Abstract Systems Bioinformatics is a relatively new approach, which lies in the intersection of
systems biology and classical bioinformatics. It focuses on integrating information across …

In cell and molecular biology, metabolism is the only system that can be fully simulated at
genome scale. Metabolic systems biology offers powerful abstraction tools to simulate all …

Polyclonal metastases frequently arise from clusters of circulating tumor cells (CTCs). CTC
clusters metastasize better than single CTCs, but the underlying molecular mechanisms are …

In this paper, we address the system identification problem in the context of biological
modelling. We present and demonstrate a methodology for (i) assessing the possibility of …

Protein–protein interactions (PPIs) describe the direct physical contact of two proteins that
usually results in specific biological functions or regulatory processes. The characterization …

Background Kinetic models of biochemical systems usually consist of ordinary differential
equations that have many unknown parameters. Some of these parameters are often …

Rapid diversification often involves complex histories of gene flow that leave variable and
conflicting signatures of evolutionary relatedness across the genome. Identifying the extent …

Combinatorial interactions among transcription factors (TFs) play essential roles in
generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid …

This review focuses on modeling methodologies of the gastrointestinal tract during digestion
that have adopted a systems-view approach and, more particularly, on physiologically …

Cell-free systems are useful tools for prototyping metabolic pathways and optimizing the
production of various bioproducts. Mechanistically-based kinetic models are uniquely suited …