Related papers: Epigenetic Tracking: Implementation Details
In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues…
Dynamic graph-level embedding aims to capture structural evolution in networks, which is essential for modeling real-world scenarios. However, existing methods face two critical yet under-explored issues: Structural Visit Bias, where random…
In tumoral cells, gene regulation mechanisms are severely altered, and these modifications in the regulations may be characteristic of different subtypes of cancer. However, these alterations do not necessarily induce differential…
The design of genetic networks with specific functions is one of the major goals of synthetic biology. However, constructing biological devices that work "as required" remains challenging, while the cost of uncovering flawed designs…
3D fluorescence microscopy of living organisms has increasingly become an essential and powerful tool in biomedical research and diagnosis. An exploding amount of imaging data has been collected, whereas efficient and effective…
Numerical models based on physics represent the state-of-the-art in earth system modeling and comprise our best tools for generating insights and predictions. Despite rapid growth in computational power, the perceived need for higher model…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Unsupervised graph representation learning has recently gained interest in several application domains such as neuroscience, where modeling the diverse morphology of cell types in the brain is one of the key challenges. It is currently…
Human anatomy, morphology, and associated diseases can be studied using medical imaging data. However, access to medical imaging data is restricted by governance and privacy concerns, data ownership, and the cost of acquisition, thus…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
Ethnomethodological fieldwork has long been acknowledged as a potentially valuable way of informing the design of technology. However, there is relatively little methodological support for this activity, particularly in relation to the…
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…
Brain-body co-evolution enables animals to develop complex behaviors in their environments. Inspired by this biological synergy, embodied co-design (ECD) has emerged as a transformative paradigm for creating intelligent agents-from virtual…
Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic…
Neuronal morphology is essential for studying brain functioning and understanding neurodegenerative disorders. As acquiring real-world morphology data is expensive, computational approaches for morphology generation have been studied.…
Different subsystems of organisms adapt over many time scales, such as rapid changes in the nervous system (learning), slower morphological and neurological change over the lifetime of the organism (postnatal development), and change over…
Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures…
Many complex systems, both in technology and nature, exhibit hierarchical modularity: smaller modules, each of them providing a certain function, are used within larger modules that perform more complex functions. Previously, we have…
Artificial Life provides the opportunity to study the emergence and evolution of simple ecosystems in real time. We give an overview of the advantages and limitations of such an approach, as well as its relation to individual-based modeling…
The relation between a structure and the function running on that structure is of central interest in many fields, including computer science, biology (organ vs. function), psychology (body vs. mind), architecture (designs vs.…