Amanda M. Kowalczyk

DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS

This paper reports the first derivation of elephant induced pluripotent stem cells (emiPSCs) using a modified reprogramming protocol that inhibits TP53 expansion genes.

Fine-mapping candidate neuropsychiatric regulatory variants using cell type-aware comparative genomics

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

Genes Underlying Adaptive Physiological Shifts Among Hibernating Mammals

The paper identifies genes under selection and evolutionary convergence in hibernating mammals using metabolomic data and bioinformatic analyses.

RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution

The paper expands RERconverge to analyze multi-categorical traits by introducing methods for ancestral state reconstruction, statistical tests, and phylogenetic permutations, showing improved performance in identifying diet-related genes and pathways.

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.