Aerts, Stein

Scenic: single-cell regulatory network inference and clustering.

Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 6,520

Phenotype molding of stromal cells in the lung tumor microenvironment

Lambrechts, D., Wauters, E., Boeckx, B., Aibar, S., Nittner, D., Burton, O., Bassez, A., Decaluwé, H., Pircher, A., Van den Eynde, K., et al. (2018) · Nature Medicine

Single-cell and spatial transcriptomicsCancer Immunotherapy and Biomarkers

Cited by 1,648

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

Toward Minimal Residual Disease-Directed Therapy in Melanoma

Rambow, F., Rogiers, A., Marin-Bejar, O., Aibar, S., Femel, J., Dewaele, M., Karras, P., Brown, D., Chang, Y. H., Debiec-Rychter, M., et al. (2018) · Cell

Melanoma and MAPK PathwaysCancer Cells and Metastasis

Cited by 771

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

Moerman, T., Aibar Santos, S., Bravo González-Blas, C., Simm, J., Moreau, Y., Aerts, J., & Aerts, S. (2019) · Bioinformatics

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 621

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

Alteration of the microRNA network during the progression of Alzheimer's disease

Lau, P., Bossers, K., Janky, R., Salta, E., Frigerio, C. S., Barbash, S., Rothman, R., Sierksma, A. S. R., Thathiah, A., Greenberg, D., et al. (2013) · EMBO Molecular Medicine

MicroRNA in disease regulationAlzheimer's disease research and treatments

Cited by 474

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

Mitochondria metabolism sets the species-specific tempo of neuronal development

Iwata, R., Casimir, P., Erkol, E., Boubakar, L., Planque, M., Gallego López, I. M., Ditkowska, M., Gaspariunaite, V., Beckers, S., Remans, D., et al. (2023) · Science

Neurogenesis and neuroplasticity mechanismsMitochondrial Function and Pathology

Cited by 312

Mapping gene regulatory networks from single-cell omics data

Fiers, M. W. E. J., Minnoye, L., Aibar, S., Bravo González-Blas, C., Kalender Atak, Z., & Aerts, S. (2018) · Briefings in Functional Genomics

Gene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

Cited by 235

Chromatin accessibility profiling methods

Minnoye, L., Marinov, G. K., Krausgruber, T., Pan, L., Marand, A. P., Secchia, S., Greenleaf, W. J., Furlong, E. E. M., Zhao, K., Schmitz, R. J., et al. (2021) · Nature Reviews Methods Primers

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 206

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

Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1

van den Berghe, V., Stappers, E., Vandesande, B., Dimidschstein, J., Kroes, R., Francis, A., Conidi, A., Lesage, F., Dries, R., Cazzola, S., et al. (2013) · Neuron

Neurogenesis and neuroplasticity mechanismsAxon Guidance and Neuronal Signaling

Cited by 120

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

An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model

Atkins, M., Potier, D., Romanelli, L., Jacobs, J., Mach, J., Hamaratoglu, F., Aerts, S., & Halder, G. (2016) · Current Biology

Hippo pathway signaling and YAP/TAZGene Regulatory Network Analysis

Cited by 88