Related papers: Design Patterns of Biological Cells
Domain-specific constraint patterns are introduced, which form the counterpart to design patterns in software engineering for the constraint programming setting. These patterns describe the expert knowledge and best-practice solution to…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
Deep learning approaches have produced substantial breakthroughs in fields such as image classification and natural language processing and are making rapid inroads in the area of protein design. Many generative models of proteins have been…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
Inherent limitations of contemporary machine learning systems in crucial areas -- importantly in continual learning, information reuse, comprehensibility, and integration with deliberate behavior -- are receiving increasing attention. To…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
We present a simple model based on a reaction-diffusion equation to explain pattern formation in a multicellular bacterium (Streptomyces). We assume competition for resources as the basic mechanism that leads to pattern formation; in…
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…
We formally characterize a set of causality-based properties of metabolic networks. This set of properties aims at making precise several notions on the production of metabolites, which are familiar in the biologists' terminology. From a…
We review theoretical approaches to the understanding of food webs. After an overview of the available food web data, we discuss three different classes of models. The first class comprise static models, which assign links between species…
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.…
Machine learning methods are increasingly employed to address challenges faced by biologists. One area that will greatly benefit from this cross-pollination is the problem of biological sequence design, which has massive potential for…
Design representation is a common task in the design process to facilitate learning, analysis, redesign, communication, and other design activities. Traditional representation techniques rely on human expertise and manual construction and…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Flow-matching generative models are increasingly used to simulate cell responses to biological perturbations. However, the design space for building such models is large and underexplored. We systematically analyse the design space of flow…