Related papers: Automated generation of bacterial resource allocat…
Recurrence quantification analysis (RQA) is a widely used tool for studying complex dynamical systems, but its standard implementation requires computationally expensive calculations of recurrence plots (RPs) and line length histograms.…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
Robust ranking and selection (R&S) is an important and challenging variation of conventional R&S that seeks to select the best alternative among a finite set of alternatives. It captures the common input uncertainty in the simulation model…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
The INLA package provides a tool for computationally efficient Bayesian modeling and inference for various widely used models, more formally the class of latent Gaussian models. It is a non-sampling based framework which provides…
Market Basket Analysis (MBA) is a popular technique to identify associations between products, which is crucial for business decision making. Previous studies typically adopt conventional frequent itemset mining algorithms to perform MBA.…
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…
The Building Block Hypothesis (BBH) states that adaptive systems combine good partial solutions (so-called building blocks) to find increasingly better solutions. It is thought that Genetic Algorithms (GAs) implement the BBH. However, for…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
An evolving yeast colony is simulated by means of a cellular automaton that takes care of many important features of the system under study. A complete survey of the properties of the colony is done and a set of scaling relations is found,…
Genetic and environmental perturbation experiments have been used to study microbes in a bid to gain insight into transcriptional regulation, adaptive evolution, and other cellular dynamics. These studies have potential in enabling rational…
BHAM is a freely avaible R pakcage that implments Bayesian hierarchical additive models for high-dimensional clinical and genomic data. The package includes functions that generalized additive model, and Cox additive model with the…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
Large-scale Bundle Adjustment (BA) requires massive memory and computation resources which are difficult to be fulfilled by existing BA libraries. In this paper, we propose MegBA, a GPU-based distributed BA library. MegBA can provide…
Chlamydiae are bacteria with an interesting unusual developmental cycle. A single bacterium in its infectious form (elementary body, EB) enters the host cell, where it converts into its dividing form (reticulate body, RB), and divides by…
The collaborative efforts of large communities in science experiments, often comprising thousands of global members, reflect a monumental commitment to exploration and discovery. Recently, advanced and complex data processing has gained…
This paper presents a new static analysis for deriving upper bounds on the expected resource consumption of probabilistic programs. The analysis is fully automatic and derives symbolic bounds that are multivariate polynomials of the inputs.…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…
Despite growth being fundamental to all aspects of cell biology, we do not yet know its organizing principles in eukaryotic cells. Classic models derived from the bacteria E. coli posit that protein-synthesis rates are set by mass-action…