S. Naranjo

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

The paper maps lymphocyte interactions in lung adenocarcinoma using spatial analysis and machine learning, revealing dynamic lymphocyte networks that support anti-tumor immune responses.

Spatial Scale of Non-Target Effects of Cotton Insecticides

The paper determines the optimal plot size for assessing non-target arthropod effects of cotton insecticides in Arizona, finding 144 m2 plots sufficient to detect treatment effects.

The little skate genome and the evolutionary emergence of wing-like fin appendages

This study identifies genomic rearrangements and regulatory changes in the little skate that contribute to the evolution of wing-like fin appendages.

Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform

This study develops a reliable alveolar type 2 organoid platform to model diverse genetic subtypes of lung adenocarcinoma in vitro and in vivo.

Multiscale profiling of enzyme activity in cancer

This paper develops methods to measure enzyme activity in cancer across multiple scales, revealing protease dysregulation and dynamic interactions between tumor cells and their microenvironment.

Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution

The paper tracks tumor evolution in a mouse model using lineage tracing and single-cell RNA-seq, revealing plasticity, fitness-associated programs, and stereotypical evolutionary trajectories.

Mismatch repair deficiency is not sufficient to increase tumor immunogenicity

This study shows that MMRd in mouse tumor models does not increase immunogenicity or ICB response, due to intratumoral heterogeneity.

Deciphering the tumor-specific immunopeptidome in vivo with genetically engineered mouse models

This paper uses genetically engineered mouse models to isolate and profile tumor-specific MHC-I peptides in vivo, revealing post-translational shaping of the immunopeptidome and novel tumor-associated antigens in lung adenocarcinoma.

The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits.

This study shows that the Shh/Gli3 gene regulatory network controls proliferation in distal fin and limb regions, revealing deep homology between these structures.

Ancient genomic regulatory blocks are a major source for gene deserts in vertebrates after whole genome duplications

The paper shows that ancient genomic regulatory blocks (GRBs) were maintained as single copies in humans after vertebrate whole genome duplications, with their duplicated copies dismantled to form gene deserts.