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Items: 39

1.

pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks.

Ulgen E, Ozisik O, Sezerman OU.

Front Genet. 2019 Sep 25;10:858. doi: 10.3389/fgene.2019.00858. eCollection 2019.

2.

Whole exome sequencing-based analysis to identify DNA damage repair deficiency as a major contributor to gliomagenesis in adult diffuse gliomas.

Ülgen E, Can Ö, Bilguvar K, Oktay Y, Akyerli CB, Danyeli AE, Yakıcıer MC, Sezerman OU, Pamir MN, Özduman K.

J Neurosurg. 2019 Apr 5:1-12. doi: 10.3171/2019.1.JNS182938. [Epub ahead of print]

PMID:
30952131
3.

Identification of epilepsy related pathways using genome-wide DNA methylation measures: A trio-based approach.

Ozdemir O, Egemen E, Ugur Iseri SA, Sezerman OU, Bebek N, Baykan B, Ozbek U.

PLoS One. 2019 Feb 8;14(2):e0211917. doi: 10.1371/journal.pone.0211917. eCollection 2019.

4.

First Report and In Silico Analysis of Leishmania virus (LRV2) identified in an autochthonous Leishmania major isolate in Turkey.

Kurt Ö, Mansur N, Çavuş İ, Özcan O, Batir MB, Gündüz C, Sezerman OU, Özbilgin A.

New Microbiol. 2019 Jan;42(1):64-67. Epub 2019 Jan 21.

5.

Comparison of Dendritic Cell Activation by Virus-Based Vaccine Delivery Vectors Emphasizes the Transcriptional Downregulation of the Oxidative Phosphorylation Pathway.

Tsitoura E, Kazazi D, Oz-Arslan D, Sever EA, Khalili S, Vassilaki N, Aslanoglou E, Dérian N, Six A, Sezerman OU, Klatzmann D, Mavromara P.

Hum Gene Ther. 2019 Apr;30(4):429-445. doi: 10.1089/hum.2018.161. Epub 2019 Jan 25.

PMID:
30351174
6.

Computational drug repurposing to predict approved and novel drug-disease associations.

Khalid Z, Sezerman OU.

J Mol Graph Model. 2018 Oct;85:91-96. doi: 10.1016/j.jmgm.2018.08.005. Epub 2018 Aug 14.

PMID:
30130693
7.
8.

Thermostability of the PYL-PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants.

Timucin E, Sezerman OU.

J Chem Inf Model. 2018 Mar 26;58(3):661-672. doi: 10.1021/acs.jcim.7b00655. Epub 2018 Feb 21.

PMID:
29437392
9.

Enhancing Reuse of Data and Biological Material in Medical Research: From FAIR to FAIR-Health.

Holub P, Kohlmayer F, Prasser F, Mayrhofer MT, Schlünder I, Martin GM, Casati S, Koumakis L, Wutte A, Kozera Ł, Strapagiel D, Anton G, Zanetti G, Sezerman OU, Mendy M, Valík D, Lavitrano M, Dagher G, Zatloukal K, van Ommen GB, Litton JE.

Biopreserv Biobank. 2018 Apr;16(2):97-105. doi: 10.1089/bio.2017.0110. Epub 2018 Jan 23. Review.

10.

ZK DrugResist 2.0: A TextMiner to extract semantic relations of drug resistance from PubMed.

Khalid Z, Sezerman OU.

J Biomed Inform. 2017 May;69:93-98. doi: 10.1016/j.jbi.2017.04.002. Epub 2017 Apr 4.

11.

Computational approaches for de novo design and redesign of metal-binding sites on proteins.

Akcapinar GB, Sezerman OU.

Biosci Rep. 2017 Mar 27;37(2). pii: BSR20160179. doi: 10.1042/BSR20160179. Print 2017 Apr 28. Review.

12.

Ligand binding pocket of a novel Allatostatin receptor type C of stick insect, Carausius morosus.

Duan Sahbaz B, Sezerman OU, Torun H, Birgül Iyison N.

Sci Rep. 2017 Jan 24;7:41266. doi: 10.1038/srep41266.

13.

Prediction of HIV Drug Resistance by Combining Sequence and Structural Properties.

Khalid Z, Sezerman OU.

IEEE/ACM Trans Comput Biol Bioinform. 2018 May-Jun;15(3):966-973. doi: 10.1109/TCBB.2016.2638821. Epub 2016 Dec 13.

PMID:
27992346
14.

RACK1 Is an Interaction Partner of ATG5 and a Novel Regulator of Autophagy.

Erbil S, Oral O, Mitou G, Kig C, Durmaz-Timucin E, Guven-Maiorov E, Gulacti F, Gokce G, Dengjel J, Sezerman OU, Gozuacik D.

J Biol Chem. 2016 Aug 5;291(32):16753-65. doi: 10.1074/jbc.M115.708081. Epub 2016 Jun 20.

15.

IDH-mutant glioma specific association of rs55705857 located at 8q24.21 involves MYC deregulation.

Oktay Y, Ülgen E, Can Ö, Akyerli CB, Yüksel Ş, Erdemgil Y, Durası IM, Henegariu OI, Nanni EP, Selevsek N, Grossmann J, Erson-Omay EZ, Bai H, Gupta M, Lee W, Turcan Ş, Özpınar A, Huse JT, Sav MA, Flanagan A, Günel M, Sezerman OU, Yakıcıer MC, Pamir MN, Özduman K.

Sci Rep. 2016 Jun 10;6:27569. doi: 10.1038/srep27569.

16.

Design and characterizations of two novel cellulases through single-gene shuffling of Cel12A (EG3) gene from Trichoderma reseei.

Yenenler A, Sezerman OU.

Protein Eng Des Sel. 2016 Jun;29(6):219-229. doi: 10.1093/protein/gzw011. Epub 2016 Apr 28.

PMID:
27129352
17.

Prediction of neddylation sites from protein sequences and sequence-derived properties.

Yavuz AS, Sözer NB, Sezerman OU.

BMC Bioinformatics. 2015;16 Suppl 18:S9. doi: 10.1186/1471-2105-16-S18-S9. Epub 2015 Dec 9.

18.

A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology.

Ozer B, Sezerman OU.

BMC Genomics. 2015;16 Suppl 12:S7. doi: 10.1186/1471-2164-16-S12-S7. Epub 2015 Dec 9.

19.

Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5.

Timucin E, Cousido-Siah A, Mitschler A, Podjarny A, Sezerman OU.

Proteins. 2016 Jan;84(1):129-42. doi: 10.1002/prot.24961. Epub 2015 Dec 9.

PMID:
26573720
20.

Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure.

Ozden S, Turgut Kara N, Sezerman OU, Durasi İM, Chen T, Demirel G, Alpertunga B, Chipman JK, Mally A.

Toxicol Appl Pharmacol. 2015 Dec 1;289(2):203-12. doi: 10.1016/j.taap.2015.09.023. Epub 2015 Sep 30.

PMID:
26431795
21.

Zinc Modulates Self-Assembly of Bacillus thermocatenulatus Lipase.

Timucin E, Sezerman OU.

Biochemistry. 2015 Jun 30;54(25):3901-10. doi: 10.1021/acs.biochem.5b00200. Epub 2015 Jun 22.

PMID:
26057387
22.

CSF Proteomics Identifies Specific and Shared Pathways for Multiple Sclerosis Clinical Subtypes.

Avsar T, Durası İM, Uygunoğlu U, Tütüncü M, Demirci NO, Saip S, Sezerman OU, Siva A, Tahir Turanlı E.

PLoS One. 2015 May 5;10(5):e0122045. doi: 10.1371/journal.pone.0122045. eCollection 2015.

23.

Molecular diversity of LysM carbohydrate-binding motifs in fungi.

Akcapinar GB, Kappel L, Sezerman OU, Seidl-Seiboth V.

Curr Genet. 2015 May;61(2):103-13. doi: 10.1007/s00294-014-0471-9. Epub 2015 Jan 15. Review.

24.

Reply to Stoimenis et al.

Bakir-Gungor B, Remmers EF, Meguro A, Mizuki N, Kastner DL, Gul A, Sezerman OU.

Eur J Hum Genet. 2015 Oct;23(10):1280. doi: 10.1038/ejhg.2014.288. Epub 2015 Jan 14. No abstract available.

25.

Predicting sumoylation sites using support vector machines based on various sequence features, conformational flexibility and disorder.

Yavuz AS, Sezerman OU.

BMC Genomics. 2014;15 Suppl 9:S18. doi: 10.1186/1471-2164-15-S9-S18. Epub 2014 Dec 8.

26.

Identification of possible pathogenic pathways in Behçet's disease using genome-wide association study data from two different populations.

Bakir-Gungor B, Remmers EF, Meguro A, Mizuki N, Kastner DL, Gul A, Sezerman OU.

Eur J Hum Genet. 2015 May;23(5):678-87. doi: 10.1038/ejhg.2014.158. Epub 2014 Sep 17.

27.

Direct in vitro selection of titanium-binding epidermal growth factor.

Tada S, Timucin E, Kitajima T, Sezerman OU, Ito Y.

Biomaterials. 2014 Apr;35(11):3497-503. doi: 10.1016/j.biomaterials.2014.01.010. Epub 2014 Jan 26.

PMID:
24477191
28.

PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data.

Bakir-Gungor B, Egemen E, Sezerman OU.

Bioinformatics. 2014 May 1;30(9):1287-9. doi: 10.1093/bioinformatics/btt743. Epub 2014 Jan 11.

PMID:
24413675
29.

The conserved lid tryptophan, W211, potentiates thermostability and thermoactivity in bacterial thermoalkalophilic lipases.

Timucin E, Sezerman OU.

PLoS One. 2013 Dec 31;8(12):e85186. doi: 10.1371/journal.pone.0085186. eCollection 2013.

30.

MIR376A is a regulator of starvation-induced autophagy.

Korkmaz G, Tekirdag KA, Ozturk DG, Kosar A, Sezerman OU, Gozuacik D.

PLoS One. 2013 Dec 16;8(12):e82556. doi: 10.1371/journal.pone.0082556. eCollection 2013. Erratum in: PLoS One. 2014;9(7):e103385.

31.

Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data.

Bakir-Gungor B, Baykan B, Ugur İseri S, Tuncer FN, Sezerman OU.

Epilepsy Res. 2013 Jul;105(1-2):92-102. doi: 10.1016/j.eplepsyres.2013.02.008. Epub 2013 Mar 14.

PMID:
23498093
32.

The identification of pathway markers in intracranial aneurysm using genome-wide association data from two different populations.

Bakir-Gungor B, Sezerman OU.

PLoS One. 2013;8(3):e57022. doi: 10.1371/journal.pone.0057022. Epub 2013 Mar 6.

33.

Prediction of peptides binding to MHC class I and II alleles by temporal motif mining.

Meydan C, Otu HH, Sezerman OU.

BMC Bioinformatics. 2013;14 Suppl 2:S13. doi: 10.1186/1471-2105-14-S2-S13. Epub 2013 Jan 21.

34.

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure.

Bakış Y, Otu HH, Taşçı N, Meydan C, Bilgin N, Yüzbaşıoğlu S, Sezerman OU.

BMC Bioinformatics. 2013 Jan 17;14:20. doi: 10.1186/1471-2105-14-20.

35.

The Vroman effect: competitive protein exchange with dynamic multilayer protein aggregates.

Hirsh SL, McKenzie DR, Nosworthy NJ, Denman JA, Sezerman OU, Bilek MM.

Colloids Surf B Biointerfaces. 2013 Mar 1;103:395-404. doi: 10.1016/j.colsurfb.2012.10.039. Epub 2012 Nov 23.

PMID:
23261559
36.

A new methodology to associate SNPs with human diseases according to their pathway related context.

Bakir-Gungor B, Sezerman OU.

PLoS One. 2011;6(10):e26277. doi: 10.1371/journal.pone.0026277. Epub 2011 Oct 25.

37.

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes.

Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A.

Brief Bioinform. 2009 Sep;10(5):475-89. doi: 10.1093/bib/bbp022. Epub 2009 Apr 21. Review.

PMID:
19383843
38.

Application of automatic mutation-gene pair extraction to diseases.

Erdogmus M, Sezerman OU.

J Bioinform Comput Biol. 2007 Dec;5(6):1261-75.

PMID:
18172928
39.

Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization.

Vajda S, Jafri MS, Sezerman OU, DeLisi C.

Biopolymers. 1993 Jan;33(1):173-92.

PMID:
8427934

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