| A comparison of single-cell trajectory inference methods W Saelens, R Cannoodt, H Todorov, Y Saeys Nature biotechnology 37 (5), 547-554, 2019 | 1300 | 2019 |
| NicheNet: modeling intercellular communication by linking ligands to target genes R Browaeys, W Saelens, Y Saeys Nature methods 17 (2), 159-162, 2020 | 998 | 2020 |
| Yolk sac macrophages, fetal liver, and adult monocytes can colonize an empty niche and develop into functional tissue-resident macrophages L van de Laar, W Saelens, S De Prijck, L Martens, CL Scott, ... Immunity 44 (4), 755-768, 2016 | 609 | 2016 |
| 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 | 602 | 2020 |
| Trajectory-based differential expression analysis for single-cell sequencing data K Van den Berge, H Roux de Bézieux, K Street, W Saelens, R Cannoodt, ... Nature communications 11 (1), 1201, 2020 | 441 | 2020 |
| Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches M Guilliams, J Bonnardel, B Haest, B Vanderborght, C Wagner, ... Cell 185 (2), 379-396. e38, 2022 | 386 | 2022 |
| Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly H Li, J Janssens, M De Waegeneer, SS Kolluru, K Davie, V Gardeux, ... Science 375 (6584), eabk2432, 2022 | 347 | 2022 |
| A comprehensive evaluation of module detection methods for gene expression data W Saelens, R Cannoodt, Y Saeys Nature communications 9 (1), 1090, 2018 | 264 | 2018 |
| Computational methods for trajectory inference from single‐cell transcriptomics R Cannoodt, W Saelens, Y Saeys European journal of immunology 46 (11), 2496-2506, 2016 | 205 | 2016 |
| The transcription factor ZEB2 is required to maintain the tissue-specific identities of macrophages CL Scott, W T’Jonck, L Martens, H Todorov, D Sichien, B Soen, ... Immunity 49 (2), 312-325. e5, 2018 | 197 | 2018 |
| The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2 CL Scott, B Soen, L Martens, N Skrypek, W Saelens, J Taminau, ... Journal of Experimental Medicine 213 (6), 897-911, 2016 | 152 | 2016 |
| Essential guidelines for computational method benchmarking LM Weber, W Saelens, R Cannoodt, C Soneson, A Hapfelmeier, ... Genome biology 20, 1-12, 2019 | 134 | 2019 |
| Live-seq enables temporal transcriptomic recording of single cells W Chen, O Guillaume-Gentil, PY Rainer, CG Gäbelein, W Saelens, ... Nature 608 (7924), 733-740, 2022 | 121 | 2022 |
| SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development R Cannoodt, W Saelens, D Sichien, S Tavernier, S Janssens, M Guilliams, ... Biorxiv, 079509, 2016 | 113* | 2016 |
| Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells R Cannoodt, W Saelens, L Deconinck, Y Saeys Nature Communications 12 (1), 3942, 2021 | 73 | 2021 |
| Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition J Bues, M Biočanin, J Pezoldt, R Dainese, A Chrisnandy, S Rezakhani, ... Nature Methods 19 (3), 323-330, 2022 | 34 | 2022 |
| Recent advances in trajectory inference from single-cell omics data L Deconinck, R Cannoodt, W Saelens, B Deplancke, Y Saeys Current Opinion in Systems Biology 27, 100344, 2021 | 29 | 2021 |
| Network inference from single-cell transcriptomic data H Todorov, R Cannoodt, W Saelens, Y Saeys Gene regulatory networks: methods and protocols, 235-249, 2019 | 25 | 2019 |
| TinGa: fast and flexible trajectory inference with Growing Neural Gas H Todorov, R Cannoodt, W Saelens, Y Saeys Bioinformatics 36 (Supplement_1), i66-i74, 2020 | 21 | 2020 |
| Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes AA Raz, GS Vida, SR Stern, S Mahadevaraju, JM Fingerhut, JM Viveiros, ... Elife 12, e82201, 2023 | 18 | 2023 |
