Related papers: piBUSS: a parallel BEAST/BEAGLE utility for sequen…
Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing…
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
We present the B-spline Encoded Action Sequence Tokenizer (BEAST), a novel action tokenizer that encodes action sequences into compact discrete or continuous tokens using B-splines. In contrast to existing action tokenizers based on vector…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
Numerous machine learning (ML) models employed in protein function and structure prediction depend on evolutionary information, which is captured through multiple-sequence alignments (MSA) or position-specific scoring matrices (PSSM) as…
Integrating population genetics into community ecology theory is a major goal in ecology and evolution, but analyzing the resulting models is computationally daunting. Here we describe sPEGG ($\underline{\textrm{s}}\textrm{imulating}$…
Peptide Optimization is a highly complex problem and it takes very long time of computation. This optimization process uses many software applications in a cluster running GNU/Linux Operating System that perform special tasks. The…
Calibration is a vital step in the development of rigorous digital models of diverse physical and chemical processes, yet one which is highly time- and labour-intensive. In this paper, we introduce a novel tool, Autonomous Calibration and…
Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…
The brain can only be fully understood through the lens of the behavior it generates -- a guiding principle in modern neuroscience research that nevertheless presents significant technical challenges. Many studies capture behavior with…
Beagle is a new software framework that enables execution of Genetic Programming tasks on the GPU. Currently available for symbolic regression, it processes individuals of the population and fitness cases for training in a way that…
Phylodynamics is used to estimate epidemic dynamics from phylogenetic trees or genomic sequences of pathogens, but the likelihood calculations needed can be challenging for complex models. We present a neural Bayes estimator (NBE) for key…
Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…
PhysiBoSS is an open-source platform that integrates agent-based modeling of cell populations with intracellular stochastic Boolean networks, enabling multiscale simulations of complex biological behaviors. To promote model sharing and…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
The Basic Local Alignment Search Tool (BLAST) is currently the most popular method for searching databases of biological sequences. BLAST compares sequences via similarity defined by a weighted edit distance, which results in it being…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Phylogenetic tree reconciliation is employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation.…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…