J. A. Capra

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

This study identifies SLC22A10 as a nonfunctional pseudogene in humans due to a missense mutation, while great ape orthologs retain functional uptake of estradiol-17β-glucuronide.

Archaic Introgression Shaped Human Circadian Traits

This paper identifies circadian gene differences between modern humans and archaic hominins, showing introgression affects human chronotype and suggests adaptation to higher latitudes.

Mosaic patterns of selection in genomic regions associated with diverse human traits

The paper develops a computational framework to analyze selection patterns in genomic regions linked to human traits using GWAS summary statistics and evolutionary measures.

Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence

This study uses deep learning to infer 3D genome organization from ancient DNA, revealing how chromatin folding influenced phenotypic and sequence divergence between Neanderthals, Denisovans, and modern humans.

The IMD and JNK pathways drive the functional integration of the immune and circulatory systems of mosquitoes

The paper identifies the IMD and JNK pathways as regulators of immune-circulatory integration in mosquitoes through RNAseq and RNAi experiments.

Function and constraint in enhancers with multiple evolutionary origins

The paper analyzes the function and evolutionary constraints of core and derived sequences in complex human enhancers, finding distinct regulatory roles and constraint profiles.

An active learning framework improves tumor variant interpretation

This study applies active learning to improve variant interpretation for tumor genomes, showing better performance than traditional methods in predicting variant effects on cancer treatment.

Diverse functions associate with trans-species polymorphisms in humans

The paper identifies functional roles for trans-species polymorphisms (TSPs) in humans, showing associations with immune traits, behavior, and other phenotypes, suggesting LTBS acts on diverse functions beyond immunity.

Modeling the evolutionary architectures of human enhancer sequences reveals distinct origins, functions, and associations with human-trait variation

The paper models human enhancer sequence evolution, identifying simple and complex architectures and their associations with trait variation.

Quantifying the contribution of Neanderthal introgression to the heritability of complex traits

This study quantifies how Neanderthal introgression affects the heritability of complex traits, finding enrichment in traits related to adaptation to non-African environments.

Evaluating Human Autosomal Loci for Sexually Antagonistic Viability Selection in Two Large Biobanks

The paper evaluates evidence for sexually antagonistic viability selection on autosomal loci in humans using two large biobanks but finds no significant replication of associations, suggesting limited ongoing selection on single locus variation.

Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations

Neanderthal introgression reintroduced ancestral alleles lost in the Eurasian out of Africa bottleneck, affecting gene expression and phenotypes in modern humans.

Accounting for diverse evolutionary forces reveals the mosaic nature of selection on genomic regions associated with human preterm birth

The paper develops an approach to analyze evolutionary forces on genomic regions linked to preterm birth and finds diverse signatures like negative and positive selection.

Signatures of recent positive selection in enhancers across 41 human tissues

The paper identifies enhancers under recent positive selection across 41 human tissues and finds tissue-specific patterns, particularly in brain and testis enhancers.

The impact of natural selection on the evolution and function of placentally expressed galectins

This study examines the molecular evolution of placental galectins across mammals and humans, identifying signatures of natural selection and structural differences in a common haplotype.

Genome wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication

This study identifies genetic variants associated with reproductive traits in dogs and links them to domestication-related traits.

Deep learning reveals evolutionary conservation and divergence of sequence properties underlying gene regulatory enhancers across mammals

The paper uses machine learning to show that short DNA sequence patterns predictive of enhancers are conserved across mammals, while more complex patterns show greater divergence.