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Holstein-Friesian cattle exhibit individually-characteristic black and white coat patterns visually akin to those arising from Turing's reaction-diffusion systems. This work takes advantage of these natural markings in order to automate…
Background: It has long been advised to account for baseline covariates in the analysis of confirmatory randomised trials, with the main statistical justifications being that this increases power and, when a randomisation scheme balanced…
In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci…
Biomolecular networks, such as protein-protein interactions, gene-gene associations, and cell-cell interactions, offer valuable insights into the complex organization of biological systems. These networks are key to understanding cellular…
Traditional field phenotyping methods are often manual, time-consuming, and destructive, posing a challenge for breeding progress. To address this bottleneck, robotics and automation technologies offer efficient sensing tools to monitor…
Motivated by empirical arguments that are well-known from the genome-wide association studies (GWAS) literature, we study the statistical properties of linear mixed models (LMMs) applied to GWAS. First, we study the sensitivity of LMMs to…
The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants…
The advent of plant phenomics, coupled with the wealth of genotypic data generated by next-generation sequencing technologies, provides exciting new resources for investigations into and improvement of complex traits. However, these new…
Machine learning techniques, specifically the k-nearest neighbour algorithm applied to optical band colours, have had some success in predicting photometric redshifts of quasi-stellar objects (QSOs): Although the mean of differences between…
Mapping expression Quantitative Trait Loci (eQTLs) represents a powerful and widely-adopted approach to identifying putative regulatory variants and linking them to specific genes. Up to now eQTL studies have been conducted in a relatively…
Transfer learning is an emerging paradigm for leveraging multiple sources to improve the statistical inference on a single target. In this paper, we propose a novel approach named residual importance weighted transfer learning (RIW-TL) for…
Using deep learning models to diagnose cancer from histology data presents several challenges. Cancer grading and localization of regions of interest (ROIs) in these images normally relies on both image- and pixel-level labels, the latter…
Identifying genetic variants that regulate quantitative traits, or QTLs, is the primary focus of the field of statistical genetics. Most current methods are limited to identifying mean effects, or associations between genotype and the mean…
This study evaluates the use of Near-Infrared spectroscopy (NIRS) combined with advanced machine learning (ML) techniques to differentiate Hanwoo beef (HNB) and Holstein beef (HLB) to address food authenticity, mislabeling, and…
GWAS in humans are revealing the genetic architecture of biomedical and anthropomorphic traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to…
Conditional testing via the knockoff framework allows one to identify -- among large number of possible explanatory variables -- those that carry unique information about an outcome of interest, and also provides a false discovery rate…
Motivation: Genome-wide association studies (GWAS) have successfully identified thousands of genetic risk loci for complex traits and diseases. Most of these GWAS loci lie in regulatory regions of the genome and the gene through which each…
Motivated by the genomic application of expression quantitative trait loci (eQTL) mapping, we propose a new procedure to perform simultaneous testing of multiple hypotheses using Bayes factors as input test statistics. One of the most…
Relaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny and more accurately model overdispersed biological data.…
Presented here is a simple method for cross-validated genome-wide association studies (cvGWAS). Focusing on phenotype prediction, the method is able to reveal a significant amount of missing heritability by properly selecting a small number…