Related papers: Molecular evolution and gene function
The theory of stellar evolution plays a central role in astrophysics as stellar models are used to infer properties for Galactic and Extragalactic stellar populations as well as exoplanetary systems. However, despite decades of experience,…
The development of multicellular organisms entails a deep connection between time-dependent biochemical processes taking place at the subcellular level, and the resulting macroscopic phenotypes that arise in populations of up to trillions…
Evolution and learning are two of the fundamental mechanisms by which life adapts in order to survive and to transcend limitations. These biological phenomena inspired successful computational methods such as evolutionary algorithms and…
Digital logic forms the functional basics of most modern electronic equipment and as such the creation of novel digital logic circuits is an active area of computer engineering research. This study demonstrates that genetic algorithms can…
Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them.…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
The two major approaches to studying macroevolution in deep time are the fossil record and reconstructed relationships among extant taxa from molecular data. Results based on one approach sometimes conflict with those based on the other,…
Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and find applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural…
We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…
Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein,…
Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
Both external environmental selection and internal lower-level evolution are essential for an integral picture of evolution. This paper proposes that the division of internal evolution into DNA/RNA pattern formation (genotype) and protein…
The Hubble tuning fork diagram, based on morphology, has always been the preferred scheme for classification of galaxies and is still the only one originally built from historical/evolutionary relationships. At the opposite, biologists have…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…