Related papers: Shotgun DNA sequencing evidence: sample-specific a…
The treatment of short-tandem-repeat (STR) loci on the Y chromosome presents special problems in the forensic analysis of DNA mixtures, chiefly but not exclusively relating to the linkage of Y-STR loci which precludes the use of the…
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in…
The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to…
Biclustering has gained interest in gene expression data analysis due to its ability to identify groups of samples that exhibit similar behaviour in specific subsets of genes (or vice versa), in contrast to traditional clustering methods…
Prediction of mRNA gene-expression profiles directly from routine whole-slide images (WSIs) using deep learning models could potentially offer cost-effective and widely accessible molecular phenotyping. While such WSI-based gene-expression…
Detection limit (DL) has become an increasingly ubiquitous issue in statistical analyses of biomedical studies, such as cytokine, metabolite and protein analysis. In regression analysis, if an explanatory variable is left-censored due to…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
The aim of this paper is to propose a novel estimation method of using genetic-predicted observations to estimate trans-ancestry genetic correlations, which describes how genetic architecture of complex traits varies among populations, in…
Polygenic risk score (PRS) analysis is a powerful method been used to estimate an individual's genetic risk towards targeted traits. PRS analysis could be used to obtain evidence of a genetic effect beyond Genome-Wide Association Studies…
Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
A common task in forensic biology is to interpret and evaluate short tandem repeat DNA profiles. The first step in these interpretations is to assign a number of contributors to the profiles, a task that is most often performed manually by…
We consider cross-sectional genetic association studies (common and rare variants) where non-genetic information is available, or feasible to obtain for $N$ individuals, but where it is infeasible to genotype all $N$ individuals. We…
Current machine learning has made great progress on computer vision and many other fields attributed to the large amount of high-quality training samples, while it does not work very well on genomic data analysis, since they are notoriously…
Several studies suggest strong correlation between different types of cancer and the relative concentration of short circulating RNA sequences (miRNA). Because of short length and low concentration, miRNA detection is not easy. Standard…
In this paper, we present a novel unsupervised algorithm for word sense disambiguation (WSD) at the document level. Our algorithm is inspired by a widely-used approach in the field of genetics for whole genome sequencing, known as the…
In genetic association studies, detecting phenotype-genotype association is a primary goal. We assume that the relationship between the data -phenotype, genetic markers and environmental covariates - can be modelled by a generalized linear…
Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…