Related papers: Universality and predictability in molecular quant…
Kernel methods have been widely applied to machine learning and other questions of approximating an unknown function from its finite sample data. To ensure arbitrary accuracy of such approximation, various denseness conditions are imposed…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
Biological approximations, which are universal for diverse species, are well known. With no other experimental data, their invariance to transformations from one species to another yields exact conservation (with respect to biological…
The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but…
Infinitely many distinct trait values may arise in populations bearing quantitative traits, and modeling their population dynamics is thus a formidable task. While classical models assume fixed or infinite population size, models in which…
Pathogens drive changes in host immune systems that in turn exert pressure for pathogens to evolve. Quantifying and understanding this constant coevolutionary process has clear practical global health implications. Yet its relatively easier…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
Many biological characteristics of evolutionary interest are not scalar variables but continuous functions. Given a dataset of function-valued traits generated by evolution, we develop a practical statistical approach to infer ancestral…
By measuring or calculating coalescence times for several models of coalescence or evolution, with and without selection, we show that the ratios of these coalescence times become universal in the large size limit and we identify a few…
Recent studies of in vitro evolution of DNA via protein binding indicate that the evolution behavior is qualitatively different in different parameter regimes. I here present a general theory that is valid for a wide range of parameters,…
Variable selection has played a critical role in modern statistical learning and scientific discoveries. Numerous regularization and Bayesian variable selection methods have been developed in the past two decades for variable selection, but…
One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments which is crucial for evolvability. Recent work showed that when selective environments…
Molecular clock (MC) is a central concept of molecular evolution according to which each gene evolves at a characteristic, near constant rate. Numerous evolutionary studies have demonstrated the validity of MC but also have shown that MC is…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
In the last years many powerful techniques have emerged to measure protein interactions as well as gene expression. Many progresses have been done since the introduction of these techniques but not toward quantitative analysis of data. In…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
Genetic and evolution algebras arise naturally from applied probability and stochastic processes. Gibbs measures describe interacting systems commonly studied in thermodynamics and statistical mechanics with applications in several fields.…
Operating quantum sensors and quantum computers would make data in the form of quantum states available for purely quantum processing, opening new avenues for studying physical processes and certifying quantum technologies. In this…