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Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
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…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
In single-cell research, tracing and analyzing high-throughput single-cell differentiation trajectories is crucial for understanding biological processes. Key to this is the robust modeling of hierarchical structures that govern cellular…
Tip-driven growth processes underlie the development of many plants. To date, tip-driven growth processes have been modelled as an elongating path or series of segments without taking into account lateral expansion during elongation.…
Evolutionary transitions occur when previously-independent replicating entities unite to form more complex individuals. Such transitions have profoundly shaped natural evolutionary history and occur in two forms: fraternal transitions…
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place --…
A blood cell lineage consists of several consecutive developmental stages from the pluripotent or multipotent stem cell to a particular stage of terminally differentiated cells. There is considerable interest in identifying the key…
Complex networks can be used to analyze structures and systems in the embryo. Not only can we characterize growth and the emergence of form, but also differentiation. The process of differentiation from precursor cell populations to…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…