Ryan N. Gutenkunst

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

This paper develops a nonlinear dynamics framework to analyze mutation-selection balance in tetraploids, revealing dominance-dependent bistability and altered temporal dynamics compared to diploids.

GHIST 2024 evaluates population genetic inference methods through four demographic history challenges, revealing the dominance of site frequency spectrum-based methods and the potential of flexible models for complex histories.

The paper shows non-hypermutator cancers adapt by reversing germline mutation bias, enabling access to driver mutations through altered mutation spectra.

ConfuseNN evaluates how genomic features affect CNN performance in population genomics by systematically shuffling input data.

The paper develops a probabilistic model to correct biases in low-pass genome sequencing data, improving population genetic inferences.

This paper introduces donni, a machine learning-based method for demographic history inference that is faster and more efficient than dadi while maintaining similar accuracy.

dadi-cli simplifies dadi usage and enables distributed computing for population genetic model inference from allele frequency spectra.

The paper expands the stdpopsim species catalog and improves genome simulations by adding non-crossover recombination and species-specific annotations, making simulations more realistic for non-model organisms.

The paper introduces Demes, a standard format for demographic models in population genetics to improve clarity and ease of use in simulations and analysis.

This paper reports the genomic profile of lymphatic malformations, identifies PIK3CA and NRAS mutations, and shows a response to the PI3K inhibitor alpelisib in a personalized trial.

BATCAVE improves somatic mutation detection by incorporating tumor-specific mutation profiles, enhancing variant calling accuracy and posterior probability calibration.

This study assesses the impact of GWAS on biomedical research publications and finds declining effects on publication rates for newly associated complex disease genes.

The paper introduces MAPEX, a BLAST-based algorithm to filter spurious genetic variant calls in xenografts and tumors, achieving comparable sensitivity and specificity to complex methods.

This study shows mRNA secondary structure and codon usage regulate gene expression in budding yeast by affecting transcription, mRNA stability, and translation, with distinct functional enrichments for low and high structure genes.

This paper develops a composite-likelihood framework using two-locus statistics to infer demographic history, showing increased sensitivity compared to single-locus methods like AFS.

The paper uses genomic data and written records to validate domestication events in Brassica rapa, finding support for specific genetic groups and domestication timelines.