Carrie Davis

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

A limited set of transcriptional programs define major cell types

The paper identifies five major cell types based on transcriptional programs in human tissues and shows their composition correlates with tissue morphology and disease.

Dynamics of microRNA expression during mouse prenatal development

The paper analyzes miRNA expression dynamics across mouse embryonic development, identifying tissue-specific clusters and their regulatory roles.

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing

The paper introduces RNA Capture Long Seq (CLS) to annotate full-length lncRNAs with high throughput and accuracy, doubling annotated complexity compared to short-read methods.

STAR: ultrafast universal RNA-seq aligner

Maximum mappable seed search in uncompressed suffix arrays, then seed clustering and stitching, aligns 550 million paired-end reads per hour on 12 cores with better sensitivity and precision.