Related papers: System-Level Genetic Codes: An Explanation for Bio…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…
Component-Based Development (CBD) is a popular approach to mitigating the costs of creating software systems. However, it is not clear to what extent the core component selection and adaptation activities of CBD can be implemented to…
Complex systems, in many different scientific sectors, show coarse-grain properties with simple growth laws with respect to fundamental microscopic algorithms. We propose a classification scheme of growth laws which includes human aging,…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
What features characterise complex system dynamics? Power laws and scale invariance of fluctuations are often taken as the hallmarks of complexity, drawing on analogies with equilibrium critical phenomena[1-3]. Here we argue that slow,…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
A good feature representation is a determinant factor to achieve high performance for many machine learning algorithms in terms of classification. This is especially true for techniques that do not build complex internal representations of…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
We present a scenario for the origin of biological coding. In this context, coding is a semiotic relationship between chemical information stored in one location that links to chemical information stored in a separate location. Coding…
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
Understanding the molecular processes that drive cellular life is a fundamental question in biological research. Ambitious programs have gathered a number of molecular datasets on large populations. To decipher the complex cellular…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…