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Items: 27

1.

Next-Generation Genome-Scale Models Incorporating Multilevel 'Omics Data: From Yeast to Human.

Çakır T, Kökrek E, Avşar G, Abdik E, Pir P.

Methods Mol Biol. 2019;2049:347-363. doi: 10.1007/978-1-4939-9736-7_20.

PMID:
31602621
2.

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.

RNA Biol. 2018;15(6):829-831. doi: 10.1080/15476286.2018.1460996. Epub 2018 May 9.

3.

PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K.

Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VY, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Clark J, Hawkins PT, Stephens LR.

Mol Cell. 2017 Nov 2;68(3):566-580.e10. doi: 10.1016/j.molcel.2017.09.024. Epub 2017 Oct 19.

4.

Photorefractive Keratectomy With Mitomycin-C for High Myopia: Three Year Follow-Up Results.

Hashemi H, Salimi Y, Pir P, Asgari S.

Acta Med Iran. 2017 Jan;55(1):42-48.

5.

Toward Community Standards and Software for Whole-Cell Modeling.

Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10.

6.

Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine.

Pir P, Le Novère N.

Methods Mol Biol. 2016;1386:331-50. doi: 10.1007/978-1-4939-3283-2_15. Review.

PMID:
26677190
7.

Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis.

Kell DB, Swainston N, Pir P, Oliver SG.

Trends Biotechnol. 2015 Apr;33(4):237-46. doi: 10.1016/j.tibtech.2015.02.001. Epub 2015 Mar 3. Review.

8.

Control analysis of the eukaryotic cell cycle using gene copy-number series in yeast tetraploids.

Alcasabas AA, de Clare M, Pir P, Oliver SG.

BMC Genomics. 2013 Oct 31;14:744. doi: 10.1186/1471-2164-14-744.

9.

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.

PMID:
24157722
10.

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.

11.

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.

Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JE, Paton NW, Westerhoff HV, Kell DB, Mendes P.

FEBS Lett. 2013 Sep 2;587(17):2832-41. doi: 10.1016/j.febslet.2013.06.043. Epub 2013 Jul 4.

12.

Yeast-based automated high-throughput screens to identify anti-parasitic lead compounds.

Bilsland E, Sparkes A, Williams K, Moss HJ, de Clare M, Pir P, Rowland J, Aubrey W, Pateman R, Young M, Carrington M, King RD, Oliver SG.

Open Biol. 2013 Feb 27;3(2):120158. doi: 10.1098/rsob.120158.

13.

A prototrophic deletion mutant collection for yeast metabolomics and systems biology.

Mülleder M, Capuano F, Pir P, Christen S, Sauer U, Oliver SG, Ralser M.

Nat Biotechnol. 2012 Dec;30(12):1176-8. doi: 10.1038/nbt.2442. No abstract available.

14.

The genetic control of growth rate: a systems biology study in yeast.

Pir P, Gutteridge A, Wu J, Rash B, Kell DB, Zhang N, Oliver SG.

BMC Syst Biol. 2012 Jan 13;6:4. doi: 10.1186/1752-0509-6-4.

15.

Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast.

Lanthaler K, Bilsland E, Dobson PD, Moss HJ, Pir P, Kell DB, Oliver SG.

BMC Biol. 2011 Oct 24;9:70. doi: 10.1186/1741-7007-9-70.

16.

Functional expression of parasite drug targets and their human orthologs in yeast.

Bilsland E, Pir P, Gutteridge A, Johns A, King RD, Oliver SG.

PLoS Negl Trop Dis. 2011 Oct;5(10):e1320. doi: 10.1371/journal.pntd.0001320. Epub 2011 Oct 4.

17.

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.

18.

Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach.

Carroll KM, Simpson DM, Eyers CE, Knight CG, Brownridge P, Dunn WB, Winder CL, Lanthaler K, Pir P, Malys N, Kell DB, Oliver SG, Gaskell SJ, Beynon RJ.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007633. doi: 10.1074/mcp.M111.007633. Epub 2011 Sep 19.

19.

Haploinsufficiency and the sex chromosomes from yeasts to humans.

de Clare M, Pir P, Oliver SG.

BMC Biol. 2011 Feb 28;9:15. doi: 10.1186/1741-7007-9-15.

20.

Further developments towards a genome-scale metabolic model of yeast.

Dobson PD, Smallbone K, Jameson D, Simeonidis E, Lanthaler K, Pir P, Lu C, Swainston N, Dunn WB, Fisher P, Hull D, Brown M, Oshota O, Stanford NJ, Kell DB, King RD, Oliver SG, Stevens RD, Mendes P.

BMC Syst Biol. 2010 Oct 28;4:145. doi: 10.1186/1752-0509-4-145.

21.

Nutrient control of eukaryote cell growth: a systems biology study in yeast.

Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, Oliver SG.

BMC Biol. 2010 May 24;8:68. doi: 10.1186/1741-7007-8-68.

22.

Make way for robot scientists.

King RD, Rowland J, Oliver SG, Young M, Aubrey W, Byrne E, Liakata M, Markham M, Pir P, Soldatova LN, Sparkes A, Whelan KE, Clare A.

Science. 2009 Aug 21;325(5943):945. doi: 10.1126/science.325_945a. No abstract available.

PMID:
19696334
23.

The automation of science.

King RD, Rowland J, Oliver SG, Young M, Aubrey W, Byrne E, Liakata M, Markham M, Pir P, Soldatova LN, Sparkes A, Whelan KE, Clare A.

Science. 2009 Apr 3;324(5923):85-9. doi: 10.1126/science.1165620.

24.

Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae.

Pir P, Kirdar B, Hayes A, Onsan ZI, Ulgen KO, Oliver SG.

Yeast. 2008 Sep;25(9):661-72. doi: 10.1002/yea.1612.

25.

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.

26.

Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches.

Pir P, Ulgen KO, Hayes A, Ilsen Onsan Z, Kirdar B, Oliver SG.

Yeast. 2006 May;23(7):553-71.

27.

Integrative investigation of metabolic and transcriptomic data.

Pir P, Kirdar B, Hayes A, Onsan ZY, Ulgen KO, Oliver SG.

BMC Bioinformatics. 2006 Apr 12;7:203.

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