| 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 | 417 | 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 | 402 | 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 | 360 | 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 | 207 | 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 | 147* | 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 | 135 | 2023 |
| 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 | 90 | 2022 |
| 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 | 62 | 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 | 55 | 2021 |
| LIANA+ provides an all-in-one framework for cell–cell communication inference D Dimitrov, PSL Schäfer, E Farr, P Rodriguez-Mier, S Lobentanzer, ... Nature Cell Biology 26 (9), 1613-1622, 2024 | 54* | 2024 |
| 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 | 41 | 2022 |
| 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 | 29 | 2023 |
| 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 |
| Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions C Lerma-Martin, P Badia-i-Mompel, RO Ramirez Flores, P Sekol, ... Nature Neuroscience, 1-12, 2024 | 21* | 2024 |
| 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 |
| Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction JD Lanzer, LM Wienecke, RO Ramirez Flores, MM Zylla, C Kley, ... Basic Research in Cardiology 119 (6), 1001-1028, 2024 | 5 | 2024 |
| Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities [Internet]. bioRxiv. 2023 [cited 2023 Apr 3 … S Müller-Dott, E Tsirvouli, M Vázquez, ROR Flores, P Badia-i-Mompel, ... https://www. biorxiv. org/content/10.1101/2023.03 30, v1, 0 | 5 | |
| 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 | 3 | 2024 |
| A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling JD Lanzer, RO Ramirez Flores, J Liñares Blanco, J Saez-Rodriguez bioRxiv, 2024.11. 04.621815, 2024 | 2 | 2024 |
| 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 | 2 | 2024 |
