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2007

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.