D. Jacobson

Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression

The paper investigates how chromatin dynamics and gene expression change after epigenetic drug treatment, finding locus-specific chromatin remodeling and gene expression alterations.

Climate adaptation in P. trichocarpa: key adaptive loci identified for stomata and leaf traits

This study identifies key genetic loci associated with stomatal and leaf traits in Populus trichocarpa that contribute to climate adaptation, showing smaller stomata in genotypes from arid regions.

Environmental and ecological signals predict periods of nutritional stress for Eastern Australian flying fox populations.

The paper uses explainable AI to predict food shortages in Eastern Australian flying foxes, identifying environmental and bat-level features that predict nutritional stress with high accuracy.

Plant inositol transport influences bacterial colonization phenotypes

The paper investigates how plant inositol transport affects bacterial colonization by combining metatranscriptomic data and genetic experiments in Arabidopsis.

Rapid expansion of SARS-CoV-2 variants of concern is a result of adaptive epistasis

The paper analyzes SARS-CoV-2 genomes to show that adaptive epistasis, not just spike mutations, drives the emergence of variants of concern.

The Core Human Fecal Metabolome

This study characterizes the core human fecal metabolome through untargeted metabolomic analysis of populations along an industrialization gradient, revealing shared and industrialization-related metabolites.

Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination

This study uses protoplast fusion in Bacillus species to show genome-wide, unbiased homologous recombination without recombination hotspots or genetic distance effects.

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

The paper introduces a method to determine the source of coprolites and paleofeces using microbiome composition and host DNA content, distinguishing between human, canine, and non-fecal materials.

Differences in resources use lead to coexistence of seed-transmitted microbial populations

The paper investigates how resource use differences affect the coexistence of microbial populations on radish seeds, identifying potential native bacteria that could limit pathogen transmission.

Atomic-level characterization of protein-protein association

The paper uses molecular dynamics simulations to study protein-protein association mechanisms, finding that native associations often involve dissociation and re-association near the native interface rather than extensive interfacial exploration.