Jeremy Johnson

The paper identifies clustered structural variant hotspots in osteosarcoma, linking them to oncogenic addiction and plasticity through transcriptional changes and clinical detectability.

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

The paper introduces the 4DN Data Portal, a resource for searching and visualizing curated nucleomics data, including Hi-C and other chromosome architecture datasets.

This study investigates the genetic basis of hibernation in the meadow jumping mouse by analyzing its genome and transcriptome, identifying key genes and pathways involved in hibernation-related processes.

The paper improves the Cactus multiple-genome aligner to handle large numbers of vertebrate genomes with high accuracy and better orthology resolution.

The paper compares genomic features of canine and human angiosarcoma, finding shared genes and pathways, suggesting dogs as a valuable model for studying this cancer.

Tibanna automates bioinformatics pipeline execution on AWS using CWL, WDL, and Docker, supporting large-scale and variable computational needs.

The paper uses an OU process to model gene expression evolution across mammals and identifies expression pathways under different selection pressures.

The paper identifies OCD-associated genes by combining evolutionary and functional data with targeted sequencing in humans and animal models.