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In early development, regulation of transcription results in precisely positioned and highly reproducible expression patterns that specify cellular identities. How transcription, a fundamentally noisy molecular process, is regulated to…
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…
To study how a zygote develops into an embryo with different tissues, large-scale 4D confocal movies of C. elegans embryos have been produced recently by experimental biologists. However, the lack of principled statistical methods for the…
Deep learning segmentation and fluorescence imaging techniques allow the cellular morphology of living embryos to be constructed spatiotemporally. These development processes involve numerous molecules distributed at the subcellular scale,…
A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model --…
Successful biological development via spatial regulation of cell differentiation relies on action of multiple signaling molecules that are known as morphogens. It is now well established that signaling molecules create non-uniform…
Identification of fine-grained embryo developmental stages during In Vitro Fertilization (IVF) is crucial for assessing embryo viability. Although recent deep learning methods have achieved promising accuracy, existing discriminative models…
We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and…
Morphogens are secreted signaling molecules that mediate tissue patterning and growth of embryonic tissues. They are secreted in a localized region and spread through the tissue to form a graded concentration profile. We present a…
Gene transcription is a critical step in gene expression. The currently accepted physical model of transcription predicts the existence of a physical limit on the maximal rate of transcription, which does not depend on the transcribed gene.…
Morphogens are proteins, often produced in a localised region, whose concentrations spatially demarcate regions of differing gene expression in developing embryos. The boundaries of expression must be set accurately and in proportion to the…
Embryonic development relies on the formation of sharp, precise gene expression boundaries. In the fruit fly Drosophila melanogaster, boundary formation has been proposed to occur at a dynamical critical point. Yet, in the paradigmatic case…
Axes of polarity (and primary morphogenetic gradients) are established in the oocyte - early embryo through active transport and localization of maternal factors. It is the oocyte - syncytial embryo of Drosophila (D. melanogaster) that is a…
We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case…
Spatial patterns in the early fruit fly embryo emerge from a network of interactions among transcription factors, the gap genes, driven by maternal inputs. Such networks can exhibit many qualitatively different behaviors, separated by…
During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process…
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…
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of…
We analyze a one dimensional version of a model of morphogen transport, a biological process governing cell differentiation. The model was proposed by Hufnagel et al. to describe the forming of morphogen gradient in the wing imaginal disc…
The developmental process of embryos follows a monotonic order. An embryo can progressively cleave from one cell to multiple cells and finally transform to morula and blastocyst. For time-lapse videos of embryos, most existing developmental…