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2011

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.

Prevosto C, McDonald S, De Riva A, Goodman R, Key T, et al. (2011) ALLELE-SPECIFIC MEASUREMENT OF MHC PROTEIN TURNOVER IN DENDRITIC CELLS: APPLICATION TO ANKYLOSING SPONDYLITIS. Rheumatology 50.

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.