Ryan Christ
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View article: The Rényi Outlier Test
The Rényi Outlier Test Open
Cox and Kartsonaki proposed a simple outlier test for a vector of p-values based on the Rényi transformation that is fast for large $p$ and numerically stable for very small p-values -- key properties for large data analysis. We propose an…
View article: Mapping and characterization of structural variation in 17,795 human genomes
Mapping and characterization of structural variation in 17,795 human genomes Open
A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and re…
View article: kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R
kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R Open
Background Approximating the recent phylogeny of N phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selection, introgress…
View article: Stable Distillation and High-Dimensional Hypothesis Testing
Stable Distillation and High-Dimensional Hypothesis Testing Open
While powerful methods have been developed for high-dimensional hypothesis testing assuming orthogonal parameters, current approaches struggle to generalize to the more common non-orthogonal case. We propose Stable Distillation (SD), a sim…
View article: kalis: A Modern Implementation of the Li & Stephens Model for Local Ancestry Inference in R
kalis: A Modern Implementation of the Li & Stephens Model for Local Ancestry Inference in R Open
Approximating the recent phylogeny of $N$ phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selection, introgression, and …
View article: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
Background Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a…
View article: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
Background Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a…
View article: Additional file 2 of Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Additional file 2 of Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
Additional file 2:. Excel format (.xlsx). Large Supplementary Tables. Contains Tables S1, S5-S8, and S10.
View article: Association of Structural Variation with Cardiometabolic Traits in Finns
Association of Structural Variation with Cardiometabolic Traits in Finns Open
The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometab…
View article: Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences Open
Mitochondrial genome copy number (MT-CN) varies among humans and across tissues and is highly heritable, but its causes and consequences are not well understood. When measured by bulk DNA sequencing in blood, MT-CN may reflect a combinatio…
View article: Improved Concentration Bounds for Gaussian Quadratic Forms
Improved Concentration Bounds for Gaussian Quadratic Forms Open
For a wide class of monotonic functions $f$, we develop a Chernoff-style concentration inequality for quadratic forms $Q_f \sim \sum\limits_{i=1}^n f(η_i) (Z_i + δ_i)^2$, where $Z_i \sim N(0,1)$. The inequality is expressed in terms of tra…
View article: Inferring adaptive gene-flow in recent African history
Inferring adaptive gene-flow in recent African history Open
Gene-flow from an ancestrally differentiated group has been shown to be a powerful source of selectively advantageous variants. To understand whether recent gene-flow may have contributed to adaptation among humans in sub-Saharan Africa, w…
View article: Ancestral trees as weighted networks : scalable screening for genome wide association studies
Ancestral trees as weighted networks : scalable screening for genome wide association studies Open
Several haplotype-based methods have been developed to identify loci where multiple mutations of low to moderate frequency and effect size modulate disease susceptibility. Most such approaches either do not scale to hundreds of thousands o…
View article: Multicohort analysis of the maternal age effect on recombination
Multicohort analysis of the maternal age effect on recombination Open
Several studies have reported that the number of crossovers increases with maternal age in humans, but others have found the opposite. Resolving the true effect has implications for understanding the maternal age effect on aneuploidies. He…