| Spatial multi-omic map of human myocardial infarction C Kuppe, RO Ramirez Flores, Z Li, S Hayat, RT Levinson, X Liao, ... Nature 608 (7924), 766-777, 2022 | 301 | 2022 |
| Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data D Dimitrov, D Türei, M Garrido-Rodriguez, PL Burmedi, JS Nagai, C Boys, ... Nature communications 13 (1), 3224, 2022 | 272* | 2022 |
| decoupleR: ensemble of computational methods to infer biological activities from omics data P Badia-i-Mompel, J Vélez Santiago, J Braunger, C Geiss, D Dimitrov, ... Bioinformatics Advances 2 (1), vbac016, 2022 | 239 | 2022 |
| Gene regulatory network inference in the era of single-cell multi-omics P Badia-i-Mompel, L Wessels, S Müller-Dott, R Trimbour, ... Nature Reviews Genetics 24 (11), 739-754, 2023 | 126 | 2023 |
| Explainable multiview framework for dissecting spatial relationships from highly multiplexed data J Tanevski, ROR Flores, A Gabor, D Schapiro, J Saez-Rodriguez Genome biology 23 (1), 97, 2022 | 109 | 2022 |
| The spatial transcriptomic landscape of the healing mouse intestine following damage SM Parigi, L Larsson, S Das, RO Ramirez Flores, A Frede, KP Tripathi, ... Nature communications 13 (1), 828, 2022 | 68 | 2022 |
| Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities S Müller-Dott, E Tsirvouli, M Vazquez, RO Ramirez Flores, ... Nucleic acids research 51 (20), 10934-10949, 2023 | 61 | 2023 |
| B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing A Frede, P Czarnewski, G Monasterio, KP Tripathi, DA Bejarano, ... Immunity 55 (12), 2336-2351. e12, 2022 | 47 | 2022 |
| Consensus transcriptional landscape of human end‐stage heart failure RO Ramirez Flores, JD Lanzer, CH Holland, F Leuschner, P Most, ... Journal of the American Heart Association 10 (7), e019667, 2021 | 46 | 2021 |
| Transcriptomic cross‐species analysis of chronic liver disease reveals consistent regulation between humans and mice CH Holland, RO Ramirez Flores, M Myllys, R Hassan, K Edlund, ... Hepatology communications 6 (1), 161-177, 2022 | 37 | 2022 |
| Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes L Balzano-Nogueira, R Ramirez, T Zamkovaya, J Dailey, AN Ardissone, ... Genome biology 22, 1-27, 2021 | 23 | 2021 |
| Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease ROR Flores, JD Lanzer, D Dimitrov, B Velten, J Saez-Rodriguez Elife 12, e93161, 2023 | 18 | 2023 |
| LIANA+: an all-in-one cell-cell communication framework D Dimitrov, PSL Schäfer, E Farr, P Rodriguez Mier, S Lobentanzer, ... BioRxiv, 2023.08. 19.553863, 2023 | 18 | 2023 |
| Spatial cell type mapping of multiple sclerosis lesions C Lerma-Martin, P Badia-i-Mompel, RO Ramirez Flores, P Sekol, ... BioRxiv, 2022.11. 03.514906, 2022 | 10 | 2022 |
| Explainable multi-view framework for dissecting inter-cellular signaling from highly multiplexed spatial data. Biorxiv 2020.05. 08.084145 (2020) J Tanevski, A Gabor, ROR Flores, D Schapiro, J Saez-Rodriguez | 7 | 2020 |
| Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice. Hepatol Commun 6 (1): 161–177 CH Holland, RO Ramirez Flores, M Myllys | 7 | 1797 |
| Explainabl e multiview framework for dissecting spatial relationships from highly multiplexe d data J Tanevski, ROR Flores, A Gabor, D Schapiro, J Saez-Rodriguez Genome Biol 23 (1), 97, 2022 | 6 | 2022 |
| Complementing cell taxonomies with a multicellular analysis of tissues RO Ramirez Flores, PSL Schäfer, L Küchenhoff, J Saez-Rodriguez Physiology 39 (3), 129-141, 2024 | 2 | 2024 |
| Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in murine heart failure with preserved ejection fraction JD Lanzer, LM Wienecke, RO Ramirez-Flores, MM Zylla, N Hartmann, ... bioRxiv, 2023.05. 09.539983, 2023 | 2 | 2023 |
| Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results V Paton, RO Ramirez Flores, A Gabor, P Badia-i-Mompel, J Tanevski, ... Nucleic Acids Research 52 (14), 8100-8111, 2024 | 1 | 2024 |
