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Gert Hulselmans
Gert Hulselmans
Adresse e-mail validée de kuleuven.be
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SCENIC: single-cell regulatory network inference and clustering
S Aibar, CB González-Blas, T Moerman, VA Huynh-Thu, H Imrichova, ...
Nature methods 14 (11), 1083-1086, 2017
32982017
iRegulon: from a gene list to a gene regulatory network using large motif and track collections
R Janky, A Verfaillie, H Imrichová, B Van de Sande, L Standaert, ...
PLoS computational biology 10 (7), e1003731, 2014
7872014
A single-cell transcriptome atlas of the aging Drosophila brain
K Davie, J Janssens, D Koldere, M De Waegeneer, U Pech, Ł Kreft, ...
Cell 174 (4), 982-998. e20, 2018
6272018
A scalable SCENIC workflow for single-cell gene regulatory network analysis
B Van de Sande, C Flerin, K Davie, M De Waegeneer, G Hulselmans, ...
Nature protocols 15 (7), 2247-2276, 2020
6132020
Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia
K De Keersmaecker, ZK Atak, N Li, C Vicente, S Patchett, T Girardi, ...
Nature genetics 45 (2), 186-190, 2013
4452013
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state
A Verfaillie, H Imrichova, ZK Atak, M Dewaele, F Rambow, G Hulselmans, ...
Nature communications 6 (1), 6683, 2015
4122015
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data
C Bravo González-Blas, L Minnoye, D Papasokrati, S Aibar, ...
Nature methods 16 (5), 397-400, 2019
3072019
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly
H Imrichová, G Hulselmans, Z Kalender Atak, D Potier, S Aerts
Nucleic acids research 43 (W1), W57-W64, 2015
1742015
Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia
Z Kalender Atak, V Gianfelici, G Hulselmans, K De Keersmaecker, ...
PLoS genetics 9 (12), e1003997, 2013
1702013
Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma
J Wouters, Z Kalender-Atak, L Minnoye, KI Spanier, M De Waegeneer, ...
Nature Cell Biology 22 (8), 986-998, 2020
1662020
JAK3 mutants transform hematopoietic cells through JAK1 activation, causing T-cell acute lymphoblastic leukemia in a mouse model
S Degryse, CE De Bock, L Cox, S Demeyer, O Gielen, N Mentens, ...
Blood, The Journal of the American Society of Hematology 124 (20), 3092-3100, 2014
1522014
The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes
J Jacobs, M Atkins, K Davie, H Imrichova, L Romanelli, V Christiaens, ...
Nature genetics 50 (7), 1011-1020, 2018
1352018
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
C Bravo González-Blas, S De Winter, G Hulselmans, N Hecker, ...
Nature methods 20 (9), 1355-1367, 2023
1122023
Decoding gene regulation in the fly brain
J Janssens, S Aibar, II Taskiran, JN Ismail, AE Gomez, G Aughey, ...
Nature 601 (7894), 630-636, 2022
1092022
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
A Verfaillie, D Svetlichnyy, H Imrichova, K Davie, M Fiers, ZK Atak, ...
Genome research 26 (7), 882-895, 2016
772016
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference
D Potier, K Davie, G Hulselmans, MN Sanchez, L Haagen, D Koldere, ...
Cell reports 9 (6), 2290-2303, 2014
772014
Cross-species analysis of enhancer logic using deep learning
L Minnoye, II Taskiran, D Mauduit, M Fazio, L Van Aerschot, ...
Genome research 30 (12), 1815-1834, 2020
752020
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
C Bravo González‐Blas, XJ Quan, R Duran‐Romaña, II Taskiran, ...
Molecular systems biology 16 (5), e9438, 2020
582020
Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning
ZK Atak, II Taskiran, J Demeulemeester, C Flerin, D Mauduit, L Minnoye, ...
Genome research 31 (6), 1082-1096, 2021
392021
Cell-type-directed design of synthetic enhancers
II Taskiran, KI Spanier, H Dickmänken, N Kempynck, A Pančíková, ...
Nature 626 (7997), 212-220, 2024
372024
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