skip to primary navigationskip to content



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.


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/ 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.



Anderson A, Buckle R, Favrin G, Friend S, Geschwind D, Hu H, Oliver S, Petersen R, Rossor M, St George-Hyslop P, Zhang B (2015) Big data approaches to dementia: Opportunities and challenges. In: Dementia Research and Care: Can Big Data Help?, OECD Publishing, Paris. DOI:

Aubrey W, Riley MC, Young M, King RD, Oliver SG, Clare A (2015) A tool for multiple targeted genome deletions that is precise, scar-free, and suitable for automation. PLoS ONE 10: e0142494. 

BilslandE, BeanDM, DevaneyE, OliverSG (2015) Yeast-based high-throughput screens to identify novel compounds active against Brugia malayi. PLoS Neglected Tropical Diseases

Binder BJ, Sundstrom JF, Gardner JM, Jiranek V, Oliver SG (2015) Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies. PLoS Comp Biol 11: e1004070.

Bitton DA, Schubert F, Dey S, Okoniewski M, Smith GC, Khadayate S, Pancaldi V, Wood V, Bähler J.  AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast.  Front Genet. 2015 Nov 16;6:330. doi: 10.3389/fgene.2015.00330. eCollection 2015. PMID: 26635866

Castrillo JI, Oliver SG (2015) Alzheimer’s as a systems-level disease involving the interplay of multiple cellular networks. Methods in Molec Biol 1303, 3-48.

Castrillo JI and Oliver SG eds. (2015) Systems Biology of Alzheimer’s Disease. (Methods in Molec Biol), Totowa, NJ: Humana/Springer. DOI 10.1007/978-1-4939-2627-5 (555 pages)

Chuang R, Hall BA, Benque D, Cook B, Ishtiaq S, Piterman N, Taylor A, Vardi MY, Koschmieder S, Gottgens B, Fisher J (2015) Drug Target Optimization in Chronic Myeloid Leukemia Using Innovative Computational Platform. Nature Publishing Group, January.

ChughM, ScheurerC, SaxS, BilslandE, van SchalkwykDA, WichtKJ, HofmannN, Sharma A, BashyamS, SinghS, OliverSG, EganTJ, MalhotraP, SutherlandCJ, BeckH-P, WittlinS, SpangenbergT, Ding XC (2015) Identification and deconvolution of antimalarial compounds cross-resistance signals using multidrug-resistant Plasmodium falciparum strains. Antimicrob Agents Chemother 59: 1110-1118.

DikiciogluD, KırdarB, OliverSG (2015) Biomass composition: the “elephant in the room” of metabolic modelling. Metabolomics DOI: 10.1007/s11306-015-0819-2 (12 pages)

FidanerIB, Cankorur-CetinkayaA, DikiciogluD, KirdarB, Ali AT, Oliver SG (2015) CLUSTERnGO: A user-defined non-linear modelling platform for two-stage clustering of time-series data. Bioinformatics DOI: 10.1093/bioinformatics/btv532

Fraca E, Julvez J, Silva M (2015) Hybrid and hybrid adaptive Petri nets: on the computation of a reachability graph. Nonlinear Analysis: Hybrid Systems 16, 24-39.

Hesketh A, Deery MJ, Hong HJ (2015) High-resolution mass spectrometry based proteomic analysis of the response to vancomycin-induced cell wall stress in Streptomyces coelicolor A3(2). J Proteome Res  DOI: 10.1021/acs.jproteome.5b00242

Hoffman CS, Wood V, Fantes PA (2015) An ancient yeast for young geneticists: A primer on the Schizosaccharomyces pombe model system. Genetics 201, 403-423.

Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira EH, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M (2015) Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. Genome Biol. 2015 Jan 29;16(1):19. [Epub ahead of print]

Huber W et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods (In Press).

Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O'Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J (2015) The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet. 2015 Feb 9. doi: 10.1038/ng.3215. [Epub ahead of print]

Kell DB, Swainston N, Pir P, Oliver SG (2015) Membrane transporter engineering in industrial biotechnology and whole-cell biocatalysis. Trends Biotechnol. 33, 237-246.

Keller MA, Piedrafita G, Ralser M (2015) The widespread role of non-enzymatic reactions in cellular metabolism. Curr Opin Biotechnol. 2015 Jan 21;34C:153-161. doi: 10.1016/j.copbio.2014.12.020. [Epub ahead of print]

McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V (2015) PomBase 2015: Updates to the fission yeast database. Nuc Acids Res 43: D656-D661.

Mendes P, Oliver SG, Kell DB (2015) Fitting transporter activities to cellular flux concentrations and fluxes: Why the bumblebee can fly. Trends Pharmacol. Sci. 1260 (14 pages).

Michel S, Keller MA, Wamelink MC, Ralser M (2015) A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance. BMC Genetics, 2015,16:13. DOI: 10.1186/s12863-015-0171-6

Moignard V, Woodhouse S, Haghverdi L, Lilly J, Tanaka Y, Wilkinson A, Buettner F, Nishikawa SI, Piterman N, Kouskoff V, Theis F, Fisher J, Gottgens B (2015) Decoding the Transcriptional Program for Blood Development from Whole Tissue Single Cell Gene Expression Measurements. Nature Biotechnology, in press, Nature Publishing Group, January.

MulveyCM, SchröterC, Gatto L, DikiciogluD, FidanerIB ChristoforouA, DeeryMJ, ChoLTJ, NiakanKK, Martinez-AriasA, Lilley KS (2015) Cell Stem Cell DOI: 10.1002/stem.2067

Munoz-Torres M. et al ....includes Harris MA, Oliver SG, Rutherford K, Wood V (2015) The Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Research. 2015;43(Database issue):D1049-D1056. doi:10.1093/nar/gku1179.

Quan Z, Cao L, Tang Y, Yan Y, Oliver SG, Zhang N (2015) The yeast GSK-3 homologue Mck1 is a key controller of quiescence entry and chronological lifespan. PLoS Genetics 11(6), e1005282.

Runyon RS, Liu R, Wang Y, Oliver SG, Fan T-P, Zhang W (2015) Deciphering ancient combinatorial formulas: The Shexiang Baoxin pill. Science (Suppl.) S40-S42.

Watschinger K, Keller MA, McNeill E, Alam MT, Lai S, Sailer S, Rauch V, Patel J, Hermetter A, Golderer G, Geley S, Werner-Felmayer G, Plumb RS, Astarita G, Ralser M, Channon KM, Werner ER (2015) Tetrahydrobiopterin and alkylglycerol monooxygenase substantially alter the murine macrophage lipidome. Proc Natl Acad Sci U S A. 2015 Feb 9. pii: 201414887.

Williams K, Bilsland E, Sparkes A, Aubrey W, Young M, Soldatova LN, De Grave K, Ramon J, de Clare M, Sirawaraporn W, Oliver SG, King RD (2015) Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases. J Roy Soc Interface 12: 20141289.

Yerbury J, Bean D, Favrin G (2015) Network approaches to the understanding of Alzheimer’s Disease: from model organisms to humans. Methods in Molec Biol 1303, 447-458.

Zabet NR,  Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Research January  43 (1): 84-94 doi:10.1093/ nar/gku1269




Abenza JF, Chessel A, Raynaud WG, Carazo-Salas RE (2014) Dynamics of cell shape inheritance in fission yeast. PLoS One. 2014 Sep 11; 9(9):e106959. doi: 10.1371/journal. pone.0106959. PMID: 25210736

Bean DM, Heimbach J, Ficorella L, Micklem G, Oliver SG, Favrin G (2014) esyN: network building, sharing and publishing. PLoS One. Sep 2; 9(9):e106035. PMID: 25181461 

Christoforou A, Arias AM, Lilley KS (2014). Determining Protein Subcellular Localization in Mammalian Cell Culture with Biochemical Fractionation and iTRAQ 8-Plex Quantification. Methods Mol Biol. 2014;1156:157-74. doi: 10.1007/978-1-4939-0685-7_10. PMID:24791987 [PubMed - in process] 

Daphne Ezer, Nicolae Radu Zabet, Boris Adryan (2014)  Physical constraints determine the logic of bacterial promoter architectures. Nucleic Acids Res. April; 42(7): 4196–4207.

Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Improving functional annotation for industrial microbes: a case study with Pichi pastoris. Trends Biotechnol. 2014 Aug;32(8):396-9.

Elliott TS, Townsley FM, Bianco A, Ernst RJ, Sachdeva A, Elsässer SJ, Davis L, Lang K, Pisa R, Greiss S, Lilley KS, Chin JW (2014) Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal. Nat Biotechnol. 2014 Apr 13. doi: 10.1038/nbt.2860. [Epub ahead of print] PMID:24727715[PubMed - as supplied by publisher]

Ezer, D., Zabet, N. R., & Adryan, B. (2014). Physical constraints determine the logic of bacterial promoter architectures.. Nucleic Acids Res. doi:10.1093/nar/gku078

Feret, R., & Lilley, K. S. (2014). Protein Profiling Using Two-Dimensional Difference Gel Electrophoresis (2-D DIGE).. Curr Protoc Protein Sci, 75, 22.2.1-22.2.17. doi:10.1002/0471140864.ps2202s75

Ferrero E, Fischer B, Russell S (2014) SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete. Genome Biology 15: R74.

Füzesi-Levi, M. G., Ben-Nissan, G., Bianchi, E., Zhou, H., Deery, M. J., Lilley, K. S., . . . Sharon, M. (2014). Dynamic Regulation of the COP9 Signalosome in Response to DNA Damage.. Mol Cell Biol, 34(6), 1066-1076. doi:10.1128/MCB.01598-13

Gatto L, Breckels LM, Burger T, Nightingale DJ, Groen AJ, Campbell C, Nikolovski N, Mulvey CM, Christoforou A, Ferro M, Lilley KS (2014) A foundation for reliable spatial proteomics data analysis. Mol Cell Proteomics. Aug;13(8):1937-52.

Gatto, L., Breckels, L. M., Wieczorek, S., Burger, T., & Lilley, K. S. (2014). Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata.. Bioinformatics. doi:10.1093/bioinformatics/btu013

Graml V, Studera X, Lawson JL, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo-Salas RE (2014) A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression. Dev Cell. Oct 27;31(2):227-39. doi: 10.1016/j.devcel.2014.09.005. PMID: 25373780 

Groen, A. J., Sancho-Andrés, G., Breckels, L. M., Gatto, L., Aniento, F., & Lilley, K. S. (2014). Identification of Trans-Golgi Network Proteins in Arabidopsis thaliana Root Tissue.. J Proteome Res. doi:10.1021/pr4008464

Grüning, N. M., Du, D., Keller, M. A., Luisi, B. F., & Ralser, M. (2014). Inhibition of triosephosphate isomerase by phosphoenolpyruvate in the feedback-regulation of glycolysis.. Open Biol, 4(3), 130232. doi:10.1098/rsob.130232

Hall B, Jackson E, Hajnal A, Fisher J (2014) Logic Programming to Predict Cell Fate Patterns and Retrodict Genotypes during Organogenesis. Royal Society Interface 11: 0140245, Royal Society Publishing, June.

Hiemstra TF, Charles PD, Gracia T, Hester SS, Gatto L, Al-Lamki R, Floto RA, Su Y, Skepper JN, Lilley KS, Karet Frankl FE (2014) Human Urinary Exosomes as Innate Immune Effectors. J Am Soc Nephrol. 2014 Apr 3. [Epub ahead of print] PMID:24700864 [PubMed - as supplied by publisher]

Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014 May 21;15(1):155.

Jones, O. A. H., Sdepanian, S., Lofts, S., Svendsen, C., Spurgeon, D. J., Maguire, M. L., . . . Griffin, J. L. (2014). Metabolomic analysis of soil communities can be used for pollution assessment. Environmental Toxicology and Chemistry, 33(1), 61-64.

Kalderimis, A., Stepan, R., Sullivan, J., Lyne, R., Lyne, M., & Micklem, G. (2014). BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs.. F1000Res, 3, 51. doi:10.12688/f1000research.3-51.v1

Keller MA, Turchyn AV, Ralser M (2014) Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. Mol Syst Biol. Apr 25;10:725. doi: 10.1002/msb.20145228. PubMed PMID: 24771084; PubMed Central PMCID: PMC4023395

Khabirova E, Moloney A, Marciniak SJ, Williams J, Lomas DA, Oliver SG, Favrin G, Sattelle DB, Crowther DC. (2014). The TRiC/CCT Chaperone Is Implicated in Alzheimer's Disease Based on Patient GWAS and an RNAi Screen in Aβ-Expressing Caenorhabditis elegans. PLoS One. 2014 Jul 31;9(7):e102985. doi: 10.1371/journal.pone.0102985. 

King, H. A., Cobbold, L. C., Pichon, X., Pöyry, T., Wilson, L. A., Booden, H., . . . Willis, A. E. (2014). Remodelling of a polypyrimidine tract-binding protein complex during apoptosis activates cellular IRESs. Cell Death and Differentiation, 21(1), 161-171.

Koulman, A., Prentice, P., Wong, M. C. Y., Matthews, L., Bond, N. J., Eiden, M., . . . Dunger, D. B. (2014). The development and validation of a fast and robust dried blood spot based lipid profiling method to study infant metabolism. Metabolomics, 1-8.

Li XW, Rees JS, Xue P, Zhang H, Hamaia SW, Sanderson B, Funk PE, Farndale RW, Lilley KS, Perrett S, Jackson AP (2014) New Insights into the DT40 B-Cell Receptor Cluster using a Proteomic Proximity Labeling Assay. J Biol Chem. 2014 Apr 4. [Epub ahead of print] PMID:24706754[PubMed - as supplied by publisher] Free Article

Neville, M. C., Nojima, T., Ashley, E., Parker, D. J., Walker, J., Southall, T.,Russell, S. . . . Goodwin, S. F. (2014). Male-specific fruitless isoforms target neurodevelopmental genes to specify a sexually dimorphic nervous system.. Curr Biol, 24(3), 229-241. doi:10.1016/j.cub.2013.11.035

Oliver, S. (2014). The harder we work ….. Yeast, 31(3), 81-82. doi:10.1002/yea.3000

Patel MN, Bernard WG, Milev NB, Cawthorn WP, Figg N, Hart D, Prieur X, Virtue S, Hegyi K, Bonnafous S, Bailly-Maitre B, Chu Y, Griffin JL, Mallat Z, Considine RV, Tran A, Gual P, Takeuchi O, Akira S, Vidal-Puig A, Bennett MR, Sethi JK (2014) Hematopoietic IKBKE limits the chronicity of inflammasome priming and metaflammation. Proc Natl Acad Sci U S A Dec, 24. pii: 201414536.

Prigione, A., Rohwer, N., Hoffmann, S., Mlody, B., Drews, K., Bukowiecki, R.,Ralser M. . . . Adjaye, J. (2014). HIF1α modulates cell fate reprogramming through early glycolytic shift and upregulation of PDK1-3 and PKM2.. Stem Cells, 32(2), 364-376. doi:10.1002/stem.1552

Roberts LD, Ashmore T, Kotwica AO, Murfitt SA, Fernandez BO, Feelisch M, Murray AJ, Griffin JL (2014) Inorganic Nitrate Promotes the Browning of White Adipose Tissue through the Nitrate-Nitrite-Nitric Oxide Pathway. Diabetes Sep 23. pii: DB_140496.

Roberts, L. D., Koulman, A., & Griffin, J. L. (2014). Towards metabolic biomarkers of insulin resistance and type 2 diabetes: Progress from the metabolome. The Lancet Diabetes and Endocrinology, 2(1), 65-75.

Roberts, L. D., West, J. A., Vidal-Puig, A., & Griffin, J. L. (2014). Methods for performing lipidomics in white adipose tissue.. Methods Enzymol, 538, 211-231. doi:10.1016/B978-0-12-800280-3.00012-8

Rutherford, K. M., Harris, M. A., Lock, A., Oliver, S. G., & Wood, V. (2014). Canto: an online tool for community literature curation.. Bioinformatics. doi:10.1093/bioinformatics/btu103

Schmidt HG, Sewitz S, Andrews SS,  Lipkow K (2014) An Integrated Model of Transcription Factor Diffusion Shows the Importance of Intersegmental Transfer and Quaternary Protein Structure for Target Site Finding. PLOS ONE 9(10), e108575.  

Schoech A P,  Zabet NR (2014) Facilitated diffusion buffers noise in gene expression. Phys. Rev. E 90(3): 032701, doi:10.1103/PhysRevE.90.032701.

Torella R, Li J, Kinrade E, Cerda-Moya G, Contreras AN, Foy R, Stojnic R, Glen RC, Kovall RA, Adryan B, Bray SJ (2014) A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL. Nucleic Acids Res.42(16):10550-63. doi: 10.1093/nar/gku730. Epub 2014 Aug 11. PMID:     25114055

Tzanis, A., Dalton, K. A., Hesketh, A., den Hengst, C. D., Buttner, M. J., Thibessard, A., . . . Kelemen, G. H. (2014). A sporulation-specific, sigF-dependent protein, SspA, affects septum positioning in Streptomyces coelicolor.. Mol Microbiol, 91(2), 363-380. doi:10.1111/mmi.12466

Walzer M, Pernas LE, .... Lilley KS, et al. (2014) qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014 Apr 23. [Epub ahead of print] PMID:24760958[PubMed - as supplied by publisher] Free Article

Vaggi, F., Schiavinotto, T., Lawson, J. L., Chessel, A., Dodgson, J., Geymonat, M., Carazo-Salas, R. E.,. . . Csikász-Nagy, A. (2014). A network approach to mixing delegates at meetings.. Elife, 3, e02273. doi:10.7554/eLife.02273

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. Mar;32(3):223-6.

Wang, Y., Lilley, K. S., & Oliver, S. G. (2014). A protocol for the sub-cellular fractionation of Saccharomyces cerevisiae using nitrogen cavitation and density gradient centrifugation.. Yeast. doi:10.1002/yea.3002

Xi, W., Schmidt, C. K., Sanchez, S., Gracias, D. H., Carazo-Salas, R. E., Jackson, S. P., . . . Schmidt, O. G. (2014). Rolled-up Functionalized Nanomembranes as Three-Dimensional Cavities for Single Cell Studies.. Nano Lett. doi:10.1021/nl4042565


Alcasabas, A. A., De Clare, M., Pir, P., & Oliver, S. G. (2013). Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids. BMC Genomics, 14(1).

Aleksic, J., Ferrero, E., Fischer, B., Shen, S. P., & Russell, S. (2013). The role of Dichaete in transcriptional regulation during Drosophila embryonic development. BMC GENOMICS, 14. doi:10.1186/1471-2164-14-861

Ament, Z., Waterman, C. L., West, J. A., Waterfield, C., Currie, R. A., Wright, J., . . . Griffin, J. L. (2013). A metabolomics investigation of non-genotoxic carcinogenicity in the rat.. J Proteome Res, 12(12), 5775-5790. doi:10.1021/pr4007766

Armean, I. M., Lilley, K. S., & Trotter, M. W. (2013). Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments.. Mol Cell Proteomics, 12(1), 1-13. doi:10.1074/mcp.R112.019554

Bajpai, A., Feoktistova, A., Chen, J. S., McCollum, D., Sato, M., Carazo-Salas, R. E., . . . Csikász-Nagy, A. (2013). Dynamics of SIN asymmetry establishment.. PLoS Comput Biol, 9(7), e1003147. doi:10.1371/journal.pcbi.1003147

Bilsland, E., Sparkes, A., Williams, K., Moss, H. J., de Clare, M., Pir, P., . . . Oliver, S. G. (2013). Yeast-based automated high-throughput screens to identify anti-parasitic lead compounds.. Open Biol, 3(2), 120158. doi:10.1098/rsob.120158

Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Ni, L., Sitnikov, D., . . . Consortium, G. O. (2013). Gene Ontology Annotations and Resources. NUCLEIC ACIDS RESEARCH, 41(D1), D530-D535. doi:10.1093/nar/gks1050

Breckenridge, R. A., Piotrowska, I., Ng, K. -E., Ragan, T. J., West, J. A., Kotecha, S., . . . Mohun, T. J. (2013). Hypoxic Regulation of Hand1 Controls the Fetal-Neonatal Switch in Cardiac Metabolism. PLoS Biology, 11(9).

Breitenbach, M., Ralser, M., Perrone, G. G., Iglseder, B., Rinnerthaler, M., & Dawes, I. W. (2013). Oxidative stress and neurodegeneration: the yeast model system.. Front Biosci (Landmark Ed), 18, 1174-1193. Retrieved from

Budczies, J., Brockmöller, S. F., Müller, B. M., Barupal, D. K., Richter-Ehrenstein, C., Kleine-Tebbe, A., . . . Fiehn, O. (2013). Comparative metabolomics of estrogen receptor positive and estrogen receptor negative breast cancer: Alterations in glutamine and beta-alanine metabolism. Journal of Proteomics, 94, 279-288.

Carobbio, S., Hagen, R. M., Lelliott, C. J., Slawik, M., Medina-Gomez, G., Tan, C. Y., . . . Vidal-Puig, A. (2013). Adaptive changes of the Insig1/SREBP1/SCD1 set point help adipose tissue to cope with increased storage demands of obesity.. Diabetes, 62(11), 3697-3708. doi:10.2337/db12-1748

Castrillo, J. I., Pir, P., & Oliver, S. G. (2013). Yeast Systems Biology: Towards a Systems Understanding of Regulation of Eukaryotic Networks in Complex Diseases and Biotechnology. Handbook of Systems Biology, 343-365.

Castro, C., Krumsiek, J., Lehrbach, N. J., Murfitt, S. A., Miska, E. A., & Griffin, J. L. (2013). A study of Caenorhabditis elegans DAF-2 mutants by metabolomics and differential correlation networks.. Mol Biosyst, 9(7), 1632-1642. doi:10.1039/c3mb25539e

Catalán, Ú., Rodríguez, M. -A., Ras, M. -R., MacIá, A., Mallol, R., Vinaixa, M., . . . Solà, R. (2013). Biomarkers of food intake and metabolite differences between plasma and red blood cell matrices; A human metabolomic profile approach. Molecular BioSystems, 9(6), 1411-1422.

Chan, Y. -S., Takeuchi, R., Jarjour, J., Huen, D. S., Stoddard, B. L., & Russell, S. (2013). The Design and In Vivo Evaluation of Engineered I-OnuI-Based Enzymes for HEG Gene Drive. PLOS ONE, 8(9). doi:10.1371/journal.pone.0074254

Chan, Y. -S., Huen, D. S., Glauert, R., Whiteway, E., & Russell, S. (2013). Optimising Homing Endonuclease Gene Drive Performance in a Semi-Refractory Species: The Drosophila melanogaster Experience. PLOS ONE, 8(1). doi:10.1371/journal.pone.0054130

Claessen, K., Fisher, J., Ishtiaq, S., Piterman, N., & Wang, Q. (2013). Model-checking signal transduction networks through decreasing reachability sets. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8044 LNCS, 85-100.

Csikász-Nagy, A., Sato, M., & Carazo Salas, R. E. (2013). Projecting cell polarity into the next decade.. Philos Trans R Soc Lond B Biol Sci, 368(1629), 20130001. doi:10.1098/rstb.2013.0001

de Clare, M., & Oliver, S. G. (2013). Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae.. BMC Biol, 11, 24. doi:10.1186/1741-7007-11-24

Dikicioglu, D., Oc, S., Rash, B. M., Dunn, W. B., Pir, P., Kell, D. B., . . . Oliver, S. G. (2014). Yeast cells with impaired drug resistance accumulate glycerol and glucose.. Mol Biosyst, 10(1), 93-102. doi:10.1039/c2mb25512j

Dikicioglu, D., Pir, P., & Oliver, S. G. (2013). Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory. Biotechnology Journal, 8(9), 1017-1034.

Dodgson, J., Chessel, A., Yamamoto, M., Vaggi, F., Cox, S., Rosten, E., . . . Carazo-Salas, R. E. (2013). Spatial segregation of polarity factors into distinct cortical clusters is required for cell polarity control.. Nat Commun, 4, 1834. doi:10.1038/ncomms2813

Emwas, A. -H. M., Salek, R. M., Griffin, J. L., & Merzaban, J. (2013). NMR-based metabolomics in human disease diagnosis: Applications, limitations, and recommendations. Metabolomics, 9(5), 1048-1072.

Gene Ontology Consortium., Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Li, N., Harris MA, Oliver SG, Rutherford K, Wood V,. . . Westerfield, M. (2013). Gene Ontology annotations and resources.. Nucleic Acids Res, 41(Database issue), D530-D535. doi:10.1093/nar/gks1050

Griffin, J. L., & Salek, R. M. (2010). 1 H MAS NMR Spectroscopy of Tissues. Encyclopedia of Spectroscopy and Spectrometry, 925-930.

Favrin, G., Bean, D. M., Bilsland, E., Boyer, H., Fischer, B. E., Russell, S., . . . Giannakou, M. E. (2013). Identification of novel modifiers of Aβ toxicity by transcriptomic analysis in the fruitfly.. Sci Rep, 3, 3512. doi:10.1038/srep03512

Fu, A. Q., Russell, S., Bray, S. J., & Tavare, S. (2013). Bayesian clustering of replicated time-course gene expression data with weak signals. ANNALS OF APPLIED STATISTICS, 7(3), 1334-1361. doi:10.1214/13-AOAS650

Harris, M. A., Lock, A., Bähler, J., Oliver, S. G., & Wood, V. (2013). FYPO: the fission yeast phenotype ontology.. Bioinformatics, 29(13), 1671-1678. doi:10.1093/bioinformatics/btt266

Haug, K., Salek, R. M., Conesa, P., Hastings, J., de Matos, P., Rijnbeek, M., . . . Steinbeck, C. (2013). MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data.. Nucleic Acids Res, 41(Database issue), D781-D786. doi:10.1093/nar/gks1004

Hayles, J., Wood, V., Jeffery, L., Hoe, K. L., Kim, D. U., Park, H. O., . . . Nurse, P. (2013). A genome-wide resource of cell cycle and cell shape genes of fission yeast.. Open Biol, 3(5), 130053. doi:10.1098/rsob.130053

Heather, L. C., Pates, K. M., Atherton, H. J., Cole, M. A., Ball, D. R., Evans, R. D., . . . Clarke, K. (2013). Differential translocation of the fatty acid transporter, FAT/CD36, and the glucose transporter, GLUT4, coordinates changes in cardiac substrate metabolism during ischemia and reperfusion. Circulation: Heart Failure, 6(5), 1058-1066.

Heather, L. C., Wang, X., West, J. A., & Griffin, J. L. (2013). A practical guide to metabolomic profiling as a discovery tool for human heart disease. Journal of Molecular and Cellular Cardiology, 55(1), 2-11.

Heather, L. C., Wang, X., West, J. A., & Griffin, J. L. (2013). A practical guide to metabolomic profiling as a discovery tool for human heart disease. Journal of Molecular and Cellular Cardiology.

Hesketh, A. R., Castrillo, J. I., Sawyer, T., Archer, D. B., & Oliver, S. G. (2013). Investigating the physiological response of Pichia (Komagataella) pastoris GS115 to the heterologous expression of misfolded proteins using chemostat cultures. Applied Microbiology and Biotechnology, 97(22), 9747-9762.

Housden, B. E., Fu, A. Q., Krejci, A., Bernard, F., Fischer, B., Tavaré, S., . . . Bray, S. J. (2013). Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes.. PLoS Genet, 9(1), e1003162. doi:10.1371/journal.pgen.1003162

Ilsley, G. R., Fisher, J., Apweiler, R., DePace, A. H., & Luscombe, N. M. (2013). Cellular resolution models for even skipped regulation in the entire Drosophila embryo. eLife, 2013(2).

Jamers, A., Blust, R., De Coen, W., Griffin, J. L., & Jones, O. A. H. (2013). Copper toxicity in the microalga Chlamydomonas reinhardtii: An integrated approach. BioMetals, 26(5), 731-740.

Jamers, A., Blust, R., De Coen, W., Griffin, J. L., & Jones, O. A. H. (2013). An omics based assessment of cadmium toxicity in the green alga Chlamydomonas reinhardtii. Aquatic Toxicology, 126, 355-364.

Jin, H., Stojnic, R., Adryan, B., Ozdemir, A., Stathopoulos, A., & Frasch, M. (2013). Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.. PLoS Genet, 9(1), e1003195. doi:10.1371/journal.pgen.1003195

Jones, O. A., Sdepanian, S., Lofts, S., Svendsen, C., Spurgeon, D. J., Maguire, M. L., . . . Griffin, J. L. (2013). Metabolomic analysis of soil communities can be used for pollution assessment. Environmental Toxicology and Chemistry.

Jones, O. A. H., Maguire, M. L., Griffin, J. L., Dias, D. A., Spurgeon, D. J., & Svendsen, C. (2013). Metabolomics and its use in ecology. Austral Ecology, 38(6), 713-720.

Jones, O. A. H., Murfitt, S., Svendsen, C., Turk, A., Turk, H., Spurgeon, D. J., . . . Griffin, J. L. (2013). Comparisons of metabolic and physiological changes in rats following short term oral dosing with pesticides commonly found in food. Food and Chemical Toxicology, 59, 438-445.

Kell, D. B., Dobson, P. D., Bilsland, E., & Oliver, S. G. (2013). The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so.. Drug Discov Today, 18(5-6), 218-239. doi:10.1016/j.drudis.2012.11.008

King, H. A., Cobbold, L. C., Pichon, X., Pöyry, T., Wilson, L. A., Booden, H., . . . Willis, A. E. (2013). Remodelling of a polypyrimidine tract-binding protein complex during apoptosis activates cellular IRESs. Cell Death and Differentiation.

Koeksal, A. S., Pu, Y., Srivastava, S., Bodik, R., Fisher, J., & Piterman, N. (2013). Synthesis of Biological Models from Mutation Experiments. ACM SIGPLAN NOTICES, 48(1), 469-482. doi:10.1145/2480359.2429125

Koutroukides, T. A., Jaros, J. A., Amess, B., Martins-de-Souza, D., Guest, P. C., Rahmoune, H., . . . Lilley, K. S. (2013). Identification of protein biomarkers in human serum using iTRAQ and shotgun mass spectrometry.. Methods Mol Biol, 1061, 291-307. doi:10.1007/978-1-62703-589-7_18

Koutsimpelas, D., Bjelopavlovic, M., Yetis, R., Frauenknecht, K., Adryan, B., Schmidtmann,       I., Gouveris, H., Fruth, K., Heinrich, U., Stauber, R., Mann, W., Brieger, J. (2013)    The      VEGF/VEGF-R Axis in Sporadic Vestibular Schwannomas Correlates with      Irradiation       and Disease Recurrence., ORL J Otorhinolaryngol Relat Spec. 2013,     74(6):330-338.

Kwun, M. J., Novotna, G., Hesketh, A. R., Hill, L., & Hong, H. J. (2013). In vivo studies suggest that induction of VanS-dependent vancomycin resistance requires binding of the drug to D-Ala-D-Ala termini in the peptidoglycan cell wall.. Antimicrob Agents Chemother, 57(9), 4470-4480. doi:10.1128/AAC.00523-13

Lawson, J. L., & Carazo Salas, R. E. (2013). Microtubules: greater than the sum of the parts.. Biochem Soc Trans, 41(6), 1736-1744. doi:10.1042/BST20130239

Marygold, S. J., Leyland, P. C., Seal, R. L., Goodman, J. L., Thurmond, J., Strelets, V. B., Adryan, B . . . FlyBase consortium. (2013). FlyBase: improvements to the bibliography.. Nucleic Acids Res, 41(Database issue), D751-D757. doi:10.1093/nar/gks1024

Moignard, V., Woodhouse, S., Fisher, J., & Göttgens, B. (2013). Transcriptional hierarchies regulating early blood cell development.. Blood Cells Mol Dis, 51(4), 239-247. doi:10.1016/j.bcmd.2013.07.007

Pan, X., Wilson, M., McConville, C., Arvanitis, T. N., Griffin, J. L., Kauppinen, R. A., . . . Peet, A. C. (2013). Increased unsaturation of lipids in cytoplasmic lipid droplets in DAOY cancer cells in response to cisplatin treatment. Metabolomics, 9(3), 722-729.

Peden, A. S., Mac, P., Fei, Y. J., Castro, C., Jiang, G., Murfitt, K. J., . . . Jorgensen, E. M. (2013). Betaine acts on a ligand-gated ion channel in the nervous system of the nematode C. elegans.. Nat Neurosci, 16(12), 1794-1801. doi:10.1038/nn.3575

Roberts, L. D., Koulman, A., & Griffin, J. L. (2013). Towards metabolic biomarkers of insulin resistance and type 2 diabetes: progress from the metabolome. The Lancet Diabetes and Endocrinology.

Schep, A., & Adryan, B. (2013). A comparative analysis of transcription factor expression during   metazoan embryonic development. Retrieved from

Shen, S. P., Aleksic, J., & Russell, S. (2013). Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins.. BMC Dev Biol, 13, 1. doi:10.1186/1471-213X-13-1

Sherwood, E., Hesketh, A. R., & Bibb, M. J. (n.d.) Cloning and analysis of the planosporicin lantibiotic biosynthetic gene cluster of Planomonospora alba.. J. Bacteriol.

Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., . . . Mendes, P. (2013). A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Letters, 587(17), 2832-2841.

Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., . . . Mendes, P. (2013). A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.. FEBS Lett, 587(17), 2832-2841. doi:10.1016/j.febslet.2013.06.043

Snoek, L. B., Van der Velde, K. J., Arends, D., Li, Y., Beyer, A., Elvin, M., . . . Swertz, M. A. (2013). WormQTL-public archive and analysis web portal for natural variation data in Caenorhabditis spp. NUCLEIC ACIDS RESEARCH, 41(D1), D738-D743. doi:10.1093/nar/gks1124

Taylor, A. S., Piterman, N., Ishtiaq, S., Fisher, J., Cook, B., Cockerton, C., . . . Benque, D. (2013). At the interface of biology and computation. Conference on Human Factors in Computing Systems - Proceedings, 493-502.

Uguru, G. C., Mondhe, M., Goh, S., Hesketh, A., Bibb, M. J., Good, L., . . . Stach, J. E. (2013). Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2).. PLoS One, 8(6), e67509. doi:10.1371/journal.pone.0067509

Wilf, N. M., Reid, A. J., Ramsay, J. P., Williamson, N. R., Croucher, N. J., Gatto, L., . . . Salmond, G. P. (2013). RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.. BMC Genomics, 14, 822. doi:10.1186/1471-2164-14-822

Zhang, N., Quan, Z., Rash, B., & Oliver, S. G. (2013). Synergistic effects of TOR and proteasome pathways on the yeast transcriptome and cell growth.. Open Biol, 3(5), 120137. doi:10.1098/rsob.120137


Chouchani, E. T., Methner, C., Nadtochiy, S. M., Logan, A., Pell, V. R., Ding, S., . . . Murphy, M. P. (2013). Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex i. Nature Medicine, 19(6), 753-759.

Chouchani, E. T., Methner, C., Nadtochiy, S. M., Logan, A., Pell, V. R., Ding, S., . . . Murphy, M. P. (2013). Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I.. Nat Med, 19(6), 753-759. doi:10.1038/nm.3212

Shliaha, P. V., Bond, N. J., Gatto, L., & Lilley, K. S. (2013). Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies.. J Proteome Res, 12(6), 2323-2339. doi:10.1021/pr300775k

Bond, N. J., Shliaha, P. V., Lilley, K. S., & Gatto, L. (2013). Improving qualitative and quantitative performance for MS(E)-based label-free proteomics.. J Proteome Res, 12(6), 2340-2353. doi:10.1021/pr300776t

Ivanov, A. R., Colangelo, C. M., Dufresne, C. P., Friedman, D. B., Lilley, K. S., Mechtler, K., . . . Weintraub, S. T. (2013). Interlaboratory studies and initiatives developing standards for proteomics. Proteomics, 13(6), 904-909.

Breckels, L. M., Gatto, L., Christoforou, A., Groen, A. J., Lilley, K. S., & Trotter, M. W. (2013). The effect of organelle discovery upon sub-cellular protein localisation.. J Proteomics, 88, 129-140. doi:10.1016/j.jprot.2013.02.019

Marondedze, C., Turek, I., Parrott, B., Thomas, L., Jankovic, B., Lilley, K. S., . . . Gehring, C. (2013). Structural and functional characteristics of cGMP-dependent methionine oxidation in Arabidopsis thaliana proteins. Cell Communication and Signaling, 11(1).

Marondedze C, Lilley K, Thomas L. (2013) Comparative gel-based phosphoproteomics in response to signaling molecules. Methods Mol Biol. 2013;1016:139-54. doi: 10.1007/978-1-62703-441-8_10.

Hemsley, P. A., Weimar, T., Lilley, K. S., Dupree, P., & Grierson, C. S. (2013). A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis. New Phytologist, 197(3), 805-814.

Claeys Bouuaert, C., Lipkow, K., Andrews, S. S., Liu, D., & Chalmers, R. (2013). The autoregulation of a eukaryotic DNA transposon.. Elife, 2, e00668. doi:10.7554/eLife.00668

Sewitz, S. and Lipkow, K. (2013) Simulating bacterial chemotaxis at high spatio-temporal detail. Current Chemical Biology, in press.  Special issue: Computational Cell Biology.

Sullivan, J., Karra, K., Moxon, S. A. T., Vallejos, A., Motenko, H., Wong, J. D., . . . Micklem, G. (2013). Erratum: InterMOD: Integrated data and tools for the unification of model organism research (Scientific Reports (2013) 3 (1802) DOI: 10.1038/srep01802). Scientific Reports, 3.

Sullivan, J., Karra, K., Moxon, S. A., Vallejos, A., Motenko, H., Wong, J. D., . . . Micklem, G. (2013). CORRIGENDUM: InterMOD: integrated data and tools for the unification of model organism research.. Sci Rep, 3, 3303. doi:10.1038/srep03303

Baumgarten, S., Bayer, T., Aranda, M., Liew, Y. J., Carr, A., Micklem, G., . . . Voolstra, C. R. (2013). Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.. BMC Genomics, 14, 704. doi:10.1186/1471-2164-14-704

Diffner, E., Beck, D., Gudgin, E., Thoms, J. A. I., Knezevic, K., Pridans, C., . . . Pimanda, J. E. (2013). Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia. BLOOD, 121(12), 2289-2300. doi:10.1182/blood-2012-07-446120

Lyne, M., Smith, R. N., Lyne, R., Aleksic, J., Hu, F., Kalderimis, A., . . . Micklem, G. (2013). metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.. Database (Oxford), 2013, bat060. doi:10.1093/database/bat060

Sullivan, J., Karra, K., Moxon, S. A., Vallejos, A., Motenko, H., Wong, J. D., . . . Micklem, G. (2013). InterMOD: integrated data and tools for the unification of model organism research.. Sci Rep, 3, 1802. doi:10.1038/srep01802

Katayama, T., Wilkinson, M. D., Micklem, G., Kawashima, S., Yamaguchi, A., Nakao, M., . . . Takagi, T. (2013). The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.. J Biomed Semantics, 4(1), 6. doi:10.1186/2041-1480-4-6

Diffner, E., Beck, D., Gudgin, E., Thoms, J. A., Knezevic, K., Pridans, C., . . . Pimanda, J. E. (2013). Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia.. Blood, 121(12), 2289-2300. doi:10.1182/blood-2012-07-446120

Breitenbach, M., Rinnerthaler, M., Hartl, J., Stincone, A., Vowinckel, J., Breitenbach-Koller, H., . . . Ralser, M. (2013). Mitochondria in ageing: there is metabolism beyond the ROS.. FEMS Yeast Res. doi:10.1111/1567-1364.12134

Krüger, A., Vowinckel, J., Mülleder, M., Grote, P., Capuano, F., Bluemlein, K., . . . Ralser, M. (2013). Tpo1-mediated spermine and spermidine export controls cell cycle delay and times antioxidant protein expression during the oxidative stress response.. EMBO Rep, 14(12), 1113-1119. doi:10.1038/embor.2013.165

Sarper, N., Zengin, E., Jakobs, C., Salomons, G. S., Wamelink, M. M. C., Ralser, M., . . . Kara, B. (2013). Mild hemolytic anemia, progressive neuromotor retardation and fatal outcome: A disorder of glycolysis, triose-phosphate isomerase deficiency. Turkish Journal of Pediatrics, 55(2), 198-202.


Prevosto, C., Usmani, F., McDonald, S., Lipinska, A. M., Key, T., Goodman, R. A., . . . Busch, R. (2013). Allele-independent protein turnover enables codominant expression of HLA class Ia alleles in human APCs. In IMMUNOLOGY Vol. 140 (pp. 40).

De Riva, A., Varley, M. C., Bluck, L. J., Cooke, A., Deery, M. J., & Busch, R. (2013). Accelerated turnover of MHC class II molecules in NOD mice is developmentally and environmentally regulated in vivo and dispensable for autoimmunity. In IMMUNOLOGY Vol. 140 (pp. 49).

De Riva, A., Varley, M. C., Bluck, L. J., Cooke, A., Deery, M. J., & Busch, R. (2013). Accelerated turnover of MHC class II molecules in nonobese diabetic mice is developmentally and environmentally regulated in vivo and dispensable for autoimmunity.. J Immunol, 190(12), 5961-5971. doi:10.4049/jimmunol.1300551


Zabet, N. R., & Adryan, B. (2013). The effects of transcription factor competition on gene regulation. Frontiers in Genetics 4:197 (2013). doi:10.3389/fgene.2013.00197

Zabet, N. R., Foy, R., & Adryan, B. (2013). The influence of transcription factor competition on the relationship  between occupancy and affinity. PLoS ONE 8:, 9, e73714. doi:10.1371/journal.pone.0073714



Adryan B, Russell S (2012) Genome mapping and genomics in Drosophila. In "Genome Mapping and Genomics in Laboratory Animals" Eds P Denny and C. Kole. Springer  (In Press).

Ament Z, Masoodi M, Griffin JL (2012) Applications of metabolomics for understanding the action of peroxisome proliferator-activated receptors (PPARs) in diabetes, obesity and cancer. Genome medicine 4.

Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG (2012) Evaluation and Properties of the Budding Yeast Phosphoproteome. Molecular & Cellular Proteomics 11.

Armean IM, Lilley KS, Trotter MW (2012) Popular computational methods to assess multi-protein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. Mol Cell Proteomics. Oct 15. [Epub ahead of print]

Atzori L, Griffin JL, Noto A, Fanos V (2012) Review Metabolomics: A New Approach to Drug Delivery in Perinatology. Current Medicinal Chemistry 19.

Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, et al. (2012) YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database : the journal of biological databases and curation 2012.

Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, et al. (2012) YeastMine-an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database-the Journal of Biological Databases and Curation.

Blake JA, Dolan M, Drabkin H, Hill DP, Ni L, et al. (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Research 40.

Bossing T, Barros CS, Fischer B, Russell S, Shepherd D (2012) Disruption of Microtubule Integrity Initiates Mitosis during CNS Repair. Developmental Cell 23.

Bossing T, Fischer B, Russell S, Shepherd D (2012) Transcriptional control of damage repair at the ventral midline of Drosophila melanogaster. Dev. Cell 23: 433-440. (Preview Article KE Prehoda (2012) Dev Cell 23: 233-234)

Breitenbach M, Laun P, Dickinson JR, Klocker A, Rinnerthaler M, et al. (2012) The Role of Mitochondria in the Aging Processes of Yeast. In: Breitenbach M, Jazwinski SM, Laun P, editors. Aging Research in Yeast.

Brockmoeller SF, Bucher E, Mueller BM, Budczies J, Hilvo M, et al. (2012) Integration of Metabolomics and Expression of Glycerol-3-phosphate Acyltransferase (GPAM) in Breast Cancer-Link to Patient Survival, Hormone Receptor Status, and Metabolic Profiling. Journal of Proteome Research 11.

Budczies J, Denkert C, Mueller BM, Brockmoeller SF, Klauschen F, et al. (2012) Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study. Bmc Genomics 13.

Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, et al. (2012) Directly e-mailing authors of newly published papers encourages community curation. Database : the journal of biological databases and curation 2012.

Busch R, De Riva A, Prevosto C, Varley MC, McDonald S, et al. (2012) Kinetics of codominant MHC protein expression and implications for disease associations. Immunology 137.

Cankorur-Cetinkaya A, Dereli E, Eraslan S, Karabekmez E, Dikicioglu D, Kirdar B. (2012) A novel strategy for selection and validation of reference genes in dynamic multidimensional experimental design in yeast. PLoS One. 2012;7(6):e38351. doi: 0.1371/journal.pone.0038351. Epub 2012 Jun 4 [PubMed]

Castro C, Sar F, Shaw WR, Mishima M, Miska EA, et al. (2012) A metabolomic strategy defines the regulation of lipid content and global metabolism by Delta 9 desaturases in Caenorhabditis elegans. Bmc Genomics 13.

Chessel A, Dodgson J, Carazo-Salas RE (2012) Spherical spatial statistics for 3D fluorescence video-microscopy. 2012 IEEE 9th International Symposium on Biomedical Imaging.

Christoforou AL, Lilley KS (2012) Isobaric tagging approaches in quantitative proteomics: the ups and downs. Analytical and Bioanalytical Chemistry 404.

Chu D, Zabet N, von der Haar T (2012) A novel and versatile computational tool to model translation. Bioinformatics 28.

Contrino S, Smith RN, Butano D, Carr A, Hu F, et al. (2012) modMine: flexible access to modENCODE data. Nucleic Acids Research 40.

Davey HM, Cross EJM, Davey CL, Gkargkas K, Delneri D, et al. (2012) Genome-wide analysis of longevity in nutrient-deprived Saccharomyces cerevisiae reveals importance of recycling in maintaining cell viability. Environmental Microbiology 14.

Dereli E, Dikicioglu D, Eraslan S, Kirdar B, Oliver SG (2012) The metabolic responses of yeast to two drug agents: rapamycin and caffeine. Febs Journal 279.

Dikicioglu D, Dunn WB, Kell DB, Kirdar B, Oliver SG (2012) Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment. Molecular Biosystems 8.

Duong A, Capstick DS, Di Berardo C, Findlay KC, Hesketh A, et al. (2012) Aerial development in Streptomyces coelicolor requires sortase activity. Molecular Microbiology 83.

Eyres I, Frangedakis E, Fontaneto D, Herniou EA, Boschetti C, et al. (2012) Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers. BMC evolutionary biology 12.

Fan J, Mohareb F, Bond NJ, Lilley KS, Bessant C (2012) MRMaid 2.0: Mining PRIDE for Evidence-Based SRM Transitions. Omics-a Journal of Integrative Biology 16.

Feiglin A, Hacohen A, Sarusi A, Fisher J, Unger R, et al. (2012) Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks. Bioinformatics (Oxford, England) 28.

Fischer BE, Wasbrough E, Meadows LA, Randlet O, Dorus S, et al. (2012) Conserved properties of Drosophila and human spermatozoal mRNA repertoires. Proceedings of the Royal Society B-Biological Sciences 279.

Fu AQ, Russell, S, Bray SJ, TavaréS (2012) Bayesian clustering of replicated time-course gene expression data with weak signals Annal. Applied Stats. (In revision).

Gatto L, Lilley KS (2012) MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics 28.

Gene Ontology C (2012) The Gene Ontology: enhancements for 2011. Nucleic acids research 40.

Gottelt M, Hesketh A, Bunet R, Puri P, Takano E (2012) Characterisation of a natural variant of the gamma-butyrolactone signalling receptor. BMC research notes 5.

Habermann K, Mirgorodskaya E, Gobom J, Lehmann V, Mueller H, et al. (2012) Functional Analysis of Centrosomal Kinase Substrates in Drosophila melanogaster Reveals a New Function of the Nuclear Envelope Component Otefin in Cell Cycle Progression. Molecular and Cellular Biology 32.

Housden BE, FuAQ, Krejci A, Bernard F, Fischer B, Tavaré S, Russell S, Bray SJ (2012) Transcriptional dynamics elicited by a short pulse of Notch activation.  PLoS Gen. (In press).

Howe PWA, Ament Z, Knowles K, Griffin JL, Wright J (2012) Combined use of filtered and edited (1) H NMR spectroscopy to detect (13) C-enriched compounds in complex mixtures. NMR in biomedicine 25.

Jones OAH, Swain SC, Svendsen C, Griffin JL, Sturzenbaum SR, et al. (2012) Potential New Method of Mixture Effects Testing Using Metabolomics and Caenorhabditis elegans. Journal of Proteome Research 11.

Kasavi C, Finore I, Lama L, Nicolaus B, Oliver SG, et al. (2012) Evaluation of industrial Saccharomyces cerevisiae strains for ethanol production from biomass. Biomass & Bioenergy 45.

McQuilton P, St Pierre SE, Thurmond J, FlyBase C (2012) FlyBase 101-the basics of navigating FlyBase. Nucleic Acids Research 40.

Mercer JR, Yu E, Figg N, Cheng K-K, Prime TA, et al. (2012) The mitochondria-targeted antioxidant MitoQ decreases features of the metabolic syndrome in ATM(+/-)/ApoE(-/-) mice. Free Radical Biology and Medicine 52.

Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, et al. (2012) Putative Glycosyltransferases and Other Plant Golgi Apparatus Proteins Are Revealed by LOPIT Proteomics. Plant Physiology 160.

Nusser-Stein S, Beyer A, Rimann I, Adamczyk M, Piterman N, et al. (2012) Cell-cycle regulation of NOTCH signaling during C. elegans vulval development. Molecular systems biology 8.

Pan X, Wilson M, McConville C, Brundler M-A, Arvanitis TN, et al. (2012) The lipid composition of isolated cytoplasmic lipid droplets from a human cancer cell line, BE(2)M17. Molecular Biosystems 8.

Pir P, Gutteridge A, Wu J, Rash B, Kell DB, et al. (2012) The genetic control of growth rate: a systems biology study in yeast. Bmc Systems Biology 6.

Ralser M, Kuhl H, Ralser M, Werber M, Lehrach H, et al. (2012) The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt. Open biology 2.

Ralser M, Michel S, Breitenbach M (2012) Sirtuins as regulators of the yeast metabolic network. Frontiers in pharmacology 3.

Roote J, Russell S (2012) Toward a complete Drosophila deficiency kit. Genome Biology 13.

Russell MR, Lilley KS. (2012) Pipeline to assess the greatest source of technical variance in quantitative proteomics using metabolic labelling J Proteomics. . [Epub ahead of print]

Russell S (2012) From sequence to function: the impact of the genome sequence on Drosophila biology. Briefings in Functional Genomics 11.

Sansone S-A, Rocca-Serra P, Field D, Maguire E, Taylor C, et al. (2012) Toward interoperable bioscience data. Nature Genetics 44.

Snoek B, van der Velde K, Arends D, Li Y, Beyer A, Elvin M, Fisher J, Hajnal A, Hengartner M, Poulin G, Rodriquez M, Schmid T, Schrimpf S, Xue F, Jansen R, Jammenga J, Swertz M (2012) WormQTL - Public archive and analysis web portal for natural variation data in Caenorhabditis spp. Nucleic Acids Research (in press).

Speretta E, Jahn TR, Tartaglia GG, Favrin G, Barros TP, et al. (2012) Expression in Drosophila of Tandem Amyloid beta Peptides Provides Insights into Links between Aggregation and Neurotoxicity. Journal of Biological Chemistry 287.

Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA, et al. (2012) On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS computational biology 8.

Ubhi BK, Cheng KK, Dong J, Janowitz T, Jodrell D, et al. (2012) Targeted metabolomics identifies perturbations in amino acid metabolism that sub-classify patients with COPD. Molecular bioSystems 8.

Ubhi BK, Riley JH, Shaw PA, Lomas DA, Tal-Singer R, et al. (2012) Metabolic profiling detects biomarkers of protein degradation in COPD patients. European Respiratory Journal 40.

Vaggi F, Dodgson J, Bajpai A, Chessel A, Jordan F, et al. (2012) Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network. PLoS computational biology 8.

Virtue S, Masoodi M, Velagapudi V, Tan CY, Dale M, et al. (2012) Lipocalin Prostaglandin D Synthase and PPAR gamma 2 Coordinate to Regulate Carbohydrate and Lipid Metabolism In Vivo. Plos One 7.

Virtue S, Masoodi M, Velagapudi V, Tan CY, Dale M, et al. (2012) Lipocalin prostaglandin D synthase and PPARgamma2 coordinate to regulate carbohydrate and lipid metabolism in vivo. PloS one 7.

Vowinckel J, Stahlberg S, Paulmann N, Bluemlein K, Grohmann M, et al. (2012) Histaminylation of glutamine residues is a novel posttranslational modification implicated in G-protein signaling. FEBS letters 586.

Watson AA, Mahajan P, Mertens HDT, Deery MJ, Zhang W, et al. (2012) The PHD and Chromo Domains Regulate the ATPase Activity of the Human Chromatin Remodeler CHD4. Journal of Molecular Biology 422.

Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, et al. (2012) PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Research 40.

Zabet NR, Adryan B (2012) A comprehensive computational model to simulate transcription factor binding in prokaryotes. Information Processing in Cells and Tissues Proceedings of the 9th International Conference, IPCAT 2012.

Zabet NR, Adryan B (2012) A comprehensive computational model of facilitated diffusion in prokaryotes. Bioinformatics 28.

Zabet NR, Adryan B (2012) Computational models for large-scale simulations of facilitated diffusion. Molecular Biosystems 8.

Zabet NR, Adryan B (2012) GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics 28.

Zabet NR (2012) System size reduction in stochastic simulations of the facilitated diffusion mechanism. BMC Systems Biology 6.


Atherton HJ, Dodd MS, Heather LC, Schroeder MA, Griffin JL, et al. (2011) Role of Pyruvate Dehydrogenase Inhibition in the Development of Hypertrophy in the Hyperthyroid Rat Heart A Combined Magnetic Resonance Imaging and Hyperpolarized Magnetic Resonance Spectroscopy Study. Circulation 123.

Atzori L, Griffin JL, Scherer PE, Irminger-Finger I (2011) Editorial for the directed issue: "Metabolic pathways in cancer". International Journal of Biochemistry & Cell Biology 43.

Baker DA, Nolan T, Fischer B, Pinder A, Crisanti A, Russell S (2011) A comprehensive atlas of tissue-specific expression in the malaria vector, Anopheles gambiae, reveals genes evolved for specialized feeding and mating behaviours. BMC Genomics 12.

Baker DA, Russell S (2011) Role of Testis-Specific Gene Expression in Sex-Chromosome Evolution of Anopheles gambiae. Genetics 189.

Bilsland E, Pir P, Gutteridge A, Johns A, King RD, et al. (2011) Functional Expression of Parasite Drug Targets and Their Human Orthologs in Yeast. Plos Neglected Tropical Diseases 5.

Bitton DA, Wood V, Scutt PJ, Grallert A, Yates T, et al. (2011) Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability. Genetics 187.

Bluemlein K, Gruening N-M, Feichtinger RG, Lehrach H, Kofler B, et al. (2011) No evidence for a shift in pyruvate kinase PKM1 to PKM2 expression during tumorigenesis. Oncotarget 2.

Bluemlein K, Ralser M (2011) Monitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MS. Nature Protocols 6.

Bonzanni N, Zhang N, Oliver SG, Fisher J (2011) The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in Saccharomyces cerevisiae. Bioinformatics 27.

Bothwell JHF, Griffin JL (2011) An introduction to biological nuclear magnetic resonance spectroscopy. Biological Reviews 86.

Capuano F, Bond NJ, Gatto L, Beaudoin F, Napier JA, et al. (2011) LC-MS/MS Methods for Absolute Quantification and Identification of Proteins Associated with Chimeric Plant Oil Bodies. Analytical Chemistry 83.

Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, et al. (2011) Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. Molecular & cellular proteomics : MCP 10.

Castrillo JI, Oliver SG (2011) Yeast Systems Biology: The Challenge of Eukaryotic Complexity. In: Castrillo JI, Oliver SG, editors. Yeast Systems Biology: Methods and Protocols.

Chan Y-S, Naujoks DA, Huen DS, Russell S (2011) Insect Population Control by Homing Endonuclease-Based Gene Drive: An Evaluation in Drosophila melanogaster. Genetics 188.

Choo SW, White R, Russell S (2011) Genome-Wide Analysis of the Binding of the Hox Protein Ultrabithorax and the Hox Cofactor Homothorax in Drosophila. Plos One 6.

Chouchani ET, James AM, Fearnley IM, Lilley KS, Murphy MP (2011) Proteomic approaches to the characterization of protein thiol modification. Current Opinion in Chemical Biology 15.

Christoforou A, Lilley KS (2011) Taming the isobaric tagging elephant in the room in quantitative proteomics. Nature Methods 8.

Chu DF, Zabet NR, Hone ANW (2011) Optimal parameter settings for information processing in gene regulatory networks. Biosystems 104.

de Clare M, Pir P, Oliver SG (2011) Haploinsufficiency and the sex chromosomes from yeasts to humans. Bmc Biology 9.

Di Carli M, Zamboni A, Pe ME, Pezzotti M, Lilley KS, et al. (2011) Two-Dimensional Differential in Gel Electrophoresis (2D-DIGE) Analysis of Grape Berry Proteome during Postharvest Withering. Journal of Proteome Research 10.

Dikicioglu D, Karabekmez E, Rash B, Pir P, Kirdar B, et al. (2011) How yeast re-programmes its transcriptional profile in response to different nutrient impulses. Bmc Systems Biology 5.

Dong J-Y, Li W, Deng L-L, Xu J-J, Griffin JL, et al. (2011) New Variable Scaling Method for NMR-based Metabolomics Data Analysis. Chemical Journal of Chinese Universities-Chinese 32.

Dong J, Cheng K-K, Xu J, Chen Z, Griffin JL (2011) Group aggregating normalization method for the preprocessing of NMR-based metabolomic data. Chemometrics and Intelligent Laboratory Systems 108.

Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R, Griffin JL (2011) Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chemical Society Reviews 40.

Falick AM, Lane WS, Lilley KS, MacCoss MJ, Phinney BS, et al. (2011) ABRF-PRG07: advanced quantitative proteomics study. Journal of biomolecular techniques : JBT 22.

Fisher J, Harel D, Henzinger TA (2011) Biology as Reactivity. Communications of the Acm 54.

Fisher J, Harel D, Henzinger TA (2011) Biology as Reactivity. Communications of the Acm 54.

Friedman DB, Andacht TM, Bunger MK, Chien AS, Hawke DH, et al. (2011) The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses. Proteomics 11.

Griffin JL (2011) Ask not what data standards can do for you but what you can do for data standards: a personal view of reporting standardisation in metabolomic experiments. Metabolomics 7.

Griffin JL, Atherton HJ, Steinbeck C, Salek RM (2011) A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human.". BMC research notes 4.

Griffin JL, Atherton H, Shockcor J, Atzori L (2011) Metabolomics as a tool for cardiac research. Nature Reviews Cardiology 8.

Gruening N-M, Ralser M (2011) CANCER Sacrifice for survival. Nature 480.

Gruening N-M, Rinnerthaler M, Bluemlein K, Muelleder M, Wamelink MMC, et al. (2011) Pyruvate Kinase Triggers a Metabolic Feedback Loop that Controls Redox Metabolism in Respiring Cells. Cell Metabolism 14.

Guo J, Garrett M, Micklem G, Brogna S (2011) Poly(A) Signals Located near the 5 ' End of Genes Are Silenced by a General Mechanism That Prevents Premature 3 '-End Processing. Molecular and Cellular Biology 31.

Hallen L, Klein H, Stoschek C, Wehrmeyer S, Nonhoff U, et al. (2011) The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2. Human Molecular Genetics 20.

Hesketh A, Hill C, Mokhtar J, Novotna G, Tran N, et al. (2011) Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope. Bmc Genomics 12.

Hiemstra TF, Charles PD, Hester SS, Karet FE, Lilley KS (2011) Uromodulin exclusion list improves urinary exosomal protein identification. Journal of biomolecular techniques : JBT 22.

Hilvo M, Denkert C, Lehtinen L, Mueller B, Brockmoeller S, et al. (2011) Novel Theranostic Opportunities Offered by Characterization of Altered Membrane Lipid Metabolism in Breast Cancer Progression. Cancer Research 71.

Huang W, Ling Q, Bedard J, Lilley K, Jarvis P (2011) In Vivo Analyses of the Roles of Essential Omp85-Related Proteins in the Chloroplast Outer Envelope Membrane. Plant Physiology 157.

Hyde MJ, Clarke L, Griffin JL, Herrera E, Byrne CD, et al. (2011) A single enteral feed prior to the commencement of parenteral nutrition ameliorates the incidence of steatosis in parenterally fed neonatal piglets. Metabolomics 7.

Jones OAH, Maguire ML, Griffin JL, Jung Y-H, Shibato J, et al. (2011) Using metabolic profiling to assess plant-pathogen interactions: an example using rice (Oryza sativa) and the blast pathogen Magnaporthe grisea. European Journal of Plant Pathology 129.

Kell DB, Dobson PD, Oliver SG (2011) Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only. Drug Discovery Today 16.

King RD, Liakata M, Lu C, Oliver SG, Soldatova LN (2011) On the formalization and reuse of scientific research. Journal of the Royal Society Interface 8.

Krueger A, Gruening N-M, Wamelink MMC, Kerick M, Kirpy A, et al. (2011) The Pentose Phosphate Pathway Is a Metabolic Redox Sensor and Regulates Transcription During the Antioxidant Response. Antioxidants & Redox Signaling 15.

Krueger A, Ralser M (2011) ATM Is a Redox Sensor Linking Genome Stability and Carbon Metabolism. Science Signaling 4.

Lanthaler K, Bilsland E, Dobson PD, Moss HJ, Pir P, et al. (2011) Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast. Bmc Biology 9.

Lilley KS, Deery MJ, Gatto L (2011) Challenges for proteomics core facilities. Proteomics 11.

Lim WK, Micklem G (2011) MicroRNAs dysregulated in breast cancer preferentially target key oncogenic pathways. Molecular Biosystems 7.

Malys N, Wishart JA, Oliver SG, McCarthy JEG (2011) PROTEIN PRODUCTION IN SACCHAROMYCES CEREVISIAE FOR SYSTEMS BIOLOGY STUDIES. In: Jameson D, Verma M, Westerhoff HV, editors. Methods in Enzymology, Vol 500: Methods in Systems Biology.

Massie CE, Lynch A, Ramos-Montoya A, Boren J, Stark R, et al. (2011) The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. Embo Journal 30.

Mirbahai L, Wilson M, Shaw CS, McConville C, Malcomson RDG, et al. (2011) (1)H magnetic resonance spectroscopy metabolites as biomarkers for cell cycle arrest and cell death in rat glioma cells. International Journal of Biochemistry & Cell Biology 43.

Mole SE, Codlin S, Griffin JL (2011) Reply to Comment on "Deletion of btn1, an orthologue of CLN3, increases glycolysis and perturbs amino acid metabolism in the fission yeast model of Batten disease". Molecular Biosystems 7.

Nurmohamed S, Vincent HA, Titman CM, Chandran V, Pears MR, et al. (2011) Polynucleotide Phosphorylase Activity May Be Modulated by Metabolites in Escherichia coli. Journal of Biological Chemistry 286.

Pan X, Wilson M, Mirbahai L, McConville C, Arvanitis TN, et al. (2011) In Vitro Metabonomic Study Detects Increases in UDP-GlcNAc and UDP-GalNAc, as Early Phase Markers of Cisplatin Treatment Response in Brain Tumor Cells. Journal of Proteome Research 10.

Prevosto C, De Riva A, Wilson A, McDonald S, Usmani MF, et al. (2011) How old are your MHC proteins? The role of protein turnover in MHC codominance. Immunology 135.


Prigione A, Lichtner B, Kuhl H, Struys EA, Wamelink M, et al. (2011) Human Induced Pluripotent Stem Cells Harbor Homoplasmic and Heteroplasmic Mitochondrial DNA Mutations While Maintaining Human Embryonic Stem Cell-like Metabolic Reprogramming. Stem Cells 29.

Quan Z, Oliver SG, Zhang N (2011) JmjN interacts with JmjC to ensure selective proteolysis of Gis1 by the proteasome. Microbiology-Sgm 157.

Ratnakumar S, Hesketh A, Gkargkas K, Wilson M, Rash BM, et al. (2011) Phenomic and transcriptomic analyses reveal that autophagy plays a major role in desiccation tolerance in Saccharomyces cerevisiae. Molecular Biosystems 7.

Rees JS, Lilley KS (2011) Method for suppressing non-specific protein interactions observed with affinity resins. Methods 54.

Rees JS, Lowe N, Armean IM, Roote J, Johnson G, et al. (2011) In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry. Molecular & cellular proteomics : MCP 10.

Rees J, Lilley K (2011) Enabling Technologies for Yeast Proteome Analysis. In: Castrillo JI, Oliver SG, editors. Yeast Systems Biology: Methods and Protocols.

Roberts IN, Oliver SG (2011) The yin and yang of yeast: biodiversity research and systems biology as complementary forces driving innovation in biotechnology. Biotechnology Letters 33.

Roberts LD, Murray AJ, Menassa D, Ashmore T, Nicholls AW, et al. (2011) The contrasting roles of PPAR delta and PPAR gamma in regulating the metabolic switch between oxidation and storage of fats in white adipose tissue. Genome Biology 12.

Rotstein B, Molnar D, Adryan B, Llimargas M (2011) Tramtrack Is Genetically Upstream of Genes Controlling Tracheal Tube Size in Drosophila. Plos One 6.

Russell S (2011) 'MiMICing' genomic flexibility. Nature Methods 8.

Salek RM, Pears MR, Cooper JD, Mitchison HM, Pearce DA, et al. (2011) A metabolomic comparison of mouse models of the Neuronal Ceroid Lipofuscinoses. Journal of Biomolecular Nmr 49.

Schroeder MA, Atherton HJ, Heather LC, Griffin JL, Clarke K, et al. (2011) Determining the in vivo regulation of cardiac pyruvate dehydrogenase based on label flux from hyperpolarised 1-C-13 pyruvate. Nmr in Biomedicine 24.

Spann N, Aldridge DC, Griffin JL, Jones OAH (2011) Size-dependent effects of low level cadmium and zinc exposure on the metabolome of the Asian clam, Corbicula fluminea. Aquatic Toxicology 105.

Sykacek P, Kreil DP, Meadows LA, Auburn RP, Fischer B, et al. (2011) The impact of quantitative optimization of hybridization conditions on gene expression analysis. Bmc Bioinformatics 12.

Szappanos B, Kovacs K, Szamecz B, Honti F, Costanzo M, et al. (2011) An integrated approach to characterize genetic interaction networks in yeast metabolism. Nature Genetics 43.

Thiel UJE, Feltens R, Adryan B, Gieringer R, Brochhausen C, et al. (2011) Analysis of differentially expressed proteins in oral squamous cell carcinoma by MALDI-TOF MS. Journal of Oral Pathology & Medicine 40.

Thorne MAS, Worland MR, Feret R, Deery MJ, Lilley KS, et al. (2011) Proteomics of cryoprotective dehydration in Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola). Insect Molecular Biology 20.

Walsh J, Kitteringham NR, Griffin JL, Goldring CEP, Williams S, et al. (2011) The role of the transcription factor Nrf2 in lipid metabolism in the liver. Toxicology 290.

Washington NL, Stinson EO, Perry MD, Ruzanov P, Contrino S, et al. (2011) The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database : the journal of biological databases and curation 2011.

Zabet NR (2011) Negative feedback and physical limits of genes. Journal of Theoretical Biology 284.

Zakrzewska A, van Eikenhorst G, Burggraaff JEC, Vis DJ, Hoefsloot H, et al. (2011) Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Molecular Biology of the Cell 22.


Adryan B, Teichmann SA (2010) The developmental expression dynamics of Drosophila melanogaster transcription factors. Genome Biology 11.

Amoutzias GD, He Y, Gordon J, Mossialos D, Oliver SG, et al. (2010) Posttranslational regulation impacts the fate of duplicated genes. Proceedings of the National Academy of Sciences of the United States of America 107.

Ashrafian H, Docherty L, Leo V, Towlson C, Neilan M, et al. (2010) A Mutation in the Mitochondrial Fission Gene Dnm1l Leads to Cardiomyopathy. Plos Genetics 6.

Barnard AML, Simpson NJL, Lilley KS, Salmond GPC (2010) Mutations in rpsL that confer streptomycin resistance show pleiotropic effects on virulence and the production of a carbapenem antibiotic in Erwinia carotovora. Microbiology-Sgm 156.

Barton MD, Delneri D, Oliver SG, Rattray M, Bergman CM (2010) Evolutionary Systems Biology of Amino Acid Biosynthetic Cost in Yeast. Plos One 5.

Berardini TZ, Li D, Huala E, Bridges S, Burgess S, et al. (2010) The Gene Ontology in 2010: extensions and refinements The Gene Ontology Consortium. Nucleic Acids Research 38.

Bernard F, Krejci A, Housden B, Adryan B, Bray SJ (2010) Specificity of Notch pathway activation: Twist controls the transcriptional output in adult muscle progenitors. Development 137.

Beyer A, Thomason P, Li X, Scott J, Fisher J (2010) Mechanistic Insights into Metabolic Disturbance during Type-2 Diabetes and Obesity Using Qualitative Networks. Transactions on Computational Systems Biology Xii 5945.

Bolognesi B, Kumita JR, Barros TP, Esbjorner EK, Luheshi LM, et al. (2010) ANS Binding Reveals Common Features of Cytotoxic Amyloid Species. Acs Chemical Biology 5.

Brieger A, Adryan B, Wolpert F, Passmann S, Zeuzem S, et al. (2010) Cytoskeletal scaffolding proteins interact with Lynch-Syndrome associated mismatch repair protein MLH1. Proteomics 10.

Brorsson A-C, Bolognesi B, Tartaglia GG, Shammas SL, Favrin G, et al. (2010) Intrinsic Determinants of Neurotoxic Aggregate Formation by the Amyloid beta Peptide. Biophysical Journal 98.

Canelas AB, Harrison N, Fazio A, Zhang J, Pitkanen J-P, et al. (2010) Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nature Communications 1.

Celik E, Calik P, Oliver SG (2010) Metabolic Flux Analysis for Recombinant Protein Production by Pichia pastoris Using Dual Carbon Sources: Effects of Methanol Feeding Rate. Biotechnology and Bioengineering 105.

Charoensawan V, Adryan B, Martin S, Soellner C, Thisse B, et al. (2010) The Impact of Gene Expression Regulation on Evolution of Extracellular Signaling Pathways. Molecular & Cellular Proteomics 9.

Cheng K-K, Benson GM, Grimsditch DC, Reid DG, Connor SC, et al. (2010) Metabolomic study of the LDL receptor null mouse fed a high-fat diet reveals profound perturbations in choline metabolism that are shared with ApoE null mice. Physiological Genomics 41.

Chouchani ET, Hurd TR, Nadtochiy SM, Brookes PS, Fearnley IM, et al. (2010) Identification of S-nitrosated mitochondrial proteins by S-nitrosothiol difference in gel electrophoresis (SNO-DIGE): implications for the regulation of mitochondrial function by reversible S-nitrosation. Biochemical Journal 430.

Cossais F, Sock E, Hornig J, Schreiner S, Kellerer S, et al. (2010) Replacement of mouse Sox10 by the Drosophila ortholog Sox100B provides evidence for co-option of SoxE proteins into vertebrate-specific gene-regulatory networks through altered expression. Developmental Biology 341.

De Riva A, Deery MJ, McDonald S, Lund T, Busch R (2010) Measurement of protein synthesis using heavy water labeling and peptide mass spectrometry: Discrimination between major histocompatibility complex allotypes. Analytical Biochemistry 403.

Dobson PD, Smallbone K, Jameson D, Simeonidis E, Lanthaler K, et al. (2010) Further developments towards a genome-scale metabolic model of yeast. Bmc Systems Biology 4.

Fisher J, Piterman N (2010) The executable pathway to biological networks. Briefings in Functional Genomics 9.

Gatto L, Vizcaino JA, Hermjako H, Huber W, Lilley KS (2010) Organelle proteomics experimental designs and analysis. Proteomics 10.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, et al. (2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 330.

Griffin JL, Steinbeck C (2010) So what have data standards ever done for us? The view from metabolomics. Genome medicine 2.

Groen AJ, Lilley KS (2010) Proteomics of total membranes and subcellular membranes. Expert Review of Proteomics 7.

Gruening N-M, Lehrach H, Ralser M (2010) Regulatory crosstalk of the metabolic network. Trends in Biochemical Sciences 35.

Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, et al. (2010) Nutrient control of eukaryote cell growth: a systems biology study in yeast. Bmc Biology 8.

Hekmatyar SK, Wilson M, Jerome N, Salek RM, Griffin JL, et al. (2010) H-1 nuclear magnetic resonance spectroscopy characterisation of metabolic phenotypes in the medulloblastoma of the SMO transgenic mice. British Journal of Cancer 103.

Huen DS, Russell S (2010) On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence. Bmc Bioinformatics 11.

Hyde MJ, Griffin JL, Herrera E, Byrne CD, Clarke L, et al. (2010) Delivery by Caesarean section, rather than vaginal delivery, promotes hepatic steatosis in piglets. Clinical Science 118.

Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV, et al. (2010) Addressing Accuracy and Precision Issues in iTRAQ Quantitation. Molecular & Cellular Proteomics 9.

Kim D-U, Hayles J, Kim D, Wood V, Park H-O, et al. (2010) Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nature Biotechnology 28.

Kim D-U, Hayles J, Kim D, Wood V, Park H-O, et al. (2010) Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe (vol 28, pg 617, 2010). Nature Biotechnology 28.

Marcone GL, Beltrametti F, Binda E, Carrano L, Foulston L, et al. (2010) Novel Mechanism of Glycopeptide Resistance in the A40926 Producer Nonomuraea sp ATCC 39727. Antimicrobial Agents and Chemotherapy 54.

Martin S, Soellner C, Charoensawan V, Adryan B, Thisse B, et al. (2010) Construction of a Large Extracellular Protein Interaction Network and Its Resolution by Spatiotemporal Expression Profiling. Molecular & Cellular Proteomics 9.

Massie C, Lynch A, Stark R, Ramos-Montoya A, Fazli L, et al. (2010) Transcriptional networks downstream of the AR identify clinically relevant prostate cancer targets. Proceedings of the American Association for Cancer Research Annual Meeting 51.

McGlincy NJ, Tan L-Y, Paul N, Zavolan M, Lilley KS, et al. (2010) Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. Bmc Genomics 11.

Meadows LA, Chan YS, Roote J, Russell S (2010) Neighbourhood Continuity Is Not Required for Correct Testis Gene Expression in Drosophila. Plos Biology 8.

Mohanty S, Irback A, Mitternacht S, Favrin G, Hansmann UHE (2010) Protein folding, aggregation and unfolding in Monte Carlo Simulations. In: Landau DP, Lewis SP, Schuttler HB, editors. Computer Simulation Studies in Condensed Matter Physics Xx, Csp-2007: Proceedings of the 20th Workshop.

Negre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, et al. (2010) A Comprehensive Map of Insulator Elements for the Drosophila Genome. Plos Genetics 6.

Nilo R, Saffie C, Lilley K, Baeza-Yates R, Cambiazo V, et al. (2010) Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). Bmc Genomics 11.

Omara WAM, Rash BM, Hayes A, Wickham MSJ, Oliver SG, et al. (2010) Conditional cell-wall mutants of Saccharomyces cerevisiae as delivery vehicles for therapeutic agents in vivo to the GI tract. Journal of Biotechnology 147.

Pan X, Wilson M, McConville CM, Brundler M, Arvanitis TN, et al. (2010) Cytoplasmic lipid droplets - A novel indicator of tumour growth and potential therapeutic target in childhood brain and nervous system tumours. Neuro-Oncology 12.

Pears MR, Codlin S, Haines RL, White IJ, Mortishire-Smith RJ, et al. (2010) Deletion of btn1, an orthologue of CLN3, increases glycolysis and perturbs amino acid metabolism in the fission yeast model of Batten disease. Molecular Biosystems 6.

Pedreschi R, Hertog M, Lilley KS, Nicolai B (2010) Proteomics for the Food Industry: Opportunities and Challenges. Critical Reviews in Food Science and Nutrition 50.

Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, et al. (2010) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Research 38.

Phochanukul N, Russell S (2010) No backbone but lots of Sox: Invertebrate Sox genes. International Journal of Biochemistry & Cell Biology 42.

Prevosto C, McDonald S, Deery MJ, Gaston JSH, Busch R (2010) Measurement of HLA-B27 (B27) turnover in primary antigen-presenting cells from patients with ankylosing spondylitis (AS). Clinical and Experimental Rheumatology 28.

Requejo R, Chouchani ET, James AM, Prime TA, Lilley KS, et al. (2010) Quantification and identification of mitochondrial proteins containing vicinal dithiols. Archives of Biochemistry and Biophysics 504.

Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, NY) 330.

Rubtsov DV, Waterman C, Currie RA, Waterfield C, Salazar JD, et al. (2010) Application of a Bayesian Deconvolution Approach for High-Resolution H-1 NMR Spectra to Assessing the Metabolic Effects of Acute Phenobarbital Exposure in Liver Tissue. Analytical Chemistry 82.

Salek RM, Xia J, Innes A, Sweatman BC, Adalbert R, et al. (2010) A metabolomic study of the CRND8 transgenic mouse model of Alzheimer's disease. Neurochemistry International 56.

Segura MP, Lilley KS, Dupree P (2010) Proteomic Complex Detection using Sedimentation (ProCoDeS): screening for proteins in stable complexes and their candidate interaction partners. Biochemical Society Transactions 38.

Stickland HG, Davenport PW, Lilley KS, Griffin JL, Welch M (2010) Mutation of nfxB Causes Global Changes in the Physiology and Metabolism of Pseudomonas aeruginosa. Journal of Proteome Research 9.

Timmermann B, Jarolim S, Russmayer H, Kerick M, Michel S, et al. (2010) A new dominant peroxiredoxin allele identified by whole-genome resequencing of random mutagenized yeast causes oxidant-resistance and premature aging. Aging-Us 2.

Trotter MWB, Sadowski PG, Dunkley TPJ, Groen AJ, Lilley KS (2010) Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics 10.

Vandenbrouck T, Jones OAH, Dom N, Griffin JL, De Coen W (2010) Mixtures of similarly acting compounds in Daphnia magna: From gene to metabolite and beyond. Environment International 36.

Wamelink MMC, Gruning NM, Jansen EEW, Bleumlein K, Lehrach H, et al. (2010) The difference between rare and exceptionally rare: molecular characterisation of ribose 5-phosphate isomerase deficiency. Journal of Inherited Metabolic Disease 33.

Wamelink MMC, Gruening N-M, Jansen EEW, Bluemlein K, Lehrach H, et al. (2010) The difference between rare and exceptionally rare: molecular characterization of ribose 5-phosphate isomerase deficiency. Journal of Molecular Medicine-Jmm 88.

Wang M, Bond NJ, Letcher AJ, Richardson JP, Lilley KS, et al. (2010) Genomic tagging reveals a random association of endogenous PtdIns5P 4-kinases II alpha and II beta and a partial nuclear localization of the II alpha isoform. Biochemical Journal 430.

Wasbrough ER, Dorus S, Hester S, Howard-Murkin J, Lilley K, et al. (2010) The Drosophila melanogaster sperm proteome-II (DmSP-II). Journal of Proteomics 73.

Waterman CL, Currie RA, Cottrell LA, Dow J, Wright J, et al. (2010) An integrated functional genomic study of acute phenobarbital exposure in the rat. Bmc Genomics 11.

Waterman CL, Kian-Kai C, Griffin JL (2010) Metabolomic strategies to study lipotoxicity in cardiovascular disease. Biochimica Et Biophysica Acta-Molecular and Cell Biology of Lipids 1801.

Wilson M, Hekmatyar SK, Jerome N, Griffin JL, Peet AC, et al. (2010) Characterising metabolite profiles of medulloblastomas in transgenic SMO mice using 1H magnetic resonance spectroscopy. Neuro-Oncology 12

Zabet NR, Chu DF (2010) Stochasticity and robustness in bi-stable systems. 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2010).

Zabet NR, Chu DF (2010) Computational limits to binary genes. Journal of the Royal Society Interface 7.

Zamboni A, Di Carli M, Guzzo F, Stocchero M, Zenoni S, et al. (2010) Identification of Putative Stage-Specific Grapevine Berry Biomarkers and Omics Data Integration into Networks. Plant Physiology 154.

Zhang N, Oliver SG (2010) The Transcription Activity of Gis1 Is Negatively Modulated by Proteasome-mediated Limited Proteolysis. Journal of Biological Chemistry 285.


Aleksic J, Lazic R, Mueller I, Russell SR, Adryan B (2009) Biases in Drosophila melanogaster protein trap screens. Bmc Genomics 10.

Aleksic J, Russell S (2009) ChIPing away at the genome: the new frontier travel guide. Molecular Biosystems 5.

Atherton HJ, Gulston MK, Bailey NJ, Cheng K-K, Zhang W, et al. (2009) Metabolomics of the interaction between PPAR-alpha and age in the PPAR-alpha-null mouse. Molecular Systems Biology 5.

Atzori L, Antonucci R, Barberini L, Griffin JL, Fanos V (2009) Metabolomics: a new tool for the neonatologist. Journal of Maternal-Fetal & Neonatal Medicine 22.

Baker DA, Russell S (2009) Gene expression during Drosophila melanogaster egg development before and after reproductive diapause. Bmc Genomics 10.

Bibb M, Hesketh A (2009) ANALYZING THE REGULATION OF ANTIBIOTIC PRODUCTION IN STREPTOMYCETES. In: Hopwood DA, editor. Complex Enzymes in Microbial Natural Product Biosynthesis, Part a: Overview Articles and Peptides.

Blagden SP, Gatt MK, Archambault V, Lada K, Ichihara K, et al. (2009) Drosophila Larp associates with poly(A)-binding protein and is required for male fertility and syncytial embryo development. Developmental Biology 334.


Calik P, Celik E, Oliver SG (2009) Recombinant protein production by Mut(+) strain of Pichia pastoris using dual carbon sources: methanol and sorbitol. New Biotechnology 25.

Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, et al. (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25.

Ccedilelik E, Ccedilalinodotk P, Oliver SG (2009) A structured kinetic model for recombinant protein production by Mut + strain of Pichia pastoris. Chemical Engineering Science 64.

Celik E, Calik P, Oliver SG (2009) A structured kinetic model for recombinant protein production by Mut(+) strain of Pichia pastoris. Chemical Engineering Science 64.

Celik E, Calik P, Oliver SG (2009) Fed-batch methanol feeding strategy for recombinant protein production by Pichia pastoris in the presence of co-substrate sorbitol. Yeast 26.

Celniker SE, Dillon LAL, Gerstein MB, Gunsalus KC, Henikoff S, et al. (2009) Unlocking the secrets of the genome. Nature 459.

Chu D, Zabet NR, Mitavskiy B (2009) Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology 257.

Deery MJ, Maywood ES, Chesham JE, Sladek M, Karp NA, et al. (2009) Proteomic Analysis Reveals the Role of Synaptic Vesicle Cycling in Sustaining the Suprachiasmatic Circadian Clock. Current Biology 19.

DePristo MA, Chang L, Vale RD, Khan SM, Lipkow K (2009) Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy. Progress in Biophysics & Molecular Biology 100.

Diaz H, Andrews BA, Hayes A, Castrillo J, Oliver SG, et al. (2009) Global gene expression in recombinant and non-recombinant yeast Saccharomyces cerevisiae in three different metabolic states. Biotechnology Advances 27.

Dickens AM, Anthony DC, Claridge TDW, Mardiguian S, Cavay A, et al. (2009) PLS models discriminate types of MS from spectroscopic analysis of plasma and urinele. Multiple Sclerosis 15.

Dobson PD, Lanthaler K, Oliver SG, Kell DB (2009) Implications of the Dominant Role of Transporters in Drug Uptake by Cells. Current Topics in Medicinal Chemistry 9.

Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, et al. (2009) The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proceedings of the National Academy of Sciences of the United States of America 106.

Fu AQ, Adryan B (2009) Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays. Molecular Biosystems 5.

Garrett M, Fullaondo A, Troxler L, Micklem G, Gubb D (2009) Identification and analysis of serpin-family genes by homology and synteny across the 12 sequenced Drosophilid genomes. Bmc Genomics 10.

Gaudet P, Chisholm R, Berardini T, Dimmer E, Engel SR, et al. (2009) The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. Plos Computational Biology 5.

Griffin JL, Des Rosiers C (2009) Applications of metabolomics and proteomics to the mdx mouse model of Duchenne muscular dystrophy: lessons from downstream of the transcriptome. Genome medicine 1.

Hall SL, Hester S, Griffin JL, Lilley KS, Jackson AP (2009) The Organelle Proteome of the DT40 Lymphocyte Cell Line. Molecular & Cellular Proteomics 8.

Hesketh A, Kock H, Mootien S, Bibb M (2009) The role of absC, a novel regulatory gene for secondary metabolism, in zinc-dependent antibiotic production in Streptomyces coelicolor A3(2). Molecular Microbiology 74.

Hodson MP, Dear GJ, Griffin JL, Haselden JN (2009) An approach for the development and selection of chromatographic methods for high-throughput metabolomic screening of urine by ultra pressure LC-ESI-ToF-MS. Metabolomics 5.

Hurd TR, James AM, Lilley KS, Murphy MR (2009) MEASURING REDOX CHANGES TO MITOCHONDRIAL PROTEIN THIOLS WITH REDOX DIFFERENCE GEL ELECTROPHORESIS (REDOX-DIGE). Methods in Enzymology, Vol 456: Mitochondrial Function, Part a: Mitochondrial Electron Transport Complexes and Reactive Oxygen Species 456.

Jameson D, Turner DA, Ankers J, Kennedy S, Ryan S, et al. (2009) Information management for high content live cell imaging. Bmc Bioinformatics 10.

Karp NA, Lilley KS (2009) Investigating sample pooling strategies for DIGE experiments to address biological variability. Proteomics 9.

Kasavi C, Finore I, Nicolaus B, Oner ET, Kirdar B, et al. (2009) Comparison of industrial Saccharomyces cerevisiae strains for second generation bioethanol production. New Biotechnology 25.

King RD, Rowland J, Aubrey W, Liakata M, Markham M, et al. (2009) THE ROBOT SCIENTIST ADAM. Computer 42.

King RD, Rowland J, Oliver SG, Young M, Aubrey W, et al. (2009) Make Way for Robot Scientists. Science 325.

King RD, Rowland J, Oliver SG, Young M, Aubrey W, et al. (2009) The Automation of Science. Science 324.

Kosebent D, Ates O, Oner ET, Oliver SG, Kirdar B (2009) Fermentation performances of amylolytic Saccharomyces cerevisiae integrands developed for bioethanol production. New Biotechnology 25.

Lan MJ, McLoughlin GA, Griffin JL, Tsang TM, Huang JTJ, et al. (2009) Metabonomic analysis identifies molecular changes associated with the pathophysiology and drug treatment of bipolar disorder. Molecular Psychiatry 14.

Lane LA, Ruotolo BT, Robinson CV, Favrin G, Benesch JLP (2009) A Monte Carlo approach for assessing the specificity of protein oligomers observed in nano-electrospray mass spectra. International Journal of Mass Spectrometry 283.

Martin S, Charoensawan V, Soellner C, Adryan B, Thisse B, et al. (2009) Regulation and evolution of an extracellular glycoprotein interaction network. Mechanisms of Development 126.

McCombie G, Browning LM, Titman CM, Song M, Shockcor J, et al. (2009) omega-3 oil intake during weight loss in obese women results in remodelling of plasma triglyceride and fatty acids. Metabolomics 5.

Mead JA, Bianco L, Ottone V, Barton C, Kay RG, et al. (2009) MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions. Molecular & Cellular Proteomics 8.

Mikkelsen H, Bond NJ, Skindersoe ME, Givskov M, Lilley KS, et al. (2009) Biofilms and type III secretion are not mutually exclusive in Pseudomonas aeruginosa. Microbiology-Sgm 155.

Nanda S, DeFalco TJ, Loh SHY, Phochanukul N, Camara N, et al. (2009) Sox100B, a Drosophila Group E Sox-domain Gene, Is Required for Somatic Testis Differentiation. Sexual Development 3.

Nasrallah FA, Griffin JL, Balcar VJ, Rae C (2009) Understanding your inhibitions: effects of GABA and GABA(A) receptor modulation on brain cortical metabolism. Journal of Neurochemistry 108.

Pedreschi R, Hertog M, Robben J, Lilley KS, Karp NA, et al. (2009) Gel-Based Proteomics Approach to the Study of Metabolic Changes in Pear Tissue during Storage. Journal of Agricultural and Food Chemistry 57.

Postma L, Lehrach H, Ralser M (2009) Surviving in the cold: yeast mutants with extended hibernating lifespan are oxidant sensitive. Aging-Us 1.

Rae C, Nasrallah FA, Griffin JL, Balcar VJ (2009) Now I know my ABC. A systems neurochemistry and functional metabolomic approach to understanding the GABAergic system. Journal of Neurochemistry 109.

Ralser M, Lehrach H (2009) Building a new bridge between metabolism, free radicals and longevity. Aging-Us 1.

Ralser M, Wamelink MMC, Latkolik S, Jansen EEW, Lehrach H, et al. (2009) Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response. Nature Biotechnology 27.

Ralser M, Zeidler U, Lehrach H (2009) Interfering with Glycolysis Causes Sir2-Dependent Hyper-Recombination of Saccharomyces cerevisiae Plasmids. Plos One 4.

Reference Genome Group of the Gene Ontology C (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS computational biology 5.

Roberts LD, Hassall DG, Winegar DA, Haselden JN, Nicholls AW, et al. (2009) Increased hepatic oxidative metabolism distinguishes the action of Peroxisome proliferator-activated receptor delta from Peroxisome proliferator-activated receptor gamma in the ob/ob mouse. Genome medicine 1.

Roberts LD, Virtue S, Vidal-Puig A, Nicholls AW, Griffin JL (2009) Metabolic phenotyping of a model of adipocyte differentiation. Physiological Genomics 39.

Ryder E, Spriggs H, Drummond E, St Johnston D, Russell S (2009) The Flannotator-a gene and protein expression annotation tool for Drosophila melanogaster. Bioinformatics 25.

Schroeder MA, Atherton HJ, Ball DR, Cole MA, Heather LC, et al. (2009) Real-time assessment of Krebs cycle metabolism using hyperpolarized C-13 magnetic resonance spectroscopy. Faseb Journal 23.

Soldatova LN, Young M, Pir P, Aubrey W, King RD, et al. (2009) The robot scientist Adam. Computer 42.

Tan DJL, Dvinge H, Christoforou A, Bertone P, Arias AM, et al. (2009) Mapping Organelle Proteins and Protein Complexes in Drosophila melanogaster. Journal of Proteome Research 8.

Titman CM, Downs JA, Oliver SG, Carmichael PL, Scott AD, et al. (2009) A metabolomic and multivariate statistical process to assess the effects of genotoxins in Saccharomyces cerevisiae. Molecular Biosystems 5.

Wang DYQ, Cardelli L, Phillips A, Piterman N, Fisher J (2009) Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics. Bmc Systems Biology 3.

Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, et al. (2009) The 2008 update of the Aspergillus nidulans genome annotation: A community effort. Fungal Genetics and Biology 46.

Zhang N, Wu J, Oliver SG (2009) Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast. Microbiology-Sgm 155.


Al-Lamki RS, Wang J, Tolkovsky AM, Bradley JA, Griffin JL, et al. (2008) TL1A both promotes and protects from renal inflammation and injury. Journal of the American Society of Nephrology 19.

Allen MJ, Howard JA, Lilley KS, Wilson WH (2008) Proteomic analysis of the EhV-86 virion. Proteome Science 6.

Amoutzias GD, Robertson DL, de Peer YV, Oliver SG (2008) Choose your partners: dimerization in eukaryotic transcription factors. Trends in Biochemical Sciences 33.

Archambault V, D'Avino PP, Deery MJ, Lilley KS, Glover DM (2008) Sequestration of Polo kinase to microtubules by phosphopriming-independent binding to Map205 is relieved by phosphorylation at a CDK site in mitosis. Genes & Development 22.

Atherton HJ, Jones OAH, Malik S, Miska EA, Griffin JL (2008) A comparative metabolomic study of NHR-49 in Caenorhabditis elegans and PPAR-alpha in the mouse. Febs Letters 582.

Breitkreutz B-J, Stark C, Reguly T, Boucher L, Breitkreutz A, et al. (2008) The BioGRID interaction database: 2008 update. Nucleic Acids Research 36.

Casasoli M, Spadoni S, Lilley KS, Cervone F, De Lorenzo G, et al. (2008) Identification by 2-D DIGE of apoplastic proteins regulated by oligogalacturonides in Arabidopsis thaliana. Proteomics 8.

Cheon M, Favrin G, Chang I, Dobson CM, Vendruscolo M (2008) Calculation of the free energy barriers in the oligomerisation of A beta peptide fragments. Frontiers in Bioscience 13.

Cobbold LC, Spriggs KA, Haines SJ, Dobbyn HC, Hayes C, et al. (2008) Identification of internal ribosome entry segment (IRES)-trans-acting factors for the Myc family of IRESs. Molecular and Cellular Biology 28.

Coulthurst SJ, Lilley KS, Hedley PE, Liu H, Toth IK, et al. (2008) DsbA plays a critical and multifaceted role in the production of secreted virulence factors by the phytopathogen Erwinia carotovora subsp atroseptica. Journal of Biological Chemistry 283.

D'Avino PP, Takeda T, Capalbo L, Zhang W, Lilley KS, et al. (2008) Interaction between Anillin and RacGAP50C connects the actomyosin contractile ring with spindle microtubules at the cell division site. Journal of Cell Science 121.

De Riva A, Deery M, McDonald S, Casey S, Bluck L, et al. (2008) Measurement of MHC class II protein turnover by heavy water labelling: rheumatoid arthritis-associated DR0401 molecules are not intrinsically unstable. Immunology 125.

Delneri D, Hoyle DC, Gkargkas K, Cross EJM, Rash B, et al. (2008) Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. Nature Genetics 40.

Dikicioglu D, Pir P, Onsan ZI, Ulgen KO, Kirdar B, et al. (2008) Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae. Applied and Environmental Microbiology 74.

Dondero F, Jones OAH, Banni M, Boatti L, Minicozzi P, et al. (2008) Molecular effects of Ni and clorpyrifos in the digestive gland tissue of Mytilus galloprovincialis: A systems biology approach. Marine Environmental Research 66.

Fisher J, Henzinger TA (2008) Dichotomies between computational and mathematical models (Correspondence). Nature Biotechnology 26.

Friedman DB, Lilley KS (2008) Optimizing the difference gel electrophoresis (DIGE) technology. In: Vlahou A, editor. Clinical Proteomics: Methods and Protocols.

Gibson F, Anderson L, Babnigg G, Baker M, Berth M, et al. (2008) Guidelines for reporting the use of gel electrophoresis in proteomics. Nature Biotechnology 26.

Gleixner E, Abriss D, Adryan B, Kraemer M, Gerlach F, et al. (2008) Oxygen-induced changes in hemoglobin expression in Drosophila. Febs Journal 275.

Gomez-Escribano JP, Martin JF, Hesketh A, Bibb MJ, Liras P (2008) Streptomyces clavuligerus reIA-null mutants overproduce clavulanic acid and cephamycin C: negative regulation of secondary metabolism by (p)ppGpp. Microbiology-Sgm 154.

Griffin JL (2008) Following the role of PPARs in controlling systemic metabolism by metabolomics. European Journal of Pharmaceutical Sciences 34.

Griffin JL, Vidal-Puig A (2008) Current challenges in metabolomics for diabetes research: a vital functional genomic tool or just a ploy for gaining funding? Physiological Genomics 34.

Groen AJ, de Vries SC, Lilley KS (2008) A proteomics approach to membrane trafficking. Plant Physiology 147.

Gulston MK, Rubtsov DV, Atherton HJ, Clarke K, Davies KE, et al. (2008) A combined metabolomic and proteomic investigation of the effects of a failure to express dystrophin in the mouse heart. Journal of Proteome Research 7.

Harris MA, Deegan JI, Lomax J, Ashburner M, Tweedie S, et al. (2008) The Gene Ontology project in 2008. Nucleic Acids Research 36.

Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26.

Huang JTJ, Wang L, Prabakaran S, Wengenroth M, Lockstone HE, et al. (2008) Independent protein-profiling studies show a decrease in apolipoprotein A1 levels in schizophrenia CSF, brain and peripheral tissues. Molecular Psychiatry 13.

Jameson D, Garwood K, Garwood C, Booth T, Alper P, et al. (2008) Data capture in bioinformatics: requirements and experiences with Pedro. Bmc Bioinformatics 9.

Jones OAH, Dondero F, Viarengo A, Griffin JL (2008) Metabolic profiling of Mytilus galloprovincialis and its potential applications for pollution assessment. Marine Ecology-Progress Series 369. Jones OAH, Maguire ML, Griffin JL (2008) Environmental pollution and diabetes: a neglected association. Lancet 371.

Jones OAH, Spurgeon DJ, Svendsen C, Griffin JL (2008) A metabolomics based approach to assessing the toxicity of the polyaromatic hydrocarbon pyrene to the earthworm Lumbricus rubellus. Chemosphere 71.

Kam Na, Kugler H, Marelly R, Appleby L, Fisher J, et al. (2008) A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification. Developmental Biology 323.

Karp NA, Feret R, Rubtsov DV, Lilley KS (2008) Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics. Proteomics 8.

Kim DW, Hesketh A, Kim ES, Song JY, Lee DH, et al. (2008) Complex extracellular interactions of proteases and a protease inhibitor influence multicellular development of Streptomyces coelicolor. Molecular Microbiology 70.

Kubis SE, Lilley KS, Jarvis P (2008) Isolation and preparation of chloroplasts from Arabidopsis thaliana plants. In: Posch A, editor. Methods in Molecular Biology.

Kuhnle GGC, Joosen AMCP, Wood TR, Runswick SA, Griffin JL, et al. (2008) Detection and quantification of sucrose as dietary biomarker using gas chromatography and liquid chromatography with mass spectrometry. Rapid Communications in Mass Spectrometry 22.

Kwong C, Adryan B, Bell I, Meadows L, Russell S, et al. (2008) Stability and Dynamics of Polycomb Target Sites in Drosophila Development. Plos Genetics 4.

Li P, Castrillo JI, Velarde G, Wassink I, Soiland-Reyes S, et al. (2008) Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data. Bmc Bioinformatics 9.

Lilley KS, Dunkley TPJ (2008) Determination of genuine residents of plant endomembrane organelles using isotope tagging and multivariate statistics. In: Pflieger D, Rossier J, editors. Methods in Molecular Biology.

Lindsay HA, Baines R, ffrench-Constant R, Lilley K, Jacobs HT, et al. (2008) The Dominant Cold-Sensitive Out-Cold Mutants of Drosophila melanogaster Have Novel Missense Mutations in the Voltage-Gated Sodium Channel Gene paralytic. Genetics 180.

Lipkow K, Odde DJ (2008) Model for Protein Concentration Gradients in the Cytoplasm. Cellular and Molecular Bioengineering 1.

Pawar A, Favrin G (2008) Finite Size Effects in Simulations of Protein Aggregation. Plos One 3.

Pir P, Kirdar B, Hayes A, Oensan ZI, Uelgen KO, et al. (2008) Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S-cerevisiae. Yeast 25.

Pollock RF, Adryan B (2008) BioSAVE: Display of scored annotation within a sequence context. Bmc Bioinformatics 9.

Prieur X, Tung YCL, Griffin JL, Farooqi IS, O'Rahilly S, et al. (2008) Leptin Regulates Peripheral Lipid Metabolism Primarily through Central Effects on Food Intake. Endocrinology 149.

Ralser M, Wamelink MM, Struys EA, Gerisch B, Heeren G, et al. (2008) Re-routing of metabolic pathways is a regulated response to oxidative stress. Free Radical Research 42.

Ralser M, Benjamin IJ (2008) Reductive stress on life span extension in C. elegans. BMC research notes 1.

Ralser M, Nebel A, Kleindorp R, Krobitsch S, Lehrach H, et al. (2008) Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans. Bmc Genetics 9.

Ralser M, Wamelink MM, Struys EA, Joppich C, Krobitsch S, et al. (2008) A catabolic block does not sufficiently explain how 2-deoxy-D-glucose inhibits cell growth. Proceedings of the National Academy of Sciences of the United States of America 105.

Rhee SY, Wood V, Dolinski K, Draghici S (2008) Use and misuse of the gene ontology annotations. Nature Reviews Genetics 9.

Roberts LD, McCombie G, Titman CM, Griffin JL (2008) A matter of fat: An introduction to lipidomic profiling methods. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 871.

Russell S (2008) SNPing and chipping away at the fly genome. Nature Methods 5.

Russell S, Meadows, LM, PR Russell (2008) Microarray Technology In Practice.  Academic Press, San Diego.

Sadot A, Fisher J, Barak D, Admanit Y, Stern MJ, et al. (2008) Toward verified biological models. Ieee-Acm Transactions on Computational Biology and Bioinformatics 5.

Sadowski PG, Groen AJ, Dupree P, Lilley KS (2008) Sub-cellular localization of membrane proteins. Proteomics 8.

Salek RM, Colebrooke RE, Macintosh R, Lynch PJ, Sweatman BC, et al. (2008) A metabolomic study of brain tissues from aged mice with low expression of the vesicular monoamine transporter 2 (VMAT2) gene. Neurochemical Research 33.

Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, et al. (2008) ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Research 36.

Soanes DM, Alam I, Cornell M, Wong HM, Hedeler C, et al. (2008) Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis. Plos One 3.

Taylor CF, Binz P-A, Aebersold R, Affolter M, Barkovich R, et al. (2008) Guidelines for reporting the use of mass spectrometry in proteomics. Nature Biotechnology 26.

Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, et al. (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453.

Wyttenbach A, Hands S, King MA, Lipkow K, Tolkovsky AM (2008) Amelioration of protein misfolding disease by rapamycin - Translation or autophagy. Autophagy 4.


Adryan B, Teichmann SA (2007) Computational identification of site-specific transcription factors in Drosophila. Fly 1.

Adryan B, Woerfel G, Birch-Machin I, Gao S, Quick M, et al. (2007) Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila. Genome Biology 8.

Alam I, Hubbard SJ, Oliver SG, Rattray M (2007) A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. Bmc Genomics 8.

Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, et al. (2007) A protein interaction atlas for the nuclear hormone receptors: properties and quality of a hub-based dimerisation network. Amino Acids 33.

Amoutzias GD, Veron AS, Weiner J, III, Robinson-Rechavi M, Bornberg-Bauer E, et al. (2007) One billion years of bZIP transcription factor evolution: Conservation and change in dimerization and DNA-binding site specificity. Molecular Biology and Evolution 24.

Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, et al. (2007) A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. Bmc Systems Biology 1.

Arslan D, Ates O, Oner ET, Oliver SG, Kirdar B (2007) Construction of amylolytic nuclear petite Saccharomyces cerevisiae strains for bioethanol production by SSF. Journal of Biotechnology 131.

Baker DA, Meadows LA, Wang J, Dow JA, Russell S (2007) Variable sexually dimorphic gene expression in laboratory strains of Drosophila melanogaster. Bmc Genomics 8.

Bray D, Levin MD, Lipkow K (2007) The chemotactic behavior of computer-based surrogate bacteria. Current Biology 17.

Broom KA, Anthony DC, Lowe JP, Griffin JL, Scott H, et al. (2007) MRI and MRS alterations in the preclinical phase of murine prion disease: Association with neuropathological and behavioural changes. Neurobiology of Disease 26.

Bundy JG, Papp B, Harmston R, Browne RA, Clayson EM, et al. (2007) Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling. Genome Research 17.

Cakir T, Efe C, Dikicioglu D, Hortacsu A, Kirdar B, et al. (2007) Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains. Biotechnology Progress 23.

Carazo-Salas R, Nurse P (2007) Sorting out interphase microtubules. Molecular Systems Biology 3.

Castrillo JI, Oliver SG (2007) Metabolic control in the eukaryotic cell, a systems biology perspective. In: Stansfield I, Stark MJR, editors. Yeast Gene Analysis, Second Edition.

Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, et al. (2007) Growth control of the eukaryote cell: a systems biology study in yeast. Journal of biology 6.

Celik E, Calik P, Halloran SM, Oliver SG (2007) Production of recombinant human erythropoietin from Pichia pastoris and its structural analysis. Journal of Applied Microbiology 103.

Celik E, Calik P, Halloran SM, Oliver SG (2007) Expression and structural characterization of recombinant human erythropoietin from Pichia pastoris. Journal of Biotechnology 131.

Chen F, Archambault V, Kar A, Lio P, D'Avino PP, et al. (2007) Multiple protein phosphatases are required for mitosis in Drosophila. Current Biology 17.

Cheon M, Chang I, Mohanty S, Luheshi LM, Dobson CM, et al. (2007) Structural reorganisation and potential toxicity of oligomeric species formed during the assembly of amyloid fibrils. Plos Computational Biology 3.

Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450.

Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450.

Cornell MJ, Alam I, Soanes DM, Wong HM, Hedeler C, et al. (2007) Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi. Genome Research 17.

D'Avino PP, Archambault V, Przewloka MR, Zhang W, Lilley KS, et al. (2007) Recruitment of Polo Kinase to the Spindle Midzone during Cytokinesis Requires the Feo/Klp3A Complex. Plos One 2.

Dikicioglu D, Rash B, Dunn WB, Pir P, Hayes A, et al. (2007) Transcriptional and metabolic response of Saccharomyces cerevisiae to a nutritional perturbation when under stress. Journal of Biotechnology 131.

Edwards-Ingram L, Gitsham P, Burton N, Warhurst G, Clarke I, et al. (2007) Genotypic and physiological characterization of Saccharomyces boulardii, the probiotic strain of Saccharomyces cerevisiaev. Applied and Environmental Microbiology 73.

Ellis DI, Dunn WB, Griffin JL, Allwood JW, Goodacre R (2007) Metabolic fingerprinting as a diagnostic tool. Pharmacogenomics 8.

Ferguson BJ, Dovey CL, Lilley K, Wyllie AH, Rich T (2007) Nuclear phospholipase C gamma: Punctate distribution and association with the promyelocytic leukemia protein. Journal of Proteome Research 6.

Fineran PC, Williamson NR, Lilley KS, Salmond GPC (2007) Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. Journal of Bacteriology 189.

Fisher J, Henzinger TA (2007) Executable cell biology. Nature Biotechnology 25.

Fisher J, Piterman N, Hajnal A, Henzinger TA (2007) Predictive Modeling of signaling crosstalk during C-elegans vulval development. Plos Computational Biology 3.

Griffin JL, Kauppinen RA (2007) A metabolomics perspective of human brain tumours. Febs Journal 274.

Griffin JL, Kauppinen RA (2007) Tumour metabolomics in animal models of human cancer. Journal of Proteome Research 6.

Griffin JL, Nicholls AW, Daykin CA, Heald S, Keun HC, et al. (2007) Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments. Metabolomics 3.

Griffin JL, Salek RM (2007) Metabolomic applications to neuroscience: more challenges than chances? Expert Review of Proteomics 4.

Griffin JL, Scott J, Nicholson JK (2007) The influence of pharmacogenetics on fatty liver disease in the Wistar and Kyoto rats: A combined transcriptomic and metabonomic study. Journal of Proteome Research 6.

Griffin JL, Titman CM, Downs J, Carmichael P (2007) Screening for DNA damage using a metabolomics approach in Saccharomyces cerevisiae. Mutagenesis 22.

Gulston MK, Titman CM, Griffin JL (2007) Applications of metabolomics to understanding obesity in mouse and man. Biomarkers in Medicine 1.

Hakes L, Lovell SC, Oliver SG, Robertson DL (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proceedings of the National Academy of Sciences of the United States of America 104.

Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL (2007) All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biology 8.

Hakes L, Robertson DL, Oliver SG, Lovell SC (2007) Protein interactions from complexes: A structural perspective. Comparative and Functional Genomics.

Harrison R, Papp B, Pal C, Oliver SG, Delneri D (2007) Plasticity of genetic interactions in metabolic networks of yeast. Proceedings of the National Academy of Sciences of the United States of America 104.

Hartman NT, Sicilia F, Lilley KS, Dupree P (2007) Proteomic complex detection using sedimentation. Analytical Chemistry 79.

Hayes A, Castrillo JI, Oliver SG, Brass A, Zeef LAH (2007) Transcript analysis: A microarray approach. In: Stansfield I, Stark MJR, editors. Yeast Gene Analysis, Second Edition.

Hedeler C, Wong HM, Cornell MJ, Alam I, Soanes DM, et al. (2007) e-Fungi: a data resource for comparative analysis of fungal genomes. Bmc Genomics 8.

Hesketh A, Chen WJ, Ryding J, Chang S, Bibb M (2007) The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2). Genome Biology 8.

Hesketh A, Bucca G, Laing E, Flett F, Hotchkiss G, et al. (2007) New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures. Bmc Genomics 8.

Hodson MP, Dear GJ, Roberts AD, Haylock CL, Ball RJ, et al. (2007) A gender-specific discriminator in Sprague-Dawley rat urine: The deployment of a metabolic profiling strategy for biomarker discovery and identification. Analytical Biochemistry 362.

Holland S, Lodwig E, Sideri T, Reader T, Clarke I, et al. (2007) Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity. Genome Biology 8.

Holohan EE, Kwong C, Adryan B, Bartkuhn M, Herold M, et al. (2007) CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex. Plos Genetics 3.

Hudson SG, Garrett MJ, Carlson JW, Micklem G, Celniker SE, et al. (2007) Phylogenetic and genomewide analyses suggest a functional relationship between kayak, the drosophila fos homolog, and fig, a predicted protein phosphatase 2C nested within a kayak intron. Genetics 177.

Hurd TR, Prime TA, Harbour ME, Lilley KS, Murphy MP (2007) Detection of reactive oxygen species-sensitive thiol proteins by redox difference gel electrophoresis - Implications for mitochondrial redox signaling. Journal of Biological Chemistry 282.

Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, et al. (2007) The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology 25.

Jones OAH, Walker LA, Nicholson JK, Shore RF, Griffin JL (2007) Cellular acidosis in rodents exposed to cadmium is caused by adaptation of the tissue rather than an early effect of toxicity. Comparative Biochemistry and Physiology D-Genomics & Proteomics 2.

Karp NA, Lilley KS (2007) Design and analysis issues in quantitative proteomics studies. Proteomics 7 Suppl 1.

Karp NA, McCormick PS, Russell MR, Lilley KS (2007) Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis. Molecular & Cellular Proteomics 6.

Lilley KS (2007) The study of organelle dynamics using stable isotope Labeling. Molecular & Cellular Proteomics 6.

Lilley KS, Dupree P (2007) Mant organelle proteomics. Current Opinion in Plant Biology 10.

Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, et al. (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biology 8.

Massie CE, Adryan B, Barbosa-Morais NL, Lynch AG, Tran MG, et al. (2007) New androgen receptor genomic targets show an interaction with the ETS1 transcription factor. Embo Reports 8.

Mikkelsen H, Duck Z, Lilley KS, Welch M (2007) Interrelationships between colonies, biofilms, and planktonic cells of Pseudomonas aeruginosa. Journal of Bacteriology 189.

Morton CO, Hayes A, Wilson M, Rash BM, Oliver SG, et al. (2007) Global phenotype screening and transcript analysis outlines the inhibitory mode(s) of action of two amphibian-derived, alpha-helical, cationic peptides on Saccharomyces cerevisiae. Antimicrobial Agents and Chemotherapy 51.

Moussa CEH, Rae C, Bubb WA, Griffin JL, Deters NA, et al. (2007) Inhibitors of glutamate transport modulate distinct patterns in brain metabolism. Journal of Neuroscience Research 85.

Nasrallah FA, Griffin JL, Balcar VJ, Rae C (2007) Understanding your inhibitions: modulation of brain cortical metabolism by GABA(B) receptors. Journal of Cerebral Blood Flow and Metabolism 27.

Nonhoff U, Ralser M, Welzel F, Piccini I, Balzereit D, et al. (2007) Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules. Molecular Biology of the Cell 18.

Oliver SG (2007) Introduction to functional analysis in yeast. In: Stansfield I, Stark MJR, editors. Yeast Gene Analysis, Second Edition.

Pears MR, Rubtsov D, Mitchison HM, Cooper JD, Pearce DA, et al. (2007) Strategies for data analyses in a high resolution (1)H NMR based metabolomics study of a mouse model of Batten disease. Metabolomics 3.

Pears MR, Salek RM, Palmer DN, Kay GW, Mortishire-Smith RJ, et al. (2007) Metabolomic investigation of CLN6 neuronal ceroid lipofuscinosis in affected South Hampshire sheep. Journal of Neuroscience Research 85.

Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology 25.

Przewloka MR, Zhang W, Costa P, Archambault V, D'Avino PP, et al. (2007) Molecular Analysis of Core Kinetochore Composition and Assembly in Drosophila melanogaster. Plos One 2.

Ralser M, Wamelink MM, Kowald A, Gerisch B, Heeren G, et al. (2007) Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. Journal of biology 6.

Reddy AB, Maywood ES, Karp NA, King VM, Inoue Y, et al. (2007) Glucocorticoid signaling synchronizes the liver circadian transcriptome. Hepatology 45.

Rubtsov DV, Griffin JL (2007) Time-domain Bayesian detection and estimation of noisy damped sinusoidal signals applied to NMR spectroscopy. Journal of Magnetic Resonance 188.

Rubtsov DV, Jenkins H, Ludwig C, Easton J, Viant MR, et al. (2007) Proposed reporting requirements for the description of NMR-based metabolomics experiments. Metabolomics 3.

Ryder E, Ashburner M, Bautista-Llacer R, Drummond J, Webster J, et al. (2007) The DrosDel deletion collection: A Drosophila genomewide chromosomal deficiency resource. Genetics 177.

Salek RM, Maguire ML, Bentley E, Rubtsov DV, Hough T, et al. (2007) A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human. Physiological Genomics 29.

Salinas S, Carazo-Salas RE, Proukakis C, Schiavo G, Warner TT (2007) Spastin and microtubules: Functions in health and disease. Journal of Neuroscience Research 85.

Samsonova AA, Niranjan M, Russell S, Brazma A (2007) Prediction of gene expression in embryonic structures of Drosophila melanogaster. Plos Computational Biology 3.

Sansone S-A, Fan T, Goodacre R, Griffin JL, Hardy NW, et al. (2007) The metabolomics standards initiative. Nature Biotechnology 25.

Sansone S-A, Fan T, Goodacre R, Griffin JL, Hardy NW, et al. (2007) The metabolomics standards initiative. Nature biotechnology 25.

Schaub MA, Henzinger TA, Fisher J (2007) Qualitative networks: a symbolic approach to analyze biological signaling networks. Bmc Systems Biology 1.

Stahl M, Schuh R, Adryan B (2007) Identification of FGF-dependent genes in the Drosophila tracheal system. Gene Expression Patterns 7.

Sumner LW, Amberg A, Barrett D, Beale MH, Beger R, et al. (2007) Proposed minimum reporting standards for chemical analysis. Metabolomics 3.

Sykacek P, Clarkson R, Print C, Furlong R, Micklem G (2007) Bayesian modelling of shared gene function. Bioinformatics 23.

Taylor CF, Paton NW, Lilley KS, Binz P-A, Julian RK, Jr., et al. (2007) The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology 25.

Turck CW, Falick AM, Kowalak JA, Lane WS, Lilley KS, et al. (2007) The Association of Biomolecular Resource Facilities Proteomics Research Group 2006 Study - Relative protein quantitation. Molecular & Cellular Proteomics 6.

Viale A, Li J, Tiesman J, Hester S, Massimi A, et al. (2007) Big results from small samples: evaluation of amplification protocols for gene expression profiling. Journal of biomolecular techniques : JBT 18.

Zakrzewska A, Boorsma A, Delneri D, Brul S, Oliver SG, et al. (2007) Cellular processes and pathways that protect Saccharomyces cerevisiae cells against the plasma membrane-perturbing compound chitosan. Eukaryotic Cell 6.