Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics 24 (8), 550-572, 2023 | 210 | 2023 |
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 | 198* | 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 | 147 | 2022 |
How will artificial intelligence and bioinformatics change our understanding of IgA Nephropathy in the next decade? RD Bülow, D Dimitrov, P Boor, J Saez-Rodriguez Seminars in Immunopathology 43 (5), 739-752, 2021 | 24 | 2021 |
BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis D Dimitrov, Q Gu PeerJ 8, e10469, 2020 | 9 | 2020 |
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 | 8 | 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 | 8 | 2023 |
Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples H Baghdassarian, D Dimitrov, E Armingol, J Saez-Rodriguez, NE Lewis BioRxiv, 2023 | 5 | 2023 |
Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system PSL Schäfer, D Dimitrov, EJ Villablanca, J Saez-Rodriguez Nature Immunology, 1-13, 2024 | 1 | 2024 |
Defining and benchmarking open problems in single-cell analysis M Luecken, S Gigante, D Burkhardt, R Cannoodt, D Strobl, N Markov, ... | | 2024 |
Clarifying the murk: Unveiling bacterial dynamics in response to crude oil pollution, Corexit-dispersant, and natural sunlight in the Gulf of Mexico S Matallana-Surget, LM Nigro, LA Waidner, P Lebaron, R Wattiez, ... Frontiers in Marine Science, 2024 | | 2024 |
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions EB Farr, D Dimitrov, D Turei, C Schmidt, S Lobentanzer, A Dugourd, ... bioRxiv, 2023.12. 30.573715, 2023 | | 2023 |