Related papers: Cellular reprogramming dynamics follow a simple on…
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…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
Cellular reprogramming can be used for both the prevention and cure of different diseases. However, the efficiency of discovering reprogramming strategies with classical wet-lab experiments is hindered by lengthy time commitments and high…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
In the genome biology research, regulatory genome modeling is an important topic for many regulatory downstream tasks, such as promoter classification, transaction factor binding sites prediction. The core problem is to model how regulatory…
Neural circuits are able to perform computations under very diverse conditions and requirements. The required computations impose clear constraints on their fine-tuning: a rapid and maximally informative response to stimuli in general…
Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…
Developments in transcriptomics techniques have caused a large demand in tailored computational methods for modelling gene expression dynamics from experimental data. Recently, so-called single-cell experiments have revolutionised genetic…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular…
In this work, a neural network is trained to replicate the code that trains it using only its own output as input. A paradigm for evolutionary self-replication in neural programs is introduced, where program parameters are mutated, and the…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
The function of the organism hinges on the performance of its information-processing networks, which convey information via molecular recognition. Many paths within these networks utilize molecular codebooks, such as the genetic code, to…
Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of a process known as spontaneous immortalization. In this process a generic series of cell state transitions occur in…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
The paper introduces a biologically and evolutionarily plausible neural architecture that allows a single group of neurons, or an entire cortical pathway, to be dynamically reconfigured to perform multiple, potentially very different…
Stem cell regeneration is a crucial biological process for most self-renewing tissues during the development and maintenance of tissue homeostasis. In developing the mathematical models of stem cell regeneration and tissue development, cell…