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Items: 16

1.

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.

Bravo González-Blas C, Minnoye L, Papasokrati D, Aibar S, Hulselmans G, Christiaens V, Davie K, Wouters J, Aerts S.

Nat Methods. 2019 May;16(5):397-400. doi: 10.1038/s41592-019-0367-1. Epub 2019 Apr 8.

2.

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain.

Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo González-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S.

Cell. 2018 Aug 9;174(4):982-998.e20. doi: 10.1016/j.cell.2018.05.057. Epub 2018 Jun 18.

3.

The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes.

Jacobs J, Atkins M, Davie K, Imrichova H, Romanelli L, Christiaens V, Hulselmans G, Potier D, Wouters J, Taskiran II, Paciello G, González-Blas CB, Koldere D, Aibar S, Halder G, Aerts S.

Nat Genet. 2018 Jul;50(7):1011-1020. doi: 10.1038/s41588-018-0140-x. Epub 2018 Jun 4.

4.

SCENIC: single-cell regulatory network inference and clustering.

Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S.

Nat Methods. 2017 Nov;14(11):1083-1086. doi: 10.1038/nmeth.4463. Epub 2017 Oct 9.

5.

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks.

Kalender Atak Z, Imrichova H, Svetlichnyy D, Hulselmans G, Christiaens V, Reumers J, Ceulemans H, Aerts S.

Genome Med. 2017 Aug 30;9(1):80. doi: 10.1186/s13073-017-0464-7.

6.

Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia.

Spanier KI, Jansen M, Decaestecker E, Hulselmans G, Becker D, Colbourne JK, Orsini L, De Meester L, Aerts S.

Genome Biol Evol. 2017 Jun 1;9(6):1821-1842. doi: 10.1093/gbe/evx127.

7.

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.

Genome Res. 2016 Jul;26(7):882-95. doi: 10.1101/gr.204149.116. Epub 2016 May 18.

8.

Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.

Naval-Sánchez M, Potier D, Hulselmans G, Christiaens V, Aerts S.

Mol Biol Evol. 2015 Sep;32(9):2441-55. doi: 10.1093/molbev/msv107. Epub 2015 May 4.

9.

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.

Imrichová H, Hulselmans G, Atak ZK, Potier D, Aerts S.

Nucleic Acids Res. 2015 Jul 1;43(W1):W57-64. doi: 10.1093/nar/gkv395. Epub 2015 Apr 29.

10.

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.

Nat Commun. 2015 Apr 9;6:6683. doi: 10.1038/ncomms7683.

11.

CD45 antigen negativity in T-lineage ALL correlates with PTPRC mutation and sensitivity to a selective JAK inhibitor.

Raponi S, Gianfelici V, Chiaretti S, Peragine N, Brugnoletti F, De Propris MS, Marinelli M, Hulselmans G, Aerts S, Geerdens E, Cools J, Foà R, Guarini A.

Br J Haematol. 2015 Dec;171(5):884-7. doi: 10.1111/bjh.13448. Epub 2015 Apr 8. No abstract available.

PMID:
25854815
12.

Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.

Potier D, Davie K, Hulselmans G, Naval Sanchez M, Haagen L, Huynh-Thu VA, Koldere D, Celik A, Geurts P, Christiaens V, Aerts S.

Cell Rep. 2014 Dec 24;9(6):2290-303. doi: 10.1016/j.celrep.2014.11.038. Epub 2014 Dec 18.

13.

JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model.

Degryse S, de Bock CE, Cox L, Demeyer S, Gielen O, Mentens N, Jacobs K, Geerdens E, Gianfelici V, Hulselmans G, Fiers M, Aerts S, Meijerink JP, Tousseyn T, Cools J.

Blood. 2014 Nov 13;124(20):3092-100. doi: 10.1182/blood-2014-04-566687. Epub 2014 Sep 5.

PMID:
25193870
14.

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.

PLoS Comput Biol. 2014 Jul 24;10(7):e1003731. doi: 10.1371/journal.pcbi.1003731. eCollection 2014 Jul.

15.

Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia.

Atak ZK, Gianfelici V, Hulselmans G, De Keersmaecker K, Devasia AG, Geerdens E, Mentens N, Chiaretti S, Durinck K, Uyttebroeck A, Vandenberghe P, Wlodarska I, Cloos J, Foà R, Speleman F, Cools J, Aerts S.

PLoS Genet. 2013;9(12):e1003997. doi: 10.1371/journal.pgen.1003997. Epub 2013 Dec 19.

16.

Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia.

De Keersmaecker K, Atak ZK, Li N, Vicente C, Patchett S, Girardi T, Gianfelici V, Geerdens E, Clappier E, Porcu M, Lahortiga I, Lucà R, Yan J, Hulselmans G, Vranckx H, Vandepoel R, Sweron B, Jacobs K, Mentens N, Wlodarska I, Cauwelier B, Cloos J, Soulier J, Uyttebroeck A, Bagni C, Hassan BA, Vandenberghe P, Johnson AW, Aerts S, Cools J.

Nat Genet. 2013 Feb;45(2):186-90. doi: 10.1038/ng.2508. Epub 2012 Dec 23.

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