相关论文: Reconstructing pedigrees: a stochastic perspective

Our understanding of past evolutionary change is often based on reconstructions based on incomplete data, raising fundamental questions about the degree to which we can make reliable inferences about past evolutionary processes. This was…

In this paper we discuss reconstruction problems for graphs. We develop some new ideas like isomorphic extension of isomorphic graphs, partitioning of vertex sets into sets of equivalent points, subdeck property, etc. and develop an…

This issue includes six articles that develop and apply statistical methods for the analysis of gene sequencing data of different types. The methods are tailored to the different data types and, in each case, lead to biological insights not…

Many innovations are inspired by past ideas in a non-trivial way. Tracing these origins and identifying scientific branches is crucial for research inspirations. In this paper, we use citation relations to identify the descendant chart,…

We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…

Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…

Kinship verification is a well-explored task: identifying whether or not two persons are kin. In contrast, kinship identification has been largely ignored so far. Kinship identification aims to further identify the particular type of…

This paper considers the problem of inferring the structure of a network from indirect observations. Each observation (a "trace") is the unordered set of nodes which are activated along a path through the network. Since a trace does not…

The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…

We introduce a general diploid population model with self-fertilization and possible overlapping generations, and study the genealogy of a sample of $n$ genes as the population size $N$ tends to infinity. Unlike traditional approach in…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

How can one visually characterize people in a decade? In this work, we assemble the Faces Through Time dataset, which contains over a thousand portrait images from each decade, spanning the 1880s to the present day. Using our new dataset,…

Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…

Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…

Inferences about the evolution of continuous traits based on reconstruction of ancestral states has often been considered more error-prone than analysis of independent contrasts. Here we show that both methods in fact yield identical…

The reconstruction of a species tree from genomic data faces a double hurdle. First, the (gene) tree describing the evolution of each gene may differ from the species tree, for instance, due to incomplete lineage sorting. Second, the…

Historical processes manifest remarkable diversity. Nevertheless, scholars have long attempted to identify patterns and categorize historical actors and influences with some success. A stochastic process framework provides a structured…

Recent trends in information management involve the periodic transcription of data onto secondary devices in a networked environment, and the proper scheduling of these transcriptions is critical for efficient data management. To assist in…