Kathleen C. Keough

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

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

Integrating gene annotation with orthology inference at scale

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

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

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

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

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

Evolutionary constraint and innovation across hundreds of placental mammals

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.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

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

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

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.

An atlas of lamina-associated chromatin across twelve human cell types revealsan intermediate chromatin subtype

The paper maps lamin-associated chromatin across twelve human cell types, identifying two subtypes with distinct features and developmental dynamics.

Two therapeutic CRISPR/Cas9 gene editing approaches revert FTD/ALS cellular pathology caused by a C9orf72 repeat expansion mutation in patient derived cells

This study evaluates three CRISPR/Cas9 approaches to correct C9orf72 repeat expansion in patient-derived neurons, finding that repeat and mutant allele excision fully eliminate dipeptide repeats.

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

The paper predicts the broad host range of SARS-CoV-2 by analyzing ACE2 conservation across vertebrates and identifying high-risk species.

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

AlleleAnalyzer designs personalized and allele-specific sgRNAs to improve CRISPR/Cas editing performance by accounting for individual genetic variants.