Related papers: The infinitely many genes model with horizontal ge…
Horizontal gene transfer events partition a gene tree $T$ and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer…
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…
How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
Pangenomics uses graph-based models to represent and study the genetic variation between individuals of the same species or between different species. In such variation graphs, a path through the graph represents one individual genome.…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
This paper develops a Bayesian graphical model for fusing disparate types of count data. The motivating application is the study of bacterial communities from diverse high dimensional features, in this case transcripts, collected from…
Transposable elements are DNA sequences that can move around to different positions in the genome. During this process, they can cause mutations, and lead to an increase in genome size. Despite representing a large genomic fraction,…
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,…
Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity of recombining segments, several studies examined whether this could lead to the…
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also be useful for this task. Notably, perfect transfer networks (PTN) explain the character…
Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…