Related papers: The physics of epigenetics
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Spatial systems with heterogeneities are ubiquitous in nature, from precipitation, temperature and soil gradients controlling vegetation growth to morphogen gradients controlling gene expression in embryos. Such systems, generally described…
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers,…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
The present view of biological phenomena is based on a biochemical paradigm that development of living organisms is defined by information stored in a molecular form as some genetic code. However, new discoveries indicate that biological…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms.…
Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
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…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
Epigenetics is most often reduced to chromatin marking in the current literature, whereas this notion was initially defined in a more general context. This restricted view ignores that epigenetic memories are in fact more robustly ensured…
Cells of the human body have nearly identical genome but exhibit very different phenotypes that allow them to carry out specific functions and react to changes in their surrounding environment. This division of labour is achieved by…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and find applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural…