B. Berger

Deciphering Salt Stress Responses in Solanum pimpinellifolium through High-Throughput Phenotyping.

This study uses high-throughput phenotyping to analyze salt stress responses in Solanum pimpinellifolium, identifying phenotypic variations and candidate genes associated with stress tolerance.

Uncovering structural ensembles from single particle cryo-EM data using cryoDRGN

This paper introduces cryoDRGN, a deep generative model for cryo-EM density maps, and provides a protocol for analyzing its results.

Identification and characterization of the T cell receptor (TCR) repertoire of the Cynomolgus macaque (Macaca Fascicularis)

The paper characterizes the T cell receptor repertoire in Cynomolgus macaques using single-cell RNA sequencing and identifies similarities with human and Rhesus macaque TCR repertoires.

HIV-specific CD8+ T-cells in tonsils express exhaustive TRM-like signatures

The paper examines HIV-specific CD8+ T-cells in tonsils, finding they exhibit TRM-like exhaustion signatures compared to blood, with differences in natural HIV controllers.

Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

The paper introduces virDTL, a phylogenetic workflow for analyzing viral evolution with recombination, and applies it to Sarbecoviruses to identify ancestral recombination events in SARS-CoV-2.

Learning the mutational landscape of the cancer genome

The paper predicts cancer-specific mutation rates genome-wide using deep neural networks to identify new putative driver mutations in understudied genomic regions.

Multimodal profiling of lung granulomas reveals cellular correlates of tuberculosis control

The paper identifies cellular and temporal factors associated with bacterial control in tuberculosis granulomas using multimodal data.

GM-CSF differentiation of human monocytes stabilizes macrophage state via oxidative signaling

This study shows that GM-CSF differentiation of human monocytes reduces IL-10 production through oxidative signaling, highlighting its role in macrophage function and plasticity.

GWAS reveals the genetic complexity of fructan accumulation patterns in barley grain

This study identifies genetic factors influencing fructan accumulation patterns in barley grain through GWAS and co-expression analysis, revealing new gene candidates and distinct biosynthesis pathways.

Greenhouse spatial effects detected in the barley (Hordeum vulgare L.) epigenome underlie stochasticity of DNA methylation

The paper shows that environmental micro-variations during growth affect DNA methylation in barley, linking previously stochastic epigenetic changes to greenhouse conditions.

A single nucleotide substitution in TaHKT1;5-D controls shoot Na+ accumulation in bread wheat

The paper identifies a single nucleotide substitution in TaHKT1;5-D that causes high shoot Na+ accumulation in a salt-tolerant wheat landrace without affecting its salinity tolerance.