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Human embryonic stem cells (ESC) are undifferentiated and are endowed with the capacities of self renewal and pluripotential differentiation. Adult stem cells renew their own tissue, but whether they can trans-differentiate to other tissues…
Developmental constraints have been postulated to limit the space of feasible phenotypes and thus shape animal evolution. These constraints have been suggested to be the strongest during either early or mid-embryogenesis, which corresponds…
We propose a new model describing the production and the establishment of the stable gradient of the Bicoid protein along the antero-posterior axis of the embryo of \textit{Drosophila}. In this model, we consider that \textit{bicoid} mRNA…
Cellular checkerboard patterns are observed at many developmental stages of embryos. We study an analytically tractable model for lateral inhibition and show that a coupling coefficient with a negative value is sufficient to obtain noisy or…
Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and macroscopic…
Gene expression of social actions in Drosophilae has been attracting wide interest from biologists, medical scientists and psychologists. Gene-edited Drosophilae have been used as a test platform for experimental investigation. For example,…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
A central feature of vertebrate immune response is affinity maturation, wherein antibody-producing B cells undergo evolutionary selection in microanatomical structures called germinal centers, which form in secondary lymphoid organs upon…
One of the most common analysis tasks in genomic research is to identify genes that are differentially expressed (DE) between experimental conditions. Empirical Bayes (EB) statistical tests using moderated genewise variances have been very…
A model of sensory information processing is presented. The model assumes that learning of internal (hidden) generative models, which can predict the future and evaluate the precision of that prediction, is of central importance for…
Despite the relative simplicity of C. elegans, its locomotion machinery is not yet well understood. We focus on the generation of dorsoventral body bends. While central pattern generators are commonly involved in animal locomotion, their…
Understanding the differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We develop a theoretical framework to quantify the underlying potential landscape and biological…
A family of repressor networks is proposed as a simple model of gene regulatory networks. We analytically show three topological classes of the repressor networks, each of which exhibits distinctly growing complexity of spatiotemporal…
Appropriate regulation of gene expression is essential to ensure that protein synthesis occurs in a selective manner. The control of transcription is the most dominant type of regulation mediated by a complex of molecules such as…
This paper reveal the selective rotation in the CNNs' forward processing. It elucidates the activation function as a discerning mechanism that unifies and quantizes the rotational aspects of the input data. Experiments show how this defined…
Morphogen profiles play a vital role in biology by specifying position in embryonic development. However, the factors that influence the shape of a morphogen profile remain poorly understood. Since morphogens should provide precise…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of…
Motivation: Spatial pattern formation of the primary anterior-posterior morphogenetic gradient of the transcription factor Bicoid (Bcd) has been studied experimentally and computationally for many years. Bcd specifies positional information…