015 Jun 11.

Castrillo JI, Oliver SG. (2016) Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks. Methods Mol Biol. 2016;1303:3-48. doi: 10.1007/978-1-4939-2627-5_1. Review.

Cox PJ, Kirk T, Ashmore T, Willerton K, Evans R, Smith A, Murray AJ, Stubbs B, West J, McLure SW, King MT, Dodd MS, Holloway C, Neubauer S, Drawer S, Veech RL, Griffin JL, Clarke K. (2016) Nutritional Ketosis Alters Fuel Preference and Thereby Endurance Performance in Athletes. Cell Metab. 2016 Aug 9;24(2):256-68. doi: 10.1016/j.cmet.2016.07.010.

Del Carratore F, Lussu M, Kowalik MA, Perra A, Griffin JL, Atzori L, Grosso M. (2016) Statistical Health Monitoring Applied to a Metabolomic Study of Experimental Hepatocarcinogenesis: An Alternative Approach to Supervised Methods for the Identification of False Positives. Anal Chem. 2016 Aug 16;88(16):7921-9. doi: 10.1021/acs.analchem.5b03078..

Forouhi NG, et al. (2016)  Association of Plasma Phospholipid n-3 and n-6 Polyunsaturated Fatty Acids with Type 2 Diabetes: The EPIC-InterAct Case-Cohort Study. PLoS Med. 2016 Jul 19;13(7):e1002094. doi: 10.1371/journal.pmed.1002094.

Hall Z, Ament Z, Wilson CH, Burkhart DL, Ashmore T, Koulman A, Littlewood T, Evan GI, Griffin JL. (2016) Myc Expression Drives Aberrant Lipid Metabolism in Lung Cancer. Cancer Res. 2016 Aug 15;76(16):4608-18. doi: 10.1158/0008-5472.CAN-15-3403. Epub  Jun 22.

Ament Z, West JA, Stanley E, Li X, Ashmore T, Roberts LD, Wright J, Nicholls AW, Griffin JL.Metabolomics dataset of PPAR-pan treated rat liver. Data Brief. 2016 May 10;8:196-202. doi: 10.1016/j.dib.2016.05.002. eCollection 2016 Sep.

West JA, Beqqali A, Ament Z, Elliott P, Pinto YM, Arbustini E, Griffin JL. (2016) A targeted metabolomics assay for cardiac metabolism and demonstration using a mouse model of dilated cardiomyopathy. Metabolomics. 2016;12:59. Epub  Mar 7.

Taegtmeyer H, et al; (2016) American Heart Association Council on Basic Cardiovascular Sciences. Assessing Cardiac Metabolism: A Scientific Statement From the American Heart Association. Circ Res. 2016 May 13;118(10):1659-701. doi: 10.1161/RES.0000000000000097. Epub Mar 24. Review.

Kale NS, Haug K, Conesa P, Jayseelan K, Moreno P, Rocca-Serra P, Nainala VC, Spicer RA, Williams M, Li X, Salek RM, Griffin JL, Steinbeck C. (2016) MetaboLights: An Open-Access Database Repository for Metabolomics Data. Curr Protoc Bioinformatics. Mar 24;53:14.13.1-18. doi: 10.1002/0471250953.bi1413s53.

Auffray C, Caulfield T, Griffin JL, Khoury MJ, Lupski JR, Schwab M. (2016) From genomic medicine to precision medicine: highlights of 2015. Genome Med. Jan 29;8(1):12. doi: 10.1186/s13073-016-0265-4. No abstract available.

 

Keller MA, Zylstra A, Castro C, Turchyn AV, Griffin JL, Ralser M. (2016) Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway. Sci Adv. Jan 15;2(1):e1501235. doi: 10.1126/sciadv.1501235. eCollection 2016 Jan.

Murray AJ, et al .(2016)  Novel ketone diet enhances physical and cognitive performance. FASEB J. 2016 Dec;30(12):4021-4032. Epub 2016 Aug 15.

Cader MZ, et al. (2016) C13orf31 (FAMIN) is a central regulator of immunometabolic function. Nat Immunol. Sep;17(9):1046-56. doi: 10.1038/ni.3532. Epub 2016 Aug 1.

Yang L, Cheriyan J, Gutterman DD, Mayer RJ, Ament Z, Griffin JL, Lazaar AL, Newby DE, Tal-Singer R, Wilkinson IB. (2016) Mechanisms of Vascular Dysfunction in COPD and Effects of a Novel Soluble Epoxide Hydrolase Inhibitor in Smokers. Chest. 2017 Mar;151(3):555-563. doi: 10.1016/j.chest.2016.10.058. Epub 2016 Nov 21.

Lotta LA, et al. (2016) Genetic Predisposition to an Impaired Metabolism of the Branched-Chain Amino Acids and Risk of Type 2 Diabetes: A Mendelian Randomisation Analysis. PLoS Med. Nov 29;13(11):e1002179. doi: 10.1371/journal.pmed.1002179. eCollection 2016 Nov.

Acharjee A, Ament Z, West JA, Stanley E, Griffin JL.(2016)  Integration of metabolomics, lipidomics and clinical data using a machine learning method. BMC Bioinformatics. Nov 22;17(Suppl 15):440. doi: 10.1186/s12859-016-1292-2.