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Caenorhabditis elegans (C. elegans) illustrated remarkable behavioral plasticities including complex non-associative and associative learning representations. Understanding the principles of such mechanisms presumably leads to constructive…
Background: Caenorhabditis elegans is a major model system in biology, yet very little is known about its biology outside the laboratory. Especially, its unusual mode of reproduction with self-fertile hermaphrodites and facultative males…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
To optimize clinical outcomes, fertility clinics must strategically select which embryos to transfer. Common selection heuristics are formulas expressed in terms of the durations required to reach various developmental milestones,…
We consider a class of biologically-motivated stochastic processes in which a unicellular organism divides its resources (volume or damaged proteins, in particular) symmetrically or asymmetrically between its progeny. Assuming the final…
Recent whole-brain calcium imaging recordings of the nematode C. elegans have demonstrated that neural activity is dominated by dynamics on a low-dimensional manifold that can be clustered according to behavioral states. Despite progress in…
At the end of the first larval stage, the C elegans larva chooses between two developmental pathways, an L2 committed to reproductive development and an L2d, which has the option of undergoing reproductive development or entering the dauer…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
We discuss a cellular automata model to study the competition between an emergent better fitted species against an existing majority species. The model implement local fights among small group of individual and a synchronous random walk on…
Neoteny, also spelled Paedomorphosis, can be defined in biological terms as the retention by an organism of juvenile or even larval traits into later life. In some species, all morphological development is retarded; the organism is…
Free-living nematode Caenorhabditis elegans is a powerful genetic model, essential for investigations ranging from behavior to neuroscience to aging, and locomotion is a key observable used in these studies. However, despite the fact that…
The motility behavior of the nematode Caenorhabditis elegans in polymeric solutions of varying concentrations is systematically investigated in experiments using tracking and velocimetry methods. As the polymer concentration is increased,…
Network flow is a powerful mathematical framework to systematically explore the relationship between structure and function in biological, social, and technological networks. We introduce a new pipelining model of flow through networks…
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…
Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur,…
Undulatory locomotion, as seen in the nematode \emph{Caenorhabditis elegans}, is a common swimming gait of organisms in the low Reynolds number regime, where viscous forces are dominant. While the nematode's motility is expected to be a…
Molecular networks act as the backbone of cellular activities, providing an {excellent} opportunity to understand the developmental changes in an organism. While network data usually constitute only stationary network graphs, constructing…