Related papers: Biological logics are restricted
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
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…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and…
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
We consider here the morphogenesis (pattern formation) problem for some genetic network models. First, we show that any given spatio-temporal pattern can be generated by a genetic network involving a sufficiently large number of genes.…
Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known…
We study the oscillatory behaviour of a gene regulatory network with interlinked positive and negative feedback loop. Frequency and amplitude are two important properties of oscillation. Studied network produces two different modes of…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
In synthetic biology, gene regulatory circuits are often constructed by combining smaller circuit components. Connections between components are achieved by transcription factors acting on promoters. If the individual components behave as…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…
Are biological self-organising systems more ``intelligent'' than artificial intelligence (AI)? If so, why? I address this question using a mathematical framework that defines intelligence in terms of adaptability. Systems are modelled as…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Gene regulatory networks are powerful tools for modeling interactions among genes to regulate their expression for homeostasis and differentiation. Single-cell sequencing offers a unique opportunity to build these networks with…
MicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription factor-regulated gene expression. Recently, a mathematical model has been proposed to…
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…