Linda Goodman

Empty drops in scRNA-seq uncover the surprising prevalence of sequestered neuropeptide mRNA and pervasive sequencing artifacts

The paper analyzes empty drops in scRNA-seq to identify sequencing artifacts and reveals the prevalence of neuropeptide mRNA, suggesting potential physiological relevance.

DEPower: approximate power analysis with DESeq2

DEPower provides a web tool for power analysis in RNA-seq experiments based on DESeq2 assumptions, enabling researchers to determine sample size requirements for detecting differential expression.

Unexpected XIST Expression in Male Hearts Associates with Disease

The paper reports endogenous XIST expression in male heart samples across multiple single-cell RNA sequencing studies and links it to heart disease and myocardial infarction.

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.