Related papers: Predicting Horizontal Gene Transfers with Perfect …
We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…
Designing fonts requires a great deal of time and effort. It requires professional skills, such as sketching, vectorizing, and image editing. Additionally, each letter has to be designed individually. In this paper, we will introduce a…
We show that for any two values $\alpha, \beta >0 $ for which $\alpha+\beta>1$ then there is a value $N$ so that for all $n \geq N$ the following holds. For any binary phylogenetic tree $T$ on $n$ leaves there is a set of $\lfloor n^\alpha…
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…
This paper develops a theory for characterisation of DNA sequences based on their measure representation. The measures are shown to be random cascades generated by an infinitely divisible distribution. This probability distribution is…
Inferring the network topology from the dynamics is a fundamental problem with wide applications in geology, biology and even counter-terrorism. Based on the propagation process, we present a simple method to uncover the network topology.…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
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…
Bayesian network structure learning algorithms with limited data are being used in domains such as systems biology and neuroscience to gain insight into the underlying processes that produce observed data. Learning reliable networks from…
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…
We study treatment effect modifiers for causal analysis in a social network, where neighbors' characteristics or network structure may affect the outcome of a unit, and the goal is to identify sub-populations with varying treatment effects…
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
In this paper, we describe the problem of cognate identification and its relation to phylogenetic inference. We introduce subsequence based features for discriminating cognates from non-cognates. We show that subsequence based features…
Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it…
How can we recognise social roles of people, given a completely unlabelled social network? We present a transfer learning approach to network role classification based on feature transformations from each network's local feature…
Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…