相关论文: Reconstructing pedigrees: a stochastic perspective

We introduce a new model of indeterminacy in graphs: instead of specifying all the edges of the graph, the input contains all triples of vertices that form a connected subgraph. In general, different (labelled) graphs may have the same set…

We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…

For families, kinship coefficients are quantifications of the amount of genetic sharing between a pair of individuals. These coefficients are critical for understanding the breeding habits and genetic diversity of diploid populations.…

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across…

We consider a neutral haploid population whose generations are not overlapping and whose size is large and constantly of $N$ individuals. Any generation is replaced by a new one and any individual has a single parent. We do not choose the…

We examine the problem of family size statistics (the number of individuals carrying the same surname, or the same DNA sequence) in a given size subsample of an exponentially growing population. We approach the problem from two directions.…

Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the…

Mechanisms leading to speciation are a major focus in evolutionary biology. In this paper, we present and study a stochastic model of population where individuals, with type a or A, are equivalent from ecological, demographical and spatial…

Ordered sequences of univariate or multivariate regressions provide statistical models for analysing data from randomized, possibly sequential interventions, from cohort or multi-wave panel studies, but also from cross-sectional or…

The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…

Evolutionary graph theory has grown to be an area of intense study. Despite the amount of interest in the field, it seems to have grown separate from other subfields of population genetics and evolution. In the current work I introduce the…

We calculate the probability distribution of repetitions of ancestors in a genealogical tree for simple neutral models of a closed population with sexual reproduction and non-overlapping generations. Each ancestor at generation g in the…

Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools…

Human history leaves fingerprints in human languages. Little is known over language evolution and its study is of great importance. Here, we construct a simple stochastic model and compare its results to statistical data of real languages.…

Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…

Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…