Related papers: Quantifying the Emergence of Selection Prior to Bi…
Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling frameworks. A long-standing hope of theoretical ecology is that…
Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts…
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.…
Configurational entropy is an important factor in the free energy change of many macromolecular recognition and binding processes, and has been intensively studied. Despite great progresses that have been made, the global sampling remains…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…
Constitutive model discovery refers to the task of identifying an appropriate model structure, usually from a predefined model library, while simultaneously inferring its material parameters. The data used for model discovery are measured…
Forming a molecular candidate set that contains a wide range of potentially effective compounds is crucial to the success of drug discovery. While most databases and machine-learning-based generation models aim to optimize particular…
We analyse the unreduced, nonperturbative dynamics of an arbitrary many-body interaction process with the help of the generalised effective potential method and reveal the well-specified universal origin of change (emergence), time and…
Bedau has developed a general set of evolutionary statistics that quantify the adaptive component of evolutionary processes. On the basis of these measures, he has proposed a set of 4 classes of evolutionary system. All artificial life…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
Deep ensembles can be considered as the current state-of-the-art for uncertainty quantification in deep learning. While the approach was originally proposed as a non-Bayesian technique, arguments supporting its Bayesian footing have been…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
The unprecedented prowess of measurement techniques provides a detailed, multi-scale look into the depths of living systems. Understanding these avalanches of high-dimensional data -- by distilling underlying principles and mechanisms --…
A fundamental question in systems biology is what combinations of mean and variance of the species present in a stochastic biochemical reaction network are attainable by perturbing the system with an external signal. To address this…
Until recently, much of the microbial world was hidden from view. A global research effort has changed this, unveiling and quantifying microbial diversity across enormous range of critically-important contexts, from the human microbiome, to…
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…
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…
In quantum mechanics, outcomes of measurements on a state have a probabilistic interpretation while the evolution of the state is treated deterministically. Here we show that one can also treat the evolution as being probabilistic in nature…
It is well known that life on Earth alters its environment over evolutionary and geological timescales. An important open question is whether this is a result of evolutionary optimization or a universal feature of life. In the latter case,…
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…