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Removing Background Co-occurrences of Transcription Factor Binding Sites Greatly Improves the Prediction of Specific Transcription Factor Cooperations.

Meckbach C, Wingender E, Gültas M.

Front Genet. 2018 May 29;9:189. doi: 10.3389/fgene.2018.00189. eCollection 2018.


Mycoplasma hyorhinis reduces sensitivity of human lung carcinoma cells to Nutlin-3 and promotes their malignant phenotype.

Boyarskikh UA, Shadrina AS, Smetanina MA, Tsepilov YA, Oscorbin IP, Kozlov VV, Kel AE, Filipenko ML.

J Cancer Res Clin Oncol. 2018 Jul;144(7):1289-1300. doi: 10.1007/s00432-018-2658-9. Epub 2018 May 8.


Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3.

Boyarskikh U, Pintus S, Mandrik N, Stelmashenko D, Kiselev I, Evshin I, Sharipov R, Stegmaier P, Kolpakov F, Filipenko M, Kel A.

BMC Med Genomics. 2018 Feb 13;11(Suppl 1):12. doi: 10.1186/s12920-018-0330-5.


Nucleotide patterns aiding in prediction of eukaryotic promoters.

Triska M, Solovyev V, Baranova A, Kel A, Tatarinova TV.

PLoS One. 2017 Nov 15;12(11):e0187243. doi: 10.1371/journal.pone.0187243. eCollection 2017.


TFClass: expanding the classification of human transcription factors to their mammalian orthologs.

Wingender E, Schoeps T, Haubrock M, Krull M, Dönitz J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D343-D347. doi: 10.1093/nar/gkx987.


mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines.

Hua X, Tang R, Xu X, Wang Z, Xu Q, Chen L, Wingender E, Li J, Zhang C, Wang J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D168-D174. doi: 10.1093/nar/gkx996.


Search for Master Regulators in Walking Cancer Pathways.

Kel AE.

Methods Mol Biol. 2017;1613:161-191. doi: 10.1007/978-1-4939-7027-8_8.


cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing.

Kechin A, Boyarskikh U, Kel A, Filipenko M.

J Comput Biol. 2017 Nov;24(11):1138-1143. doi: 10.1089/cmb.2017.0096. Epub 2017 Jul 17.


Ablation of Key Oncogenic Pathways by RITA-Reactivated p53 Is Required for Efficient Apoptosis.

Grinkevich VV, Nikulenkov F, Shi Y, Enge M, Bao W, Maljukova A, Gluch A, Kel A, Sangfelt O, Selivanova G.

Cancer Cell. 2017 May 8;31(5):724-726. doi: 10.1016/j.ccell.2017.04.014. No abstract available.


Defined Engineered Human Myocardium With Advanced Maturation for Applications in Heart Failure Modeling and Repair.

Tiburcy M, Hudson JE, Balfanz P, Schlick S, Meyer T, Chang Liao ML, Levent E, Raad F, Zeidler S, Wingender E, Riegler J, Wang M, Gold JD, Kehat I, Wettwer E, Ravens U, Dierickx P, van Laake LW, Goumans MJ, Khadjeh S, Toischer K, Hasenfuss G, Couture LA, Unger A, Linke WA, Araki T, Neel B, Keller G, Gepstein L, Wu JC, Zimmermann WH.

Circulation. 2017 May 9;135(19):1832-1847. doi: 10.1161/CIRCULATIONAHA.116.024145. Epub 2017 Feb 6.


c-Jun N-terminal kinase 2 promotes enterocyte survival and goblet cell differentiation in the inflamed intestine.

Mandić AD, Bennek E, Verdier J, Zhang K, Roubrocks S, Davis RJ, Denecke B, Gassler N, Streetz K, Kel A, Hornef M, Cubero FJ, Trautwein C, Sellge G.

Mucosal Immunol. 2017 Sep;10(5):1211-1223. doi: 10.1038/mi.2016.125. Epub 2017 Jan 18.


GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.

Yevshin I, Sharipov R, Valeev T, Kel A, Kolpakov F.

Nucleic Acids Res. 2017 Jan 4;45(D1):D61-D67. doi: 10.1093/nar/gkw951. Epub 2016 Oct 24.


Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data.

Kondrakhin Y, Valeev T, Sharipov R, Yevshin I, Kolpakov F, Kel A.

EuPA Open Proteom. 2016 Sep 15;13:14-23. doi: 10.1016/j.euprot.2016.09.001. eCollection 2016 Dec.


Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer.

Kel AE, Stegmaier P, Valeev T, Koschmann J, Poroikov V, Kel-Margoulis OV, Wingender E.

EuPA Open Proteom. 2016 Sep 9;13:1-13. doi: 10.1016/j.euprot.2016.09.002. eCollection 2016 Dec.


NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class.

Haubrock M, Hartmann F, Wingender E.

PLoS One. 2016 Aug 12;11(8):e0160803. doi: 10.1371/journal.pone.0160803. eCollection 2016.


Editorial: Systems Biology of Transcription Regulation.

Shelest E, Wingender E.

Front Genet. 2016 Jul 6;7:124. doi: 10.3389/fgene.2016.00124. eCollection 2016. No abstract available.


Identifying cell-specific microRNA transcriptional start sites.

Hua X, Chen L, Wang J, Li J, Wingender E.

Bioinformatics. 2016 Aug 15;32(16):2403-10. doi: 10.1093/bioinformatics/btw171. Epub 2016 Apr 19.


Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines.

Wlochowitz D, Haubrock M, Arackal J, Bleckmann A, Wolff A, Beißbarth T, Wingender E, Gültas M.

Front Genet. 2016 Apr 5;7:42. doi: 10.3389/fgene.2016.00042. eCollection 2016.

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