Related papers: Global Epigenetic State Network Governs Cellular P…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
Gradual transformation of the epidermal stem cells to corneocytes involves a chain of chronologically well-arranged events that mostly stimulated locally by their neighbors. Cell diversity that observed during the differentiation through…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
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…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
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…
Recent experimental advances in biology allow researchers to obtain gene expression profiles at single-cell resolution over hundreds, or even thousands of cells at once. These single-cell measurements provide snapshots of the states of the…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…
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…