Related papers: Bridging physiological and evolutionary time scale…
Biological transport networks are highly optimized structures that ensure power-efficient distribution of fluids across various domains, including animal vasculature and plant venation. Theoretically, these networks can be described as…
Gene regulatory networks (GRNs) orchestrate cellular decision making and survival strategies. Inferring the structure of these networks from high-dimensional transcriptomics data is a central challenge in systems biology. Traditional…
Transport networks are crucial for the functioning of natural and technological systems. We study a mathematical model of vascular network adaptation, where the network structure dynamically adjusts to changes in blood flow and pressure.…
We study a version of the Tangled Nature model of evolutionary ecology redefined in a phenotype space where mutants have properties correlated to their parents. The model has individual-based dynamics whilst incorporating species scale…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Rapidly evolving viruses use antigenic drift as a key mechanism to evade host immunity and persist in real populations. While traditional models of antigenic drift and epidemic spread rely on low-dimensional antigenic spaces, genomic…
Gene Regulatory Networks(GRNs) with feedback are essential components of many cellular processes and may exhibit oscillatory behavior. Analyzing such systems becomes increasingly complex as the number of components increases. Since gene…
Gene regulatory networks (GRNs) perform a wide range of biological functions. It is, however, often challenging to reveal their functioning mechanism with the conventional approach focusing on the network topological structure from a…
Biomolecular networks underpin emerging technologies in synthetic biology-from robust biomanufacturing and metabolic engineering to smart therapeutics and cell-based diagnostics-and also provide a mechanistic language for understanding…
Gene regulatory networks (GRNs) are essential for understanding cell fate decisions and disease mechanisms, yet cross-species GRN inference from single-cell RNA-seq data remains challenging due to noise, sparsity, and cross-species…
There is increasing need for highly predictive and stable models for the prediction of drought as an aid to better planning for drought response. This paper presents the performance of both homogenous and heterogenous model ensembles in the…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Complex distribution networks are pervasive in biology. Examples include nutrient transport in the slime mold \emph{Physarum polycephalum} as well as mammalian and plant venation. Adaptive rules are believed to guide development of these…
Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's…
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…
Time-series of high throughput gene sequencing data intended for gene regulatory network (GRN) inference are often short due to the high costs of sampling cell systems. Moreover, experimentalists lack a set of quantitative guidelines that…
We investigate response selection for multi-turn conversation in retrieval-based chatbots. Existing studies pay more attention to the matching between utterances and responses by calculating the matching score based on learned features,…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
The rapid advancement in high-throughput techniques has fueled the generation of large volume of biological data rapidly with low cost. Some of these techniques are microarray and next generation sequencing which provides genome level…