Karl W. Broman

This study identifies genetic loci affecting lifespan dynamics, sex differences, and body weight trade-offs in mice using an actuarial approach.

This paper establishes a pluripotent stem cell platform using genetically diverse mouse lines to study the impact of natural genetic variation on development and gene regulation.

BulkLMM accelerates genome-wide scans for multiple quantitative traits using LMMs by employing vectorized operations and regularization, achieving fast results on large datasets.

QTLViewer provides an interactive webtool for QTL mapping and exploration in CC and DO mouse populations, enhancing accessibility to genetic analysis resources.

The paper develops a MAGIC population in maize to map flowering time and plant height, finding that predictive models perform better when trained on direct data rather than indirect data from hybrids.

The paper introduces a generic hidden Markov model for genotype reconstruction in multi-parent populations and demonstrates its application using R/qtl2 on mouse data.

The paper identifies sample mix-ups and mixtures in microbiome data from Diversity Outbred mice using shotgun sequencing reads.

The paper develops GPU-accelerated algorithms for fast eQTL scans in BXD mice, reducing runtime to seconds for large transcriptome datasets.

The paper extends a penalized likelihood method for multiple-QTL analysis to handle the X chromosome appropriately, demonstrating its performance through simulation and eQTL data.

The paper introduces GBRS, a method to reconstruct diploid genomes and quantify gene expression in multi-parent populations using RNA-Seq data without requiring genotype information.

This study identifies genetic loci associated with gut microbiota composition and bile acid profiles in mice using QTL analysis and validation experiments.

The paper develops statistical methods to test for pleiotropy or separate QTL in multiparental populations and applies them to find two distinct loci in a genomic region of mice.

The paper describes a process for cleaning SNP genotype data from Diversity Outbred mice, focusing on identifying and handling low-quality samples and markers.

R/qtl2 is a software tool for QTL mapping in multi-parent populations and high-dimensional data, offering features like linear mixed models and SNP imputation.