Affiliation: Katholieke Universiteit Leuven
Potier D, Davie K, Hulselmans G, Naval Sanchez M, Haagen L, Huynh Thu V, et al
. Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. Cell Rep. 2014;9:2290-303 pubmed publisher
..We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general cofactor in the eye network, being bound to thousands of nucleosome-free regions. ..
ImrichovÃ¡ H, Hulselmans G, Atak Z, Potier D, Aerts S. i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. Nucleic Acids Res. 2015;43:W57-64 pubmed publisher
..Use of i-cisTarget is free and open to all, and there is no login requirement. Address: http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget. ..
Aerts S, Quan X, Claeys A, Naval Sanchez M, Tate P, Yan J, et al
. Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. PLoS Biol. 2010;8:e1000435 pubmed publisher
..The validated set of novel Ato targets exhibit functional enrichment of signaling molecules and a subset is predicted to be coregulated by other TFs within the retinal gene regulatory network. ..
Jin M, Aibar S, Ge Z, Chen R, Aerts S, Mardon G. Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets. Dev Biol. 2016;415:157-167 pubmed publisher
..Moreover, since So is highly conserved throughout the metazoa, our results provide the basis for future functional studies in a wide variety of organisms. ..
Atkins M, Potier D, Romanelli L, Jacobs J, Mach J, Hamaratoglu F, et al
. An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model. Curr Biol. 2016;26:2101-13 pubmed publisher
..Thus, modeling regulatory networks identified an ectopic andÂ ordered network of master regulators that control aÂ large part of tumor cell-specific gene expression. ..
Janky R, Binda M, Allemeersch J, Van den Broeck A, Govaere O, Swinnen J, et al
. Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma. BMC Cancer. 2016;16:632 pubmed publisher
..The study was registered at ClinicalTrials.gov under the number NCT01116791 (May 3, 2010). ..
Potier D, Seyres D, Guichard C, Iché Torres M, Aerts S, Herrmann C, et al
. Identification of cis-regulatory modules encoding temporal dynamics during development. BMC Genomics. 2014;15:534 pubmed publisher
..In addition, our results suggest a modular architecture of the regulatory machinery, in which the temporal and spatial regulation can be uncoupled and encoded by distinct CRMs. ..
Dabrowski M, Aerts S, Kaminska B. Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus. BMC Bioinformatics. 2006;7:367 pubmed
Naval Sanchez M, Potier D, Hulselmans G, Christiaens V, Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Mol Biol Evol. 2015;32:2441-55 pubmed publisher
..In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence. ..