相关论文: A renewal theory approach to IBD sharing

Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…

Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…

Cycling tissues such as the intestinal epithelium, germ line, and hair follicles, require a constant flux of differentiated cells. These tissues are maintained by a population of stem cells, which generate differentiated progenies and…

We propose in this article a brief description of the work, over almost a decade, resulting from a collaboration between mathematicians and biologists from four different research laboratories, identifiable as the co-authors of the articles…

We analyze the convergence rate of a simplified version of a popular Gibbs sampling method used for statistical discovery of gene regulatory binding motifs in DNA sequences. This sampler satisfies a very strong form of ergodicity (uniform).…

Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements -…

The sequentially Markov coalescent (SMC) is a Markov jump process which models correlations in local genealogies across a chromosome. It has been used as a theoretical tool for studying linkage disequilibrium and identity-by-descent, and it…

We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…

This paper studies a Markov chain for phylogenetic reconstruction which uses a popular transition between tree topologies known as subtree pruning-and-regrafting (SPR). We analyze the Markov chain in the simpler setting that the generating…

Kingman's coalescent is a widely used process to model sample genealogies in population genetics. Recently there have been studies on the inference of quantities related to the genealogy of additional individuals given a known sample. This…

A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…

We model the growth of a cell population by a piecewise deterministic Markov branching tree. Each cell splits into two offsprings at a division rate $B(x)$ that depends on its size $x$. The size of each cell grows exponentially in time, at…

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…

Integrating heterogeneous datasets across different measurement platforms is a fundamental challenge in many scientific applications. A common example arises in deconvolution problems, such as cell type deconvolution, where one aims to…

Novel Markov Chain Monte Carlo (MCMC) methods have enabled the generation of large ensembles of redistricting plans through graph partitioning. However, existing algorithms such as Reversible Recombination (RevReCom) and Metropolized Forest…

Distributed storage systems with replication are well known for storing large amount of data. A large number of replication is done in order to provide reliability. This makes the system expensive. Various methods have been proposed over…

Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…

We propose a method based on deep learning to perform cardiac segmentation on short axis MRI image stacks iteratively from the top slice (around the base) to the bottom slice (around the apex). At each iteration, a novel variant of U-net is…

Filtering---estimating the state of a partially observable Markov process from a sequence of observations---is one of the most widely studied problems in control theory, AI, and computational statistics. Exact computation of the posterior…

The problem of reconstructing a source sequence with the presence of decoder side-information that is mis-synchronized to the source due to deletions is studied in a distributed source coding framework. Motivated by practical applications,…