Saeys, Yvan

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

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

Van Hove, H., Martens, L., Scheyltjens, I., De Vlaminck, K., Pombo Antunes, A. R., De Prijck, S., Vandamme, N., De Schepper, S., Van Isterdael, G., Scott, C. L., et al. (2019) · Nature Neuroscience

Neuroinflammation and Neurodegeneration MechanismsSingle-cell and spatial transcriptomics

Cited by 1,074

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

Bone marrow-derived monocytes give rise to self-renewing and fully differentiated Kupffer cells

Scott, C. L., Zheng, F., De Baetselier, P., Martens, L., Saeys, Y., De Prijck, S., Lippens, S., Abels, C., Schoonooghe, S., Raes, G., et al. (2016) · Nature Communications

Liver physiology and pathologyImmune cells in cancer

Cited by 860

Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization

Pombo Antunes, A. R., Scheyltjens, I., Lodi, F., Messiaen, J., Antoranz, A., Duerinck, J., Kancheva, D., Martens, L., De Vlaminck, K., Van Hove, H., et al. (2021) · Nature Neuroscience

Immune cells in cancerGlioma Diagnosis and Treatment

Cited by 704

Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

Bonnardel, J., T’Jonck, W., Gaublomme, D., Browaeys, R., Scott, C. L., Martens, L., Vanneste, B., De Prijck, S., Nedospasov, S. A., Kremer, A., et al. (2019) · Immunity

Liver physiology and pathologyImmune cells in cancer

Cited by 631

Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver

Remmerie, A., Martens, L., Thoné, T., Castoldi, A., Seurinck, R., Pavie, B., Roels, J., Vanneste, B., De Prijck, S., Vanhockerhout, M., et al. (2020) · Immunity

Liver Disease Diagnosis and TreatmentLiver physiology and pathology

Cited by 592

Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity

Vanderbeke, L., Van Mol, P., Van Herck, Y., De Smet, F., Humblet-Baron, S., Martinod, K., Antoranz, A., Arijs, I., Boeckx, B., Bosisio, F. M., et al. (2021) · Nature Communications

COVID-19 Clinical Research StudiesSARS-CoV-2 and COVID-19 Research

Cited by 247

The unfolded-protein-response sensor IRE-1α regulates the function of CD8α+ dendritic cells

Osorio, F., Tavernier, S. J., Hoffmann, E., Saeys, Y., Martens, L., Vetters, J., Delrue, I., De Rycke, R., Parthoens, E., Pouliot, P., et al. (2014) · Nature Immunology

Endoplasmic Reticulum Stress and DiseaseImmunotherapy and Immune Responses

Cited by 235

CytoNorm: A Normalization Algorithm for Cytometry Data

Van Gassen, S., Gaudilliere, B., Angst, M. S., Saeys, Y., & Aghaeepour, N. (2020) · Cytometry Part A

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 234

A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma

Pozniak, J., Pedri, D., Landeloos, E., Van Herck, Y., Antoranz, A., Vanwynsberghe, L., Nowosad, A., Roda, N., Makhzami, S., Bervoets, G., et al. (2024) · Cell

Cancer Immunotherapy and BiomarkersMelanoma and MAPK Pathways

Cited by 199

Targeting ferroptosis protects against experimental (multi)organ dysfunction and death

Van Coillie, S., Van San, E., Goetschalckx, I., Wiernicki, B., Mukhopadhyay, B., Tonnus, W., Choi, S. M., Roelandt, R., Dumitrascu, C., Lamberts, L., et al. (2022) · Nature Communications

Ferroptosis and cancer prognosisIron Metabolism and Disorders

Cited by 186

Targeting ferroptosis protects against multiorgan dysfunction and death.

VandenBerghe, T., Coillie, S. V., Goetschalckx, I., Wiernicki, B., Mukhopadhyay, B., Tonnus, W., San, E. V., Choi, S. M., Roelandt, R., Dumitrascu, C., et al. (2021) · Nature Communications

Ferroptosis and cancer prognosisIron Metabolism and Disorders

Cited by 186

Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition

Mamantopoulos, M., Ronchi, F., Van Hauwermeiren, F., Vieira-Silva, S., Yilmaz, B., Martens, L., Saeys, Y., Drexler, S. K., Yazdi, A. S., Raes, J., et al. (2017) · Immunity

Gut microbiota and healthInflammasome and immune disorders

Cited by 181

The RNA Atlas expands the catalog of human non-coding RNAs

Lorenzi, L., Chiu, H.-S., Avila Cobos, F., Gross, S., Volders, P.-J., Cannoodt, R., Nuytens, J., Vanderheyden, K., Anckaert, J., Lefever, S., et al. (2021) · Nature Biotechnology

Cancer-related molecular mechanisms researchRNA Research and Splicing

Cited by 163

An evolutionary perspective on the necroptotic pathway

Dondelinger, Y., Hulpiau, P., Saeys, Y., Bertrand, M. J. M., & Vandenabeele, P. (2016) · Trends in Cell Biology

Cell death mechanisms and regulationImmune Response and Inflammation

Cited by 159

Myeloid cell heterogeneity in cancer: not a single cell alike

Kiss, M., Van Gassen, S., Movahedi, K., Saeys, Y., & Laoui, D. (2018) · Cellular Immunology

Immune cells in cancerImmunotherapy and Immune Responses

Cited by 159

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

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

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

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