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2012

 

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.