相关论文: Reconstructing pedigrees: a stochastic perspective

Recent improvements in high-throughput genotyping and sequencing technologies have afforded the collection of massive, genome-wide datasets of DNA information from hundreds of thousands of individuals. These datasets, in turn, provide…

We define symmetric and asymmetric branching trees, a class of processes particularly suited for modeling genealogies of inhomogeneous populations where individuals may reproduce throughout life. In this framework, a broad class of…

Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

In this paper, we investigate the computational complexity of subgraph reconfiguration problems in directed graphs. More specifically, we focus on the problem of reconfiguring arborescences in a digraph, where an arborescence is a directed…

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…

De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…

DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…

Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

We review recent progress on ancestral processes related to mutation-selection models, both in the deterministic and the stochastic setting. We mainly rely on two concepts, namely, the killed ancestral selection graph and the pruned…

The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…

We propose a partitioning of the set of unlabelled, connected cubic graphs into two disjoint subsets named genes and descendants, where the cardinality of the descendants is much larger than that of the genes. The key distinction between…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…

Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…

We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…

We consider two versions of stochastic population models with mutation and selection. The first approach relies on a multitype branching process; here, individuals reproduce and change type (i.e., mutate) independently of each other,…

A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…

Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…

Due to the mutual occlusion, severe scale variation, and complex spatial distribution, the current multi-person mesh recovery methods cannot produce accurate absolute body poses and shapes in large-scale crowded scenes. To address the…