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A central idea in understanding brains and building artificial intelligence is that structure determines function. Yet, how the brain's complex structure arises from a limited set of genetic instructions remains a key question. The ultra…
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…
Artificial and natural neural network models are a new toolkit which could be potentially have been used for clarifying of complex brain functions. To attend this goal, such models need to be neurobiologically realistic. However, although…
The brain is a complex organ characterized by heterogeneous patterns of structural connections supporting unparalleled feats of cognition and a wide range of behaviors. New noninvasive imaging techniques now allow these patterns to be…
Social network structures play an important role in the lives of animals by affecting individual fitness and the spread of disease and information. Nevertheless, we still lack a good understanding of how these structures emerge from the…
We describe and analyze algorithms for shape-constrained symbolic regression, which allows the inclusion of prior knowledge about the shape of the regression function. This is relevant in many areas of engineering -- in particular whenever…
Space-saving design is a requirement that is encountered in biological systems and the development of modern technological devices alike. Many living organisms dynamically pack their polymer chains, filaments or membranes inside of…
Large-scale force generation is essential for biological functions such as cell motility, embryonic development, and muscle contraction. In these processes, forces generated at the molecular level by motor proteins are transmitted by…
Geometric modeling by constraints, whose applications are of interest to communities from various fields such as mechanical engineering, computer aided design, symbolic computation or molecular chemistry, is now integrated into standard…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…
Segmentation in arthropod embryogenesis represents a well-known example of body plan diversity. Striped patterns of gene expression that lead to the future body segments appear simultaneously or sequentially in long and short germ-band…
The correlations that can be observed between a set of variables depend on the causal structure underpinning them. Causal structures can be modeled using directed acyclic graphs, where nodes represent variables and edges denote functional…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
Connecting cell behavior to tissue shape and mechanics is a key challenge in the physics of morphogenesis. Cytoskeletal turnover precludes a fixed reference state, and tensions are actively generated independently of strain; so conventional…
This article discusses how the individual morphological properties of basic objects (e.g. neurons, molecules and aggregates), jointly with their particular spatial distribution, can determine the connectivity and dynamics of systems…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic…