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iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
Janky R, Verfaillie A, Imrichová H, Van de Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Naval Sanchez M, Potier D, Svetlichnyy D, Kalender Atak Z, Fiers M, Marine JC, Aerts S. Janky R, et al. Among authors: svetlichnyy d. PLoS Comput Biol. 2014 Jul 24;10(7):e1003731. doi: 10.1371/journal.pcbi.1003731. eCollection 2014 Jul. PLoS Comput Biol. 2014. PMID: 25058159 Free PMC article.
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state.
Verfaillie A, Imrichova H, Atak ZK, Dewaele M, Rambow F, Hulselmans G, Christiaens V, Svetlichnyy D, Luciani F, Van den Mooter L, Claerhout S, Fiers M, Journe F, Ghanem GE, Herrmann C, Halder G, Marine JC, Aerts S. Verfaillie A, et al. Among authors: svetlichnyy d. Nat Commun. 2015 Apr 9;6:6683. doi: 10.1038/ncomms7683. Nat Commun. 2015. PMID: 25865119 Free PMC article.
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic.
Verfaillie A, Svetlichnyy D, Imrichova H, Davie K, Fiers M, Kalender Atak Z, Hulselmans G, Christiaens V, Aerts S. Verfaillie A, et al. Among authors: svetlichnyy d. Genome Res. 2016 Jul;26(7):882-95. doi: 10.1101/gr.204149.116. Epub 2016 May 18. Genome Res. 2016. PMID: 27197205 Free PMC article.
Single-Cell Gene Expression Analysis Revealed Immune Cell Signatures of Delta COVID-19.
Shaymardanov AM, Antonova OA, Sokol AD, Deinichenko KA, Kazakova PG, Milovanov MM, Zakubansky AV, Akinshina AI, Tsypkina AV, Romanova SV, Muhin VE, Mitrofanov SI, Yudin VS, Yudin SM, Makhotenko AV, Keskinov AA, Kraevoy SA, Snigir EA, Svetlichnyy DV, Skvortsova VI. Shaymardanov AM, et al. Among authors: svetlichnyy dv. Cells. 2022 Sep 21;11(19):2950. doi: 10.3390/cells11192950. Cells. 2022. PMID: 36230912 Free PMC article.
Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer.
Katzenelenbogen Y, Sheban F, Yalin A, Yofe I, Svetlichnyy D, Jaitin DA, Bornstein C, Moshe A, Keren-Shaul H, Cohen M, Wang SY, Li B, David E, Salame TM, Weiner A, Amit I. Katzenelenbogen Y, et al. Among authors: svetlichnyy d. Cell. 2020 Aug 20;182(4):872-885.e19. doi: 10.1016/j.cell.2020.06.032. Epub 2020 Aug 11. Cell. 2020. PMID: 32783915 Free article.