相关论文: Systematics and symmetry in molecular phylogenetic…

Rapid developments in genetics and biology have led to phylogenetic methods becoming an important direction in the study of cancer and viral evolution. Although our understanding of gene biology and biochemistry has increased and is…

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…

How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…

A calculational framework is proposed for phylogenetics, using nonlocal quantum field theories in hypercubic geometry. Quadratic terms in the Hamiltonian give the underlying Markov dynamics, while higher degree terms represent branching…

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…

In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…

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…

Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…

The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…

The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…

The idea that all life on earth traces back to a common beginning dates back at least to Charles Darwin's {\em Origin of Species}. Ever since, biologists have tried to piece together parts of this `tree of life' based on what we can observe…

Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…

Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…

In this article, the notion of a mathematical model in science is attempted to be enlightened from several points of view. In particular, it is shown that mathematical models are introduced differently and used differently in different…

Correctly capturing the symmetry transformations of data can lead to efficient models with strong generalization capabilities, though methods incorporating symmetries often require prior knowledge. While recent advancements have been made…

The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…