Alyssa J. Lawler

The paper introduces CTACIT to fine-map neuropsychiatric regulatory variants by integrating conservation scores with cell type-specific open chromatin data across species.

This study trains CNNs to predict chromatin accessibility across species but finds poor performance in predicting quantitative differences between species.

The paper introduces WhAMPRA, an in vivo MPRA platform in mice, to assess tissue-specific regulatory functions of genetic variants and enhancers.

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 SNAIL, a virus-based method using machine learning to design cell type-specific enhancer probes for targeted nuclear isolation and characterization.

The paper introduces a machine learning method to predict tissue-specific regulatory conservation by analyzing open chromatin patterns across mammals, showing improved performance over nucleotide alignment-based approaches.

The paper characterizes chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development, identifying changes in regulatory elements and microRNAs associated with key biological processes.

The paper identifies addiction-associated genetic variants in brain cell type- and region-specific cis-regulatory elements using GWAS and machine learning.

The paper compares open chromatin regions in motor cortex subdivisions across primates and rodents to identify gene regulatory programs involved in the evolution of fine motor skills.