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Items: 1 to 50 of 55

1.

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.

PMID:
30985253
2.

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.

3.

Doxorubicin induces an extensive transcriptional and metabolic rewiring in yeast cells.

Taymaz-Nikerel H, Karabekmez ME, Eraslan S, Kırdar B.

Sci Rep. 2018 Sep 12;8(1):13672. doi: 10.1038/s41598-018-31939-9.

4.

Transcriptomic response of yeast cells to ATX1 deletion under different copper levels.

Cankorur-Cetinkaya A, Eraslan S, Kirdar B.

BMC Genomics. 2016 Jul 11;17:489. doi: 10.1186/s12864-016-2771-6.

5.

Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations.

Taymaz-Nikerel H, Cankorur-Cetinkaya A, Kirdar B.

Front Bioeng Biotechnol. 2016 Feb 18;4:17. doi: 10.3389/fbioe.2016.00017. eCollection 2016. Review.

6.

A novel topological centrality measure capturing biologically important proteins.

Karabekmez ME, Kirdar B.

Mol Biosyst. 2016 Feb;12(2):666-73. doi: 10.1039/c5mb00732a.

PMID:
26699451
7.

An integrative analysis of transcriptomic response of ethanol tolerant strains to ethanol in Saccharomyces cerevisiae.

Kasavi C, Eraslan S, Oner ET, Kirdar B.

Mol Biosyst. 2016 Feb;12(2):464-76. doi: 10.1039/c5mb00622h.

PMID:
26661334
8.

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.

9.

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.

10.

A system based network approach to ethanol tolerance in Saccharomyces cerevisiae.

Kasavi C, Eraslan S, Arga KY, Oner ET, Kirdar B.

BMC Syst Biol. 2014 Aug 8;8:90. doi: 10.1186/s12918-014-0090-6.

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.

PMID:
24157722
12.

Transcriptional remodelling in response to changing copper levels in the Wilson and Menkes disease model of Saccharomyces cerevisiae.

Cankorur-Cetinkaya A, Eraslan S, Kirdar B.

Mol Biosyst. 2013 Nov;9(11):2889-908. doi: 10.1039/c3mb70276f.

PMID:
24056782
13.

Complex disease interventions from a network model for type 2 diabetes.

Rende D, Baysal N, Kirdar B.

PLoS One. 2013 Jun 11;8(6):e65854. doi: 10.1371/journal.pone.0065854. Print 2013.

14.

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.

15.

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.

PMID:
22491778
16.

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.

17.

A novel integrative network approach to understand the interplay between cardiovascular disease and other complex disorders.

Rende D, Baysal N, Kirdar B.

Mol Biosyst. 2011 Jul;7(7):2205-19. doi: 10.1039/c1mb05064h. Epub 2011 May 11.

PMID:
21559538
18.

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.

PMID:
21266995
19.

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB.

Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492.

20.

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.

21.

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.

22.
23.

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.

PMID:
17373823
25.

Understanding signaling in yeast: Insights from network analysis.

Arga KY, Onsan ZI, Kirdar B, Ulgen KO, Nielsen J.

Biotechnol Bioeng. 2007 Aug 1;97(5):1246-58.

PMID:
17252576
26.

Integration of metabolome data with metabolic networks reveals reporter reactions.

Cakir T, Patil KR, Onsan Zi, Ulgen KO, Kirdar B, Nielsen J.

Mol Syst Biol. 2006;2:50. Epub 2006 Oct 3.

27.

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.

28.

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.

29.

Sequence variations within the genes related to hemostatic imbalance and their impact on coronary artery disease in Turkish population.

Taymaz H, Erarslan S, Oner ET, Alkan T, Ağirbaşli M, Kirdar B.

Thromb Res. 2007;119(1):55-62. Epub 2006 Feb 10.

PMID:
16472842
30.

Production of ethanol from starch by respiration-deficient recombinant Saccharomyces cerevisiae.

Toksoy Oner E, Oliver SG, Kirdar B.

Appl Environ Microbiol. 2005 Oct;71(10):6443-5.

31.

Effect of wastewater composition on archaeal population diversity.

Akarsubasi AT, Ince O, Kirdar B, Oz NA, Orhon D, Curtis TP, Head IM, Ince BK.

Water Res. 2005 Apr;39(8):1576-84.

PMID:
15878030
32.

Why nut? The aspiration of hazelnuts has become a public health problem among small children in the central and eastern Black Sea regions of Turkey.

Tander B, Kirdar B, Aritürk E, Rizalar R, Bernay F.

Pediatr Surg Int. 2004 Jul;20(7):502-4. Epub 2004 Jun 3.

PMID:
15175891
33.

Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks.

Cakir T, Kirdar B, Ulgen KO.

Biotechnol Bioeng. 2004 May 5;86(3):251-60.

PMID:
15083505
34.

A simple structured model for biomass and extracellular enzyme production with recombinant Saccharomyces cerevisiae YPB-G.

Birol G, Kirdar B, Onsan ZI.

J Ind Microbiol Biotechnol. 2002 Sep;29(3):111-6.

PMID:
12242631
35.

Prenatal prediction of childhood-onset spinal muscular atrophy (SMA) in Turkish families.

Savas S, Eraslan S, Kantarci S, Karaman B, Acarsoz D, Tükel T, Cogulu O, Ozkinay F, Basaran S, Aydinli K, Yuksel-Apak M, Kirdar B.

Prenat Diagn. 2002 Aug;22(8):703-9.

PMID:
12210580
36.

High-level production of TaqI restriction endonuclease by three different expression systems in Escherichia coli cells using the T7 phage promoter.

Toksoy E, Onsan ZI, Kirdar B.

Appl Microbiol Biotechnol. 2002 Jul;59(2-3):239-45. Epub 2002 May 4.

PMID:
12111152
37.

Recovery of antithrombin III from milk by expanded bed chromatography.

Ozyurt S, Kirdar B, Ulgen KO.

J Chromatogr A. 2002 Jan 25;944(1-2):203-10.

PMID:
11831754
38.

Cystic fibrosis mutations and associated haplotypes in Turkish cystic fibrosis patients.

Onay T, Zielenski J, Topaloglu O, Gokgoz N, Kayserili H, Apak MY, Camcioglu Y, Cokugras H, Akcakaya N, Tsui LC, Kirdar B.

Hum Biol. 2001 Apr;73(2):191-203.

PMID:
11446424
39.

Screening of deletions in SMN, NAIP and BTF2p44 genes in Turkish spinal muscular atrophy patients.

Savas S, Gokgoz N, Kayserili H, Ozkinay F, Yuksel-Apak M, Kirdar B.

Hum Hered. 2000 May-Jun;50(3):162-5.

PMID:
10686493
40.
42.

Analysis of infertile brothers with congenital bilateral absence of vas deferens for mutations in the CFTR gene.

Onay T, Kayserili H, Apak MY, Kirdar B.

Clin Genet. 1999 Jan;55(1):63-4. No abstract available.

PMID:
10066035
43.

Study of 15 protein polymorphisms in a sample of the Turkish population.

Brega A, Scacchi R, Cuccia M, Kirdar B, Peloso G, Corbo RM.

Hum Biol. 1998 Aug;70(4):715-28.

PMID:
9686482
44.

Analysis of the CFTR gene in Turkish cystic fibrosis patients: identification of three novel mutations (3172delAC, P1013L and M1028I).

Onay T, Topaloglu O, Zielenski J, Gokgoz N, Kayserili H, Camcioglu Y, Cokugras H, Akcakaya N, Apak M, Tsui LC, Kirdar B.

Hum Genet. 1998 Feb;102(2):224-30.

PMID:
9521595
45.

Identification of the parental origin of polysomy in two 49,XXXXY cases.

Celik A, Eraslan S, Gökgöz N, Ilgin H, Başaran S, Bökesoy I, Kayserili H, Yüksel-Apak M, Kirdar B.

Clin Genet. 1997 Jun;51(6):426-9.

PMID:
9237509
46.

Modeling of recombinant yeast cells: reduction of phase space.

Birol G, Birol I, Kirdar B, Onsan ZI.

Biomed Sci Instrum. 1997;34:163-8.

PMID:
9603032
47.

Polymorphisms associated with the FVIII and FIX genes in the Turkish population.

Cçaǧlayan SH, Gökmen Y, Kirdar B.

Haemophilia. 1995 Jul;1(3):184-9. doi: 10.1111/j.1365-2516.1995.tb00065.x.

PMID:
27214537
48.

A novel 13 Bp deletion in the 3'UTR of the beta-globin gene causes beta-thalassemia in a Turkish patient.

Başak AN, Ozer A, Kirdar B, Akar N.

Hemoglobin. 1993 Dec;17(6):551-5. No abstract available.

PMID:
8144356
49.

A novel deletion in a Turkish beta-thalassemia patient detected by DGGE and direct sequencing: FSC 22-24 (-7 bp).

Ozçelik H, Başak AN, Tüzmen S, Kirdar B, Akar N.

Hemoglobin. 1993 Aug;17(4):387-91. No abstract available.

PMID:
8226099
50.

Screening of deletions and RFLP analysis in Turkish DMD/BMD families by PCR.

Gökgöz N, Kuseyri F, Topaloğlu H, Yüksel-Apak M, Kirdar B.

Clin Genet. 1993 May;43(5):261-6.

PMID:
8104108

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