Related papers: The Mathematics of Phylogenomics
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
Cancer, as the uncontrollable cell growth, is related to many branches of biology. In this review, we will discuss three mathematical approaches for studying cancer biology: population dynamics, gene regulation, and developmental biology.…
A century ago physicists and mathematicians worked in tandem and established quantum mechanism. Indeed, algebras, partial differential equations, group theory, and functional analysis underpin the foundation of quantum mechanism. Currently,…
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…
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…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
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…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
The origin and early evolution of eukaryotes are one of the major transitions in the evolution of life on earth. One of its most interesting aspects is the emergence of cellular organelles, their dynamics, their functions, and their…
Mathematical modelling has a long history in the context of collective cell migration, with applications throughout development, disease and regenerative medicine. The aim of modelling in this context is to provide a framework in which to…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
Genomics methods have uncovered patterns in a range of biological systems, but obscure important aspects of cell behavior: the shape, relative locations of, movement of, and interactions between cells in space. Spatial technologies that…
The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems.…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
It is generally accepted that "diversity" is associated with success in evolutionary algorithms. However, diversity is a broad concept that can be measured and defined in a multitude of ways. To date, most evolutionary computation research…