Related papers: Design principles of multi-map variation in biolog…
Real-world design processes often involve the evolution and divergence of design paths (by branching, revising, merging, etc.), especially when multiple stakeholders or teams operate concurrently and/or explore different alternatives for…
Non-uniform rates of morphological evolution and evolutionary increases in organismal complexity, captured in metaphors like "adaptive zones", "punctuated equilibrium" and "blunderbuss patterns", require more elaborate explanations than a…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
The emerging field of morphogenetic engineering proposes to design complex heterogeneous system focused on the paradigm of emergence. Necessarily at the interface of disciplines, its concepts can be defined through multiple viewpoints. This…
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.…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Current analyses of genomes from numerous species show that the diversity of organism's functional and behavioral characters is not proportional to the number of genes that encode the organism. We investigate the hypothesis that the…
Our understanding of evolution is shaped strongly by how we conceive of its fundamental causes. In the original Modern Synthesis, evolution was defined as a process of shifting the frequencies of available alleles at many loci affecting a…
The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
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…
All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments…
Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
In this paper, an approach to facilitate the treatment with variabilities in system families is presented by explicitly modelling variants. The proposed method of managing variability consists of a variant part, which models variants and a…
In this paper, an approach to facilitate the treatment with variabilities in system families is presented by explicitly modelling variants. The proposed method of managing variability consists of a variant part, which models variants and a…
Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora 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…