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Items: 17

1.

A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State.

Szczerbinska I, Gonzales KAU, Cukuroglu E, Ramli MNB, Lee BPG, Tan CP, Wong CK, Rancati GI, Liang H, Göke J, Ng HH, Chan YS.

Stem Cell Reports. 2019 Oct 8;13(4):612-626. doi: 10.1016/j.stemcr.2019.08.005. Epub 2019 Sep 12.

2.

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.

Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J.

Cell. 2019 Sep 5;178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018.

PMID:
31491388
3.

Tumor-associated B cells and humoral immune response in head and neck squamous cell carcinoma.

Lechner A, Schlößer HA, Thelen M, Wennhold K, Rothschild SI, Gilles R, Quaas A, Siefer OG, Huebbers CU, Cukuroglu E, Göke J, Hillmer A, Gathof B, Meyer MF, Klussmann JP, Shimabukuro-Vornhagen A, Theurich S, Beutner D, von Bergwelt-Baildon M.

Oncoimmunology. 2019 Jan 10;8(3):1535293. doi: 10.1080/2162402X.2018.1535293. eCollection 2019.

4.

B cells in esophago-gastric adenocarcinoma are highly differentiated, organize in tertiary lymphoid structures and produce tumor-specific antibodies.

Schlößer HA, Thelen M, Lechner A, Wennhold K, Garcia-Marquez MA, Rothschild SI, Staib E, Zander T, Beutner D, Gathof B, Gilles R, Cukuroglu E, Göke J, Shimabukuro-Vornhagen A, Drebber U, Quaas A, Bruns CJ, Hölscher AH, Von Bergwelt-Baildon MS.

Oncoimmunology. 2018 Nov 2;8(1):e1512458. doi: 10.1080/2162402X.2018.1512458. eCollection 2019.

PMID:
30546950
5.

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.

Schmidt F, List M, Cukuroglu E, Köhler S, Göke J, Schulz MH.

Bioinformatics. 2018 Sep 1;34(17):i908-i916. doi: 10.1093/bioinformatics/bty553.

6.

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

Do DV, Strauss B, Cukuroglu E, Macaulay I, Wee KB, Hu TX, Igor RLM, Lee C, Harrison A, Butler R, Dietmann S, Jernej U, Marioni J, Smith CWJ, Göke J, Surani MA.

Cell Discov. 2018 Jun 19;4:33. doi: 10.1038/s41421-018-0032-3. eCollection 2018.

7.

EZH2 promotes neoplastic transformation through VAV interaction-dependent extranuclear mechanisms.

Venkatesan N, Wong JF, Tan KP, Chung HH, Yau YH, Cukuroglu E, Allahverdi A, Nordenskiöld L, Göke J, Geifman-Shochat S, Lin VCL, Madhusudhan MS, Su IH.

Oncogene. 2018 Jan 25;37(4):461-477. doi: 10.1038/onc.2017.309. Epub 2017 Oct 2.

PMID:
28967906
8.

Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins.

Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A.

Sci Rep. 2017 Aug 3;7(1):7180. doi: 10.1038/s41598-017-07351-0.

9.

Disrupting Interactions Between β-Catenin and Activating TCFs Reconstitutes Ground State Pluripotency in Mouse Embryonic Stem Cells.

Saj A, Chatterjee SS, Zhu B, Cukuroglu E, Gocha T, Zhang X, Göke J, DasGupta R.

Stem Cells. 2017 Aug;35(8):1924-1933. doi: 10.1002/stem.2647. Epub 2017 Jun 15.

10.

Midbrain-like Organoids from Human Pluripotent Stem Cells Contain Functional Dopaminergic and Neuromelanin-Producing Neurons.

Jo J, Xiao Y, Sun AX, Cukuroglu E, Tran HD, Göke J, Tan ZY, Saw TY, Tan CP, Lokman H, Lee Y, Kim D, Ko HS, Kim SO, Park JH, Cho NJ, Hyde TM, Kleinman JE, Shin JH, Weinberger DR, Tan EK, Je HS, Ng HH.

Cell Stem Cell. 2016 Aug 4;19(2):248-257. doi: 10.1016/j.stem.2016.07.005. Epub 2016 Jul 28.

11.

Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells.

Itahana Y, Zhang J, Göke J, Vardy LA, Han R, Iwamoto K, Cukuroglu E, Robson P, Pouladi MA, Colman A, Itahana K.

Sci Rep. 2016 Jun 27;6:28112. doi: 10.1038/srep28112.

12.

Molecular Features Underlying Neurodegeneration Identified through In Vitro Modeling of Genetically Diverse Parkinson's Disease Patients.

Lin L, Göke J, Cukuroglu E, Dranias MR, VanDongen AM, Stanton LW.

Cell Rep. 2016 Jun 14;15(11):2411-26. doi: 10.1016/j.celrep.2016.05.022. Epub 2016 Jun 2.

13.

Hot spots in protein-protein interfaces: towards drug discovery.

Cukuroglu E, Engin HB, Gursoy A, Keskin O.

Prog Biophys Mol Biol. 2014 Nov-Dec;116(2-3):165-73. doi: 10.1016/j.pbiomolbio.2014.06.003. Epub 2014 Jul 2. Review.

PMID:
24997383
14.

PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.

Baspinar A, Cukuroglu E, Nussinov R, Keskin O, Gursoy A.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W285-9. doi: 10.1093/nar/gku397. Epub 2014 May 14.

15.

Non-redundant unique interface structures as templates for modeling protein interactions.

Cukuroglu E, Gursoy A, Nussinov R, Keskin O.

PLoS One. 2014 Jan 27;9(1):e86738. doi: 10.1371/journal.pone.0086738. eCollection 2014.

16.

HotRegion: a database of predicted hot spot clusters.

Cukuroglu E, Gursoy A, Keskin O.

Nucleic Acids Res. 2012 Jan;40(Database issue):D829-33. doi: 10.1093/nar/gkr929. Epub 2011 Nov 12.

17.

Analysis of hot region organization in hub proteins.

Cukuroglu E, Gursoy A, Keskin O.

Ann Biomed Eng. 2010 Jun;38(6):2068-78. doi: 10.1007/s10439-010-0048-9. Epub 2010 May 1.

PMID:
20437205

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