Related papers: Epigenetic Tracking: Implementation Details
New approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, enforced by new crossover operators, especially worked out for…
The Game of Life (GoL), one well known 2D cellular automaton, does not typically ensure interesting long-term phenotypic dynamics. Therefore, while being Turing complete, GoL cannot be said to be open-ended. In this work, we extend GoL with…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
Generative modelling for shapes is a prerequisite for In-Silico Clinical Trials (ISCTs), which aim to cost-effectively validate medical device interventions using synthetic anatomical shapes, often represented as 3D surface meshes. However,…
We propose and analyze a stochastic model to investigate epigenetic mutations, i.e., modifications of the genetic information that control gene expression patterns in a cell but do not alter the DNA sequence. Epigenetic mutations are…
Cellular development follows a stochastic yet rule-governed trajectory, though the underlying principles remain elusive. Here, we propose that cellular development follows paths of least action, aligning with foundational physical laws that…
Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions.…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
The image synthesis technique is relatively well established which can generate facial images that are indistinguishable even by human beings. However, all of these approaches uses gradients to condition the output, resulting in the…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
Cellular Electron CryoTomography (CECT) is a 3D imaging technique that captures information about the structure and spatial organization of macromolecular complexes within single cells, in near-native state and at sub-molecular resolution.…
Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point…
Morphogenesis, the process by which an adult organism emerges from a single cell, has fascinated humans for a long time. Modelling this process can provide novel insights into development and the principles that orchestrate the…
Tree-based Genetic Programming (TGP) is a widely used evolutionary algorithm for tasks such as symbolic regression, classification, and robotic control. Due to the intensive computational demands of running TGP, GPU acceleration is crucial…
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…
Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative…
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…