Related papers: Shotgun DNA sequencing evidence: sample-specific a…
DNA samples crime cases analysed in forensic genetics, frequently contain DNA from multiple contributors. These occur as convolutions of the DNA profiles of the individual contributors to the DNA sample. Thus, in cases where one or more of…
In the idealized Morgan model of crossover, we study the probability distributions of shared DNA (identical by descent) between individuals having a wide range of relationships (not just lineal descendants), especially cases for which…
DNA is now routinely used in criminal investigations and court cases, although DNA samples taken at crime scenes are of varying quality and therefore present challenging problems for their interpretation. We present a statistical model for…
Understanding how genetic variants influence cellular-level processes is an important step towards understanding how they influence important organismal-level traits, or "phenotypes", including human disease susceptibility. To this end…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate…
An early detection of different tumor subtypes is crucial for an effective guidance to personalized therapy. While much efforts focus on decoding the sequence of DNA basis to detect the genetic mutations related to cancer, it is becoming…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously…
Dose-finding studies in oncology often include an up-and-down dose transition rule that assigns a dose to each cohort of patients based on accumulating data on dose-limiting toxicity (DLT) events. In making a dose transition decision, a key…
Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…
Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new…
Imputation using external reference panels is a widely used approach for increasing power in GWAS and meta-analysis. Existing HMM-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian…
Genetical genomics experiments have now been routinely conducted to measure both the genetic markers and gene expression data on the same subjects. The gene expression levels are often treated as quantitative traits and are subject to…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
Single-strand breaks (SSBs) are the major DNA damage in the genome arising spontaneously as the outcome of genotoxins and intermediates of DNA transactions. SSBs play a crucial role in various biological processes and show a non-random…