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2015

 

Anderson A, Buckle R, Favrin G, Friend S, Geschwind D, Hu H, Oliver S, Petersen R, Rossor M, St George-Hyslop P, Zhang B (2015) Big data approaches to dementia: Opportunities and challenges. In: Dementia Research and Care: Can Big Data Help?, OECD Publishing, Paris. DOI: http://dx.doi.org/10.1787/9789264228429-6-en

Aubrey W, Riley MC, Young M, King RD, Oliver SG, Clare A (2015) A tool for multiple targeted genome deletions that is precise, scar-free, and suitable for automation. PLoS ONE 10: e0142494. 

BilslandE, BeanDM, DevaneyE, OliverSG (2015) Yeast-based high-throughput screens to identify novel compounds active against Brugia malayi. PLoS Neglected Tropical Diseases

Binder BJ, Sundstrom JF, Gardner JM, Jiranek V, Oliver SG (2015) Quantifying two-dimensional filamentous and invasive growth spatial patterns in yeast colonies. PLoS Comp Biol 11: e1004070.

Bitton DA, Schubert F, Dey S, Okoniewski M, Smith GC, Khadayate S, Pancaldi V, Wood V, Bähler J.  AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast.  Front Genet. 2015 Nov 16;6:330. doi: 10.3389/fgene.2015.00330. eCollection 2015. PMID: 26635866

Castrillo JI, Oliver SG (2015) Alzheimer’s as a systems-level disease involving the interplay of multiple cellular networks. Methods in Molec Biol 1303, 3-48.

Castrillo JI and Oliver SG eds. (2015) Systems Biology of Alzheimer’s Disease. (Methods in Molec Biol), Totowa, NJ: Humana/Springer. DOI 10.1007/978-1-4939-2627-5 (555 pages)

Chuang R, Hall BA, Benque D, Cook B, Ishtiaq S, Piterman N, Taylor A, Vardi MY, Koschmieder S, Gottgens B, Fisher J (2015) Drug Target Optimization in Chronic Myeloid Leukemia Using Innovative Computational Platform. Nature Publishing Group, January.

ChughM, ScheurerC, SaxS, BilslandE, van SchalkwykDA, WichtKJ, HofmannN, Sharma A, BashyamS, SinghS, OliverSG, EganTJ, MalhotraP, SutherlandCJ, BeckH-P, WittlinS, SpangenbergT, Ding XC (2015) Identification and deconvolution of antimalarial compounds cross-resistance signals using multidrug-resistant Plasmodium falciparum strains. Antimicrob Agents Chemother 59: 1110-1118.

DikiciogluD, KırdarB, OliverSG (2015) Biomass composition: the “elephant in the room” of metabolic modelling. Metabolomics DOI: 10.1007/s11306-015-0819-2 (12 pages)

FidanerIB, Cankorur-CetinkayaA, DikiciogluD, KirdarB, Ali AT, Oliver SG (2015) CLUSTERnGO: A user-defined non-linear modelling platform for two-stage clustering of time-series data. Bioinformatics DOI: 10.1093/bioinformatics/btv532

Fraca E, Julvez J, Silva M (2015) Hybrid and hybrid adaptive Petri nets: on the computation of a reachability graph. Nonlinear Analysis: Hybrid Systems 16, 24-39.

Hesketh A, Deery MJ, Hong HJ (2015) High-resolution mass spectrometry based proteomic analysis of the response to vancomycin-induced cell wall stress in Streptomyces coelicolor A3(2). J Proteome Res  DOI: 10.1021/acs.jproteome.5b00242

Hoffman CS, Wood V, Fantes PA (2015) An ancient yeast for young geneticists: A primer on the Schizosaccharomyces pombe model system. Genetics 201, 403-423.

Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira EH, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M (2015) Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. Genome Biol. 2015 Jan 29;16(1):19. [Epub ahead of print]

Huber W et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods (In Press).

Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O'Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J (2015) The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet. 2015 Feb 9. doi: 10.1038/ng.3215. [Epub ahead of print]

Kell DB, Swainston N, Pir P, Oliver SG (2015) Membrane transporter engineering in industrial biotechnology and whole-cell biocatalysis. Trends Biotechnol. 33, 237-246.

Keller MA, Piedrafita G, Ralser M (2015) The widespread role of non-enzymatic reactions in cellular metabolism. Curr Opin Biotechnol. 2015 Jan 21;34C:153-161. doi: 10.1016/j.copbio.2014.12.020. [Epub ahead of print]

McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V (2015) PomBase 2015: Updates to the fission yeast database. Nuc Acids Res 43: D656-D661.

Mendes P, Oliver SG, Kell DB (2015) Fitting transporter activities to cellular flux concentrations and fluxes: Why the bumblebee can fly. Trends Pharmacol. Sci. 1260 (14 pages).

Michel S, Keller MA, Wamelink MC, Ralser M (2015) A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance. BMC Genetics, 2015,16:13. DOI: 10.1186/s12863-015-0171-6

Moignard V, Woodhouse S, Haghverdi L, Lilly J, Tanaka Y, Wilkinson A, Buettner F, Nishikawa SI, Piterman N, Kouskoff V, Theis F, Fisher J, Gottgens B (2015) Decoding the Transcriptional Program for Blood Development from Whole Tissue Single Cell Gene Expression Measurements. Nature Biotechnology, in press, Nature Publishing Group, January.

MulveyCM, SchröterC, Gatto L, DikiciogluD, FidanerIB ChristoforouA, DeeryMJ, ChoLTJ, NiakanKK, Martinez-AriasA, Lilley KS (2015) Cell Stem Cell DOI: 10.1002/stem.2067

Munoz-Torres M. et al ....includes Harris MA, Oliver SG, Rutherford K, Wood V (2015) The Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Research. 2015;43(Database issue):D1049-D1056. doi:10.1093/nar/gku1179.

Quan Z, Cao L, Tang Y, Yan Y, Oliver SG, Zhang N (2015) The yeast GSK-3 homologue Mck1 is a key controller of quiescence entry and chronological lifespan. PLoS Genetics 11(6), e1005282.

Runyon RS, Liu R, Wang Y, Oliver SG, Fan T-P, Zhang W (2015) Deciphering ancient combinatorial formulas: The Shexiang Baoxin pill. Science (Suppl.) S40-S42.

Watschinger K, Keller MA, McNeill E, Alam MT, Lai S, Sailer S, Rauch V, Patel J, Hermetter A, Golderer G, Geley S, Werner-Felmayer G, Plumb RS, Astarita G, Ralser M, Channon KM, Werner ER (2015) Tetrahydrobiopterin and alkylglycerol monooxygenase substantially alter the murine macrophage lipidome. Proc Natl Acad Sci U S A. 2015 Feb 9. pii: 201414887.

Williams K, Bilsland E, Sparkes A, Aubrey W, Young M, Soldatova LN, De Grave K, Ramon J, de Clare M, Sirawaraporn W, Oliver SG, King RD (2015) Cheaper faster drug development validated by the repositioning of drugs against neglected tropical diseases. J Roy Soc Interface 12: 20141289.

Yerbury J, Bean D, Favrin G (2015) Network approaches to the understanding of Alzheimer’s Disease: from model organisms to humans. Methods in Molec Biol 1303, 447-458.

Zabet NR,  Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Research January  43 (1): 84-94 doi:10.1093/ nar/gku1269