Gene regulatory network inference in the era of single-cell multi-omics
- Pau Badia-I-Mompel, Lorna Wessels, Sophia Müller-Dott, …, Ricardo O Ramirez Flores, Ricard Argelaguet, Julio Saez-Rodriguez
- Nat Rev Genet, 10.1038/s41576-023-00618-5
decoupleR: ensemble of computational methods to infer biological activities from omics data
- Pau Badia-I-Mompel, Jesús Vélez Santiago, Jana Braunger, …, Christian H Holland, Ricardo O Ramirez Flores, Julio Saez-Rodriguez
- None, 10.1093/bioadv/vbac016
B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing
- Annika Frede, Paulo Czarnewski, Gustavo Monasterio, …, Andreas Schlitzer, Srustidhar Das, Eduardo J Villablanca
- Immunity, 10.1016/j.immuni.2022.11.002
Spatial multi-omic map of human myocardial infarction
- Christoph Kuppe, Ricardo O Ramirez Flores, Zhijian Li, …, Ivan G Costa, Julio Saez-Rodriguez, Rafael Kramann
- Nature, 10.1038/s41586-022-05060-x
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data
- Daniel Dimitrov, Dénes Türei, Martin Garrido-Rodriguez, …, Alberto Valdeolivas, Aurélien Dugourd, Julio Saez-Rodriguez
- Nat Commun, 10.1038/s41467-022-30755-0
Explainable multiview framework for dissecting spatial relationships from highly multiplexed data
- Jovan Tanevski, Ricardo Omar Ramirez Flores, Attila Gabor, Denis Schapiro, Julio Saez-Rodriguez
- Genome Biol, 10.1186/s13059-022-02663-5
The spatial transcriptomic landscape of the healing mouse intestine following damage
- Sara M Parigi, Ludvig Larsson, Srustidhar Das, …, Julio Saez-Rodriguez, Joakim Lundeberg, Eduardo J Villablanca
- Nat Commun, 10.1038/s41467-022-28497-0
Integrative analyses of TEDDY Omics data reveal lipid metabolism abnormalities, increased intracellular ROS and heightened inflammation prior to autoimmunity for type 1 diabetes
- Leandro Balzano-Nogueira, Ricardo Ramirez, Tatyana Zamkovaya, …, Desmond A Schatz, Eric W Triplett, Ana Conesa
- Genome Biol, 10.1186/s13059-021-02262-w