Saelens, Wouter

NicheNet: Modeling intercellular communication by linking ligands to target genes

Browaeys, R., Saelens, W., & Saeys, Y. (2020) · Nature Methods

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 2,192

A comparison of single-cell trajectory inference methods

Saelens, W., Cannoodt, R., Todorov, H., & Saeys, Y. (2019) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 1,670

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

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

Guilliams, M., Bonnardel, J., Haest, B., Vanderborght, B., Wagner, C., Remmerie, A., Bujko, A., Martens, L., Thoné, T., Browaeys, R., et al. (2022) · Cell

Single-cell and spatial transcriptomicsLiver physiology and pathology

Cited by 985

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Cannoodt, R., Saelens, W., Deconinck, L., & Saeys, Y. (2021) · Nature Communications

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 124

dyngen: a multi-modal simulator for spearheading new single-cell omics analyses

Cannoodt, R., Saelens, W., Deconinck, L., & Saeys, Y. (2020) · Nature Communications

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 124

Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair

De Ponti, F. F., Bujko, A., Liu, Z., Collins, P. J., Schuermans, S., Maueroder, C., Amstelveen, S., Thoné, T., Martens, L., McKendrick, J. G., et al. (2025) · Immunity

Liver physiology and pathologyImmune cells in cancer

Cited by 94

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

Bues, J., Biočanin, M., Pezoldt, J., Dainese, R., Chrisnandy, A., Rezakhani, S., Saelens, W., Gardeux, V., Gupta, R., Sarkis, R., et al. (2022) · Nature Methods

Single-cell and spatial transcriptomicsInnovative Microfluidic and Catalytic Techniques Innovation

Cited by 71

Essential guidelines for computational method benchmarking

Weber, L. M., Saelens, W., Cannoodt, R., Soneson, C., Hapfelmeier, A., Gardner, P. P., Boulesteix, A.-L., Saeys, Y., & Robinson, M. D. (2019) · Genome Biology

Scientific Computing and Data ManagementGenomics and Phylogenetic Studies

Cited by 21

Spatially restricted and ontogenically distinct hepatic macrophages are required for tissue repair

De Ponti, F. F., Bujko, A., Liu, Z., Collins, P. J., Schuermans, S., Maueröder, C., Amstelveen, S., Thoné, T., Martens, L., McKendrick, J. G., et al. (2025) · Immunity

Liver physiology and pathologyImmune cells in cancer

Cited by 13