相关论文: A model for the clustered distribution of SNPs in …
Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing…
Single nucleotide polymorphisms (SNPs) often appear in clusters along the length of a chromosome. This is due to variation in local coalescent times caused by,for example, selection or recombination. Here we investigate whether…
We develop a feature allocation model for inference on genetic tumor variation using next-generation sequencing data. Specifically, we record single nucleotide variants (SNVs) based on short reads mapped to human reference genome and…
We introduce and analyse an individual-based evolutionary model, in which a population of genetically diverse organisms compete with each other for limited resources. Through theoretical analysis and stochastic simulations, we show that the…
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…
When a population inhabits an inhomogeneous environment, the fitness value of traits can vary with the position in the environment. Gene flow caused by random mating can nevertheless prevent that a sexually reproducing population splits…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have…
This work focuses on clustering populations with a hierarchical dependency structure that can be described by a tree. A particular example that is the focus of our work is the phylogenetic tree, with nodes often representing biological…
We propose a new approach for clustering DNA features using array CGH data from multiple tumor samples. We distinguish data-collapsing: joining contiguous DNA clones or probes with extremely similar data into regions, from clustering:…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
Motivated by the fundamental problem of measuring species diversity, this paper introduces the concept of a cluster structure to define an exchangeable cluster probability function that governs the joint distribution of a random count and…
Consider a sample of size $N$ from a population governed by a hierarchical species sampling model. We study the large $N$ asymptotic behavior of the number ${\bf K}_N$ of clusters and the number ${\bf M}_{r,N}$ of clusters with frequency…
Recent theoretical studies have shown that demographic stochasticity can greatly increase the tendency of asexually reproducing phenotypically diverse organisms to spontaneously evolve into localised clusters, suggesting a simple mechanism…
We study a family of selection-mutation models of a sexual population structured by a phenotypical trait. The main feature of these models is the asymmetric trait heredity or fecundity between the parents : we assume that each individual…
A model-based approach is developed for clustering categorical data with no natural ordering. The proposed method exploits the Hamming distance to define a family of probability mass functions to model the data. The elements of this family…
The Bayesian approach to inference stands out for naturally allowing borrowing information across heterogeneous populations, with different samples possibly sharing the same distribution. A popular Bayesian nonparametric model for…
To study population dynamics, ecologists and wildlife biologists use relative abundance data, which are often subject to temporal preferential sampling. Temporal preferential sampling occurs when sampling effort varies across time. To…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…
We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises…