Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

Biological processes are often dynamic, thus researchers must monitor their activity at
multiple time points. The most abundant source of information regarding such dynamic …

Existing methods for gene regulatory network (GRN) inference rely on gene expression data
alone or on lower resolution bulk data. Despite the recent integration of chromatin …

Motivation The analysis of RNA-Seq data from individual differentiating cells enables us to
reconstruct the differentiation process and the degree of differentiation (in pseudo-time) of …

The intestinal microbiota is a microbial ecosystem of crucial importance to human health.
Understanding how the microbiota confers resistance against enteric pathogens and how …

Genome-wide identification of the mechanism of action (MoA) of small-molecule compounds
characterizing their targets, effectors, and activity modulators represents a highly relevant yet …

The elucidation of gene regulatory networks is one of the major challenges of systems
biology. Measurements about genes that are exploited by network inference methods are …

Gene regulatory networks have an important role in every process of life, including cell
differentiation, metabolism, the cell cycle and signal transduction. By understanding the …

Background and objective Mechanistic-based Model simulations (MM) are an effective
approach commonly employed, for research and learning purposes, to better investigate …

Background Inferring the structure of gene regulatory networks (GRN) from a collection of
gene expression data has many potential applications, from the elucidation of complex …