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2010

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.