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Items: 25


Metabolic response to Parkinson's disease recapitulated by the haploinsufficient diploid yeast cells hemizygous for the adrenodoxin reductase gene.

Dikicioglu D, Coxon JWMT, Oliver SG.

Mol Omics. 2019 Aug 20. doi: 10.1039/c9mo00090a. [Epub ahead of print]


Metaheuristic approaches in biopharmaceutical process development data analysis.

Gangadharan N, Turner R, Field R, Oliver SG, Slater N, Dikicioglu D.

Bioprocess Biosyst Eng. 2019 Sep;42(9):1399-1408. doi: 10.1007/s00449-019-02147-0. Epub 2019 May 22. Review.


Identification of Novel Components of Target-of-Rapamycin Signaling Pathway by Network-Based Multi-Omics Integrative Analysis.

Dereli Eke E, Arga KY, Dikicioglu D, Eraslan S, Erkol E, Celik A, Kirdar B, Di Camillo B.

OMICS. 2019 May;23(5):274-284. doi: 10.1089/omi.2019.0021. Epub 2019 Apr 13.


Dynamic modelling of the killing mechanism of action by virus-infected yeasts.

Sheppard S, Dikicioglu D.

J R Soc Interface. 2019 Mar 29;16(152):20190064. doi: 10.1098/rsif.2019.0064.


Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae.

Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG.

FEMS Yeast Res. 2019 Mar 1;19(2). pii: foz014. doi: 10.1093/femsyr/foz014.


Enhancing the functionality of a microscale bioreactor system as an industrial process development tool for mammalian perfusion culture.

Sewell DJ, Turner R, Field R, Holmes W, Pradhan R, Spencer C, Oliver SG, Slater NK, Dikicioglu D.

Biotechnol Bioeng. 2019 Jun;116(6):1315-1325. doi: 10.1002/bit.26946. Epub 2019 Feb 20.


A heuristic approach to handling missing data in biologics manufacturing databases.

Mante J, Gangadharan N, Sewell DJ, Turner R, Field R, Oliver SG, Slater N, Dikicioglu D.

Bioprocess Biosyst Eng. 2019 Apr;42(4):657-663. doi: 10.1007/s00449-018-02059-5. Epub 2019 Jan 8.


Saccharomyces cerevisiae adapted to grow in the presence of low-dose rapamycin exhibit altered amino acid metabolism.

Dikicioglu D, Dereli Eke E, Eraslan S, Oliver SG, Kirdar B.

Cell Commun Signal. 2018 Nov 20;16(1):85. doi: 10.1186/s12964-018-0298-y.


Handling variability and incompleteness of biological data by flexible nets: a case study for Wilson disease.

Júlvez J, Dikicioglu D, Oliver SG.

NPJ Syst Biol Appl. 2018 Jan 11;4:7. doi: 10.1038/s41540-017-0044-x. eCollection 2018.


Erratum: CamOptimus: a tool for exploiting complex adaptive evolution to optimise experiments and processes in biotechnology.

Cankorur-Cetinkaya A, Dias JML, Kludas J, Slater NKH, Rousu J, Oliver SG, Dikicioglu D.

Microbiology. 2017 Sep;163(9):1369. doi: 10.1099/mic.0.000530. Epub 2017 Sep 8.


Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification.

Cankorur-Cetinkaya A, Dikicioglu D, Oliver SG.

Biotechnol Bioeng. 2017 Nov;114(11):2605-2615. doi: 10.1002/bit.26380. Epub 2017 Aug 15.


CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology.

Cankorur-Cetinkaya A, Dias JML, Kludas J, Slater NKH, Rousu J, Oliver SG, Dikicioglu D.

Microbiology. 2017 Jun;163(6):829-839. doi: 10.1099/mic.0.000477. Epub 2017 Jun 21. Erratum in: Microbiology. 2017 Sep;163(9):1369.


Biomass composition: the "elephant in the room" of metabolic modelling.

Dikicioglu D, Kırdar B, Oliver SG.

Metabolomics. 2015;11(6):1690-1701. Epub 2015 Jun 11.


CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.

Fidaner IB, Cankorur-Cetinkaya A, Dikicioglu D, Kirdar B, Cemgil AT, Oliver SG.

Bioinformatics. 2016 Feb 1;32(3):388-97. doi: 10.1093/bioinformatics/btv532. Epub 2015 Sep 26.


Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells.

Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS.

Stem Cells. 2015 Sep;33(9):2712-25. doi: 10.1002/stem.2067. Epub 2015 Jun 23.


Improving functional annotation for industrial microbes: a case study with Pichia pastoris.

Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG.

Trends Biotechnol. 2014 Aug;32(8):396-9. doi: 10.1016/j.tibtech.2014.05.003. Epub 2014 Jun 11.


Yeast cells with impaired drug resistance accumulate glycerol and glucose.

Dikicioglu D, Oc S, Rash BM, Dunn WB, Pir P, Kell DB, Kirdar B, Oliver SG.

Mol Biosyst. 2014 Jan;10(1):93-102. doi: 10.1039/c2mb25512j.


Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory.

Dikicioglu D, Pir P, Oliver SG.

Biotechnol J. 2013 Sep;8(9):1017-34. doi: 10.1002/biot.201300138. Epub 2013 Aug 23. Review. Erratum in: Biotechnol J. 2014 May;9(5):709.


A novel strategy for selection and validation of reference genes in dynamic multidimensional experimental design in yeast.

Cankorur-Cetinkaya A, Dereli E, Eraslan S, Karabekmez E, Dikicioglu D, Kirdar B.

PLoS One. 2012;7(6):e38351. doi: 10.1371/journal.pone.0038351. Epub 2012 Jun 4.


Short- and long-term dynamic responses of the metabolic network and gene expression in yeast to a transient change in the nutrient environment.

Dikicioglu D, Dunn WB, Kell DB, Kirdar B, Oliver SG.

Mol Biosyst. 2012 Jun;8(6):1760-74. doi: 10.1039/c2mb05443d. Epub 2012 Apr 11.


How yeast re-programmes its transcriptional profile in response to different nutrient impulses.

Dikicioglu D, Karabekmez E, Rash B, Pir P, Kirdar B, Oliver SG.

BMC Syst Biol. 2011 Sep 25;5:148. doi: 10.1186/1752-0509-5-148.


Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.

Canelas AB, Harrison N, Fazio A, Zhang J, Pitkänen JP, van den Brink J, Bakker BM, Bogner L, Bouwman J, Castrillo JI, Cankorur A, Chumnanpuen P, Daran-Lapujade P, Dikicioglu D, van Eunen K, Ewald JC, Heijnen JJ, Kirdar B, Mattila I, Mensonides FI, Niebel A, Penttilä M, Pronk JT, Reuss M, Salusjärvi L, Sauer U, Sherman D, Siemann-Herzberg M, Westerhoff H, de Winde J, Petranovic D, Oliver SG, Workman CT, Zamboni N, Nielsen J.

Nat Commun. 2010;1:145. doi: 10.1038/ncomms1150.


Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae.

Dikicioglu D, Pir P, Onsan ZI, Ulgen KO, Kirdar B, Oliver SG.

Appl Environ Microbiol. 2008 Sep;74(18):5809-16. doi: 10.1128/AEM.00009-08. Epub 2008 Jun 27.


Flux balance analysis of a genome-scale yeast model constrained by exometabolomic data allows metabolic system identification of genetically different strains.

Cakir T, Efe C, Dikicioglu D, Hortaçsu A, Kirdar B, Oliver SG.

Biotechnol Prog. 2007 Mar-Apr;23(2):320-6. Epub 2007 Mar 21.


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