Related papers: evolSOM: an R Package for evolutionary conservatio…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
Biogenic Volatile Organic Compounds (BVOCs) play a critical role in biosphere-atmosphere interactions, being a key factor in the physical and chemical properties of the atmosphere and climate. Acquiring large and fine-grained BVOC emission…
Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…
An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
In last decades optimization and control of complex systems that possessed various conflicted objectives simultaneously attracted an incremental interest of scientists. This is because of the vast applications of these systems in various…
Evolvability refers to the ability of an individual genotype (solution) to produce offspring with mutually diverse phenotypes. Recent research has demonstrated that divergent search methods, particularly novelty search, promote evolvability…
Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Recent work pairs LLMs with evolutionary search to iteratively generate, modify, and select code using task-specific feedback. These systems have produced strong results in mathematical discovery and algorithm design, yet a fundamental…
In view of the problem that each subchain in the chain-of-model (CoM) relies only on the information of the previous subchain and may lose long-range dependencies due to the causal mask blocking the global context flow between multi-level…
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…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
Real-time autonomous systems utilize multi-layer computational frameworks to perform critical tasks such as perception, goal finding, and path planning. Traditional methods implement perception using occupancy grid mapping (OGM), segmenting…
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…
BPEC is an R package for Bayesian Phylogeographic and Ecological Clustering which allows geographical, environmental and phenotypic measurements to be combined with DNA sequences in order to reveal clustered structure resulting from…
We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…
The R package SamplingStrata was developed in 2011 as an instrument to optimize the design of stratified samples. The optimization is performed by considering the stratification variables available in the sampling frame, and the precision…