Related papers: Reconstructing pedigrees using probabilistic analy…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Sampling geographically dispersed minority populations poses substantial challenges when individual group membership cannot be directly observed. Although stratified sampling can offer efficiency gains, these gains are typically modest…
Although geographic isolation has been shown to play a key role in promoting reproductive isolation, it is now believed that speciation can also happen in sympatry and with considerable gene flow. Here we present a model of sympatric…
In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex $v$ of an evolutionary tree $T$ from the states that are observed at the leaves of the tree. A simple and fast…
This thesis studies high-dimensional, continuous-valued pairwise Markov Random Fields. We are particularly interested in approximating pairwise densities whose logarithm belongs to a Sobolev space. For this problem we propose the method of…
Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…
The doubly robust estimator, which models both the propensity score and outcomes, is a popular approach to estimate the average treatment effect in the potential outcome setting. The primary appeal of this estimator is its theoretical…
Recombination is a fundamental evolutionary force, but it is difficult to quantify because the effect of a recombination event on patterns of variation in a sample of genetic data can be hard to discern. Estimators for the recombination…
Understanding the interplay between recombination and resampling is a significant challenge in mathematical population genetics and of great practical relevance. Asymptotic results about the distribution of samples when recombination is…
In the postgenome era many efforts have been dedicated to systematically elucidate the complex web of interacting genes and proteins. These efforts include experimental and computational methods. Microarray technology offers an opportunity…
We consider the classic Moran process modeling the spread of genetic mutations, as extended to structured populations by Lieberman et al.\ (Nature, 2005). In this process, individuals are the vertices of a connected graph $G$. Initially,…
An unusual and surprising expansion of the form \[ p_n = \rho^{-n-1}(6n +\tfrac{18}5+ \tfrac{336}{3125} n^{-5}+\tfrac{1008}{3125} n^{-6} +\text{smaller order terms}), \] as $n\to\infty$, is derived for the probability $p_n$ that two…
The "rare type match problem" is the situation in which the suspect's DNA profile, matching the DNA profile of the crime stain, is not in the database of reference. The evaluation of this match in the light of the two competing hypotheses…
Recent empirical work has shown that human children are adept at learning and reasoning with probabilities. Here, we model a recent experiment investigating the development of school-age children's non-symbolic probability reasoning ability…
Genetic association study is an essential step to discover genetic factors that are associated with a complex trait of interest. In this paper we present a novel generalized quasi-likelihood score (GQLS) test that is suitable for a study…
The original version of Bayesian reconstruction, a method for estimating age-specific fertility, mortality, migration and population counts of the recent past with uncertainty, produced estimates for female-only populations. Here we show…
Among many efforts to facilitate timely access to safe and effective medicines to children, increased attention has been given to extrapolation. Loosely, it is the leveraging of conclusions or available data from adults or older age groups…
The number of complete chloroplastic genomes increases day after day, making it possible to rethink plants phylogeny at the biomolecular era. Given a set of close plants sharing in the order of one hundred of core chloroplastic genes, this…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Biclustering is a class of techniques that simultaneously clusters the rows and columns of a matrix to sort heterogeneous data into homogeneous blocks. Although many algorithms have been proposed to find biclusters, existing methods suffer…