The current survey aims to describe the main methodologies for extending the
reconstruction and analysis of genome-scale metabolic models and phenotype simulation …

The genome-scale cellular network has become a necessary tool in the systematic analysis
of microbes. In a cell, there are several layers (ie, types) of the molecular networks, for …

Given the extensive heterogeneity and variability, understanding cellular functions and
regulatory mechanisms through the analysis of multi‐omics datasets becomes extremely …

Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to
heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present …

Most bacteria are surrounded by their cell wall, containing a highly cross-linked protective
envelope of peptidoglycan. To grow, bacteria must continuously remodel their wall, inserting …

We present RegulomePA, a database that contains biological information on regulatory
interactions between transcription factors (TFs), sigma factor (SFs) and target genes in …

Background As an important prokaryotic model organism, Bacillus subtilis has been widely
used in the industrial production of a variety of target products. The efficient secretion of …

Introduction Staphylococcus aureus is one of the most prevalent and relevant pathogens
responsible for a wide spectrum of hospital-associated or community-acquired infections. In …

Many bacterial genes encoding components of the translation and transcription machinery
occupy genomic positions close to the origin of genome replication. These positional biases …

Symmetry principles have proven important in physics, deep learning and geometry,
allowing for the reduction of complicated systems to simpler, more comprehensible models …