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2008

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.