Hulselmans, Gert

A scalable SCENIC workflow for single-cell gene regulatory network analysis

Van de Sande, B., Flerin, C., Davie, K., De Waegeneer, M., Hulselmans, G., Aibar, S., Seurinck, R., Saelens, W., Cannoodt, R., Rouchon, Q., et al. (2020) · Nature Protocols

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 1,494

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., et al. (2014) · PLoS Computational Biology

Gene Regulatory Network AnalysisGenomics and Chromatin Dynamics

Cited by 900

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., et al. (2018) · Cell

Single-cell and spatial transcriptomicsGenetics, Aging, and Longevity in Model Organisms

Cited by 840

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

Bravo González-Blas, C., De Winter, S., Hulselmans, G., Hecker, N., Matetovici, I., Christiaens, V., Poovathingal, S., Wouters, J., Aibar, S., & Aerts, S. (2023) · Nature Methods

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 778

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

González-Blas, C. B., De Winter, S., Hulselmans, G., Hecker, N., Matetovici, I., Christiaens, V., Poovathingal, S., Wouters, J., Aibar, S., & Aerts, S. (2022) · Nature Methods

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 778

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

Verfaillie, A., Imrichova, H., Atak, Z. K., Dewaele, M., Rambow, F., Hulselmans, G., Christiaens, V., Svetlichnyy, D., Luciani, F., Van den Mooter, L., et al. (2015) · Nature Communications

Melanoma and MAPK PathwaysGenomics and Chromatin Dynamics

Cited by 489

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. (2019) · Nature Methods

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 456

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

Imrichová, H., Hulselmans, G., Kalender Atak, Z., Potier, D., & Aerts, S. (2015) · Nucleic Acids Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 202

Cell-type-directed design of synthetic enhancers

Taskiran, I. I., Spanier, K. I., Dickmänken, H., Kempynck, N., Pančíková, A., Ekşi, E. C., Hulselmans, G., Ismail, J. N., Theunis, K., Vandepoel, R., et al. (2024) · Nature

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 175

Decoding gene regulation in the fly brain

Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Gomez, A. E., Aughey, G., Spanier, K. I., De Rop, F. V., González-Blas, C. B., Dionne, M., et al. (2022) · Nature

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 170

Decoding gene regulation in the fly brain

Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Spanier, K. I., Bravo González-Blas, C., Quan, X. J., Papasokrati, D., Hulselmans, G., Makhzami, S., et al. (2021) · Nature

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 170

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, I. I., et al. (2018) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 155

Cross-species analysis of enhancer logic using deep learning

Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Van Aerschot, L., Hulselmans, G., Christiaens, V., Makhzami, S., Seltenhammer, M., Karras, P., et al. (2020) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 116

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

Bravo González‐Blas, C., Quan, X., Duran‐Romaña, R., Taskiran, I. I., Koldere, D., Davie, K., Christiaens, V., Makhzami, S., Hulselmans, G., de Waegeneer, M., et al. (2020) · Molecular Systems Biology

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 88

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

Bravo González-Blas, C., Matetovici, I., Hillen, H., Taskiran, I. I., Vandepoel, R., Christiaens, V., Sansores-García, L., Verboven, E., Hulselmans, G., Poovathingal, S., et al. (2024) · Nature Cell Biology

Genomics and Chromatin DynamicsSingle-cell and spatial transcriptomics

Cited by 85

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. (2016) · Genome Research

Genomics and Chromatin DynamicsCancer-related Molecular Pathways

Cited by 82

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Mylka, V., Matetovici, I., Poovathingal, S., Aerts, J., Vandamme, N., Seurinck, R., Verstaen, K., Hulselmans, G., Van den Hoecke, S., Scheyltjens, I., et al. (2022) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 53

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

Atak, Z. K., Taskiran, I. I., Demeulemeester, J., Flerin, C., Mauduit, D., Minnoye, L., Hulselmans, G., Christiaens, V., Ghanem, G.-E., Wouters, J., et al. (2021) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 48

Shared enhancer gene regulatory networks between wound and oncogenic programs

Floc'hlay, S., Balaji, R., Stanković, D., Christiaens, V. M., Bravo González-Blas, C., De Winter, S., Hulselmans, G. J., De Waegeneer, M., Quan, X., Koldere, D., et al. (2023) · eLife

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 27

Enhancer grammar of liver cell types and hepatocyte zonation states

González-Blas, C. B., Matetovici, I., Hillen, H., Taskiran, I. I., Vandepoel, R., Christiaens, V., Sansores-García, L., Verboven, E., Hulselmans, G., Poovathingal, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 5