Kirk E. Lohmueller

The paper uses Neanderthal ancestry patterns to identify genomic regions enriched with recessive deleterious mutations using a machine learning classifier.

This study evaluates how selective sweeps affect DFE inference using fitdadi, finding that performance declines at low recombination rates and with unfolded SFS, but remains largely unbiased with a flexible demographic model.

The paper uses simulations to study how hitchhiking and repulsion of deleterious alleles affect linkage disequilibrium during selective sweeps, finding criss-crossing patterns and exceptions in empirical data.

This paper uses causal inference to show that background selection and mutation rate variation jointly shape human genetic diversity, with mutation rate variation having comparable impact in some chromosomes.

The paper reconstructs the demographic history of Rice's whale using whole-genome sequences and assesses its genomic health, finding long-term isolation and a recent population collapse increase extinction risk.

This study detects pervasive cryptic negative selection in human noncoding regions using a statistical test, finding that at least 7% of the genome is under negative selection, surpassing previous estimates from conservation-based methods.

The paper shows that demographic inference results vary with sample size, shifting from ancient contraction to recent expansion signals in population history.

The paper extends SISTR to jointly estimate selection coefficients across STRs, showing variation in mutation and selection parameters and greater selective burden of de novo STR mutations compared to standing variation.

The paper extends the stdpopsim simulation framework to include realistic selection models, enabling studies of selection's impact on genetic variation across species.

The paper infers the fitness effects of noncoding mutations in humans using genomic annotations and polymorphism data, finding distinct selection patterns across different noncoding regions.

This study examines the distribution of fitness effects (DFE) across eleven animal species, finding that DFE co-varies with phylogeny and that mammals have more deleterious mutations than insects and birds.

The paper compares the distribution of fitness effects of new amino acid changing mutations between dogs and wolves to assess the impact of domestication on selective pressures.

This paper estimates dominance and selection parameters for nonsynonymous mutations in humans using site frequency spectra and explores their implications for genetic load and inbreeding depression.

Admix-kit provides tools for genetic analysis of admixed populations, enabling simulation, association testing, and polygenic scoring.

This study shows that selection on synonymous mutations can bias inferences of the DFE for nonsynonymous mutations when using demographic parameters estimated from synonymous variants.

This study presents a high-quality genome and methylome analysis of Quercus lobata, identifying genomic features linked to oak evolutionary success, including gene duplications and methylation patterns.

The paper shows that negative selection on complex traits leads to population-specific genetic architectures, reducing the accuracy of genetic risk prediction in non-European populations using European-derived variants.

The paper develops CNEP to predict constrained non-exonic bases using epigenomic and transcription factor data, and introduces CSS-CNEP to improve prediction for underperforming bases.

This study examines how identity-by-descent and inbreeding affect disease and fitness in Canid populations, finding that ROH burden correlates with disease and that breed popularity influences OMIA variant counts.

The paper evaluates how GERP scores relate to purifying selection and functional turnover across mammalian evolution, finding that 4.51% of noncoding human genome is under purifying selection with significant selection coefficient changes.

This study identifies de novo tandem repeat mutations in ASD probands and shows they are more prevalent, larger, and evolutionarily deleterious compared to unaffected siblings.

The paper analyzes genomic diversity in Latin American population isolates, finding increased genetic diversity and consanguinity compared to the Finnish isolate.

This study uses whole-genome sequencing of 3,514 Sardinians to explore population history, finding genetic isolation in the Gennargentu region and sex-biased demographic patterns.

The paper uses population genomic data to characterize the degree of dominance for new mutations and develops a new theory for its evolution.