Related papers: Advancing Risk Gene Discovery Across the Allele Fr…

Angle encoding has emerged as a popular feature map for embedding classical data into quantum models, naturally generating truncated Fourier series with universal function approximation capabilities. Despite this expressive capability,…

Cross-sectional HIV incidence estimation leverages recency test results to determine the HIV incidence of a population of interest, where recency test uses biomarker profiles to infer whether an HIV-positive individual was "recently"…

A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected…

In genetic studies of complex diseases, the underlying mode of inheritance is often not known. Thus, the most powerful test or other optimal procedure for one model, e.g. recessive, may be quite inefficient if another model, e.g. dominant,…

In clinical trials and other applications, we often see regions of the feature space that appear to exhibit interesting behaviour, but it is unclear whether these observed phenomena are reflected at the population level. Focusing on a…

The value of research containing novel combinations of molecules can be seen in many innovative and award-winning research programs. Despite calls to use innovative approaches to address common diseases, an increasing majority of research…

DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…

The site frequency spectrum describes variation among a set of n DNA sequences. Its i'th entry (i=1,2,...,n-1) is the number of nucleotide sites at which the mutant allele is present in i copies. Under selective neutrality, random mating,…

This issue includes six articles that develop and apply statistical methods for the analysis of gene sequencing data of different types. The methods are tailored to the different data types and, in each case, lead to biological insights not…

The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…

The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…

The genetic basis of multiple phenotypes such as gene expression, metabolite levels, or imaging features is often investigated by testing a large collection of hypotheses, probing the existence of association between each of the traits and…

Designing protein binders targeting specific sites, which requires to generate realistic and functional interaction patterns, is a fundamental challenge in drug discovery. Current structure-based generative models are limited in generating…

The prevalence of dementia has increased over time as global life expectancy improves and populations age. An individual's risk of developing dementia is influenced by various genetic, lifestyle, and environmental factors, among others.…

In healthcare, clinical risks are crucial for treatment decisions, yet the analysis of their associations is often overlooked. This gap is particularly significant when balancing risks that are weighed against each other, as in the case of…

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…

Many theoretical and experimental studies suggest that range expansions can have severe consequences for the gene pool of the expanding population. Due to strongly enhanced genetic drift at the advancing frontier, neutral and weakly…

In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to…

The mutant allele frequencies in oncogenes peak around 0.40 and rapidly decrease. In this article, we explain why this is the case. Invoking a key result from mathematical analysis in our model, namely, the inverse function theorem, we…

Recent domain generalization (DG) approaches typically use the hypothesis learned on source domains for inference on the unseen target domain. However, such a hypothesis can be arbitrarily far from the optimal one for the target domain,…