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There are two phases of Wnt signalling in early vertebrate embryogenesis: very early, maternal Wnt signalling promotes dorsal development, and slightly later, zygotic Wnt signalling promotes ventral and lateral mesoderm induction. However,…
The canonical Wnt signaling pathway, mediated by $\beta$-catenin, is crucially involved in development, adult stem cell tissue maintenance and a host of diseases including cancer. We undertake analysis of different mathematical models of…
Signal transduction pathways are largely conserved throughout the animal kingdom. The repertoire of pathways is limited and each pathway is used in different intercellular signaling events during the development of a given animal. For…
The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate specification is coordinated via Notch's interaction with the canonical Wnt pathway.…
A new suggestion for pattern formation in biological systems is proposed. The interaction of two signaling pathways provides complex patterning. The interaction of two pathways involves few of the biochemical complexities of the pathways.…
Spatially annotated single-cell datasets provide unprecedented opportunities to dissect cell-cell communication in development and disease. Heterotypic signaling includes interactions between different cell types and is well established in…
Computational modeling of Wnt signaling pathway has gained prominence for its use as computer aided diagnostic tool to develop therapeutic cancer target drugs and predict of test samples as cancerous and non cancerous. This manuscript…
Genes and proteins regulate cellular functions through complex circuits of biochemical reactions. Fluctuations in the components of these regulatory networks result in noise that invariably corrupts the signal, possibly compromising…
Transforming Growth Factor-beta (TGF-beta) signalling is an important regulator of cellular growth and differentiation. The principal intracellular mediators of TGF-beta signalling are the Smad proteins, which upon TGF-beta stimulation…
Using a stochastic individual-based modelling approach, we examine the role that Delta-Notch signalling plays in the regulation of a robust and reliable somite segmentation clock. We find that not only can Delta-Notch signalling synchronise…
This work investigates dynamical quantum phase transitions (DQPTs) in a one-dimensional Ising model subjected to a periodically modulated transverse field. In contrast to sudden quenches, we demonstrate that a DQPT can be induced in two…
Transforming growth factor beta (TGF$\beta$) plays a central role in morphogenesis, growth, and cell differentiation. This cytokine is particularly important in cartilage where it regulates cell proliferation and extracellular matrix…
Understanding how gene regulatory networks (GRNs) give rise to stable and dynamic cellular states remains a central challenge in theoretical biology, particularly when slow epigenetic feedback reshapes the underlying regulatory landscape.…
The cell cycle is tightly regulated by cyclins and their catalytic moieties, the cyclin-dependent kinases (CDKs). Cyclin D1, in association with CDK4/6, acts as a mitogenic sensor and integrates extracellular mitogenic signals and cell…
We present a parameter-efficient Diffusion Transformer (DiT) for generating 200bp cell-type-specific regulatory DNA sequences. By replacing the U-Net backbone of DNA-Diffusion with a transformer denoiser equipped with a 2D CNN input…
We present the mechanism of interaction of Wnt network module, which is responsible for periodic sometogenesis, with p53 regulatory network, which is one of the main regulators of various cellular functions, and switching of various…
The mating pathway in \emph{Saccharomyces cerevisiae} is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and…
Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently…
Notch signaling is an evolutionary conserved cell-cell communication pathway. Besides regulating cell-fate decisions at an individual cell level, Notch signaling coordinates the emergent spatiotemporal patterning in a tissue through…
Brain development in the first few months of human life is a critical phase characterized by rapid structural growth and functional organization. Accurately predicting developmental outcomes during this time is crucial for identifying…