Related papers: Finding the center reliably: robust patterns of de…
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including…
Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help coordinate these cascades by attracting regulatory proteins to enhance…
We present a novel framework for central pattern generator design that leverages the intrinsic rebound excitability of neurons in combination with winner-takes-all computation. Our approach unifies decision-making and rhythmic pattern…
We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric…
How intelligence emerges from living beings has been a fundamental question in neuroscience. However, it remains largely unanswered due to the complex neuronal dynamics and intricate connections between neurons in real neural systems. To…
Understanding how living organisms spontaneously develop complex functional structures inspires innovative approaches in engineering design. Here, we introduce a decentralized generative model based on morphogenesis to autonomously grow…
Understanding how deep learning models represent data is currently difficult due to the limited number of methodologies available. This paper demonstrates a versatile and novel visualisation tool for determining the axis alignment of…
Respondent-Driven Sampling is a popular technique for sampling hidden populations. This paper models Respondent-Driven Sampling as a Markov process indexed by a tree. Our main results show that the Volz-Heckathorn estimator is…
Reconstruction of gene regulatory networks is the process of identifying gene dependency from gene expression profile through some computation techniques. In our human body, though all cells pose similar genetic material but the activation…
A fully self-consistent calculation of the bosonic dynamics of the Hubbard model is developed within the Composite Operator Method. From one side we consider a basic set of fermionic composite operators (Hubbard fields) and calculate the…
A fully self-consistent calculation of the bosonic dynamics of the Hubbard model is developed within the Composite Operator Method. From one side we consider a basic set of fermionic composite operators (Hubbard fields) and calculate the…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
We revisit the dynamics of a gene repressed by its own protein in the case where the transcription rate does not adapt instantaneously to protein concentration but is a dynamical variable. We derive analytical criteria for the appearance of…
This study is focused on the mechanisms of rhythmogenesis and robustness of anti-phase bursting in half-center-oscillators (HCOs) consisting of two reciprocally inhibitory coupled neurons. There is a growing body of experimental evidence…
Grid cells in the medial entorhinal cortex (MEC) respond when an animal occupies a periodic lattice of "grid fields" in the environment. The grids are organized in modules with spatial periods, or scales, clustered around discrete values…
Many generative models synthesize data by transforming a standard Gaussian random variable using a deterministic neural network. Among these models are the Variational Autoencoders and the Generative Adversarial Networks. In this work, we…