In order to understand the functioning of organisms on the molecular level, we need to know
which genes are expressed, when and where in the organism, and to which extent. The …

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 …

The use of multiple omics techniques (ie, genomics, transcriptomics, proteomics, and
metabolomics) is becoming increasingly popular in all facets of life science. Omics …

INTRODUCTION The generation of biological data is presenting us with one of the most
demanding analysis challenges the world has ever faced, not only in terms of storage and …

Understanding how complex phenotypes arise from individual molecules and their
interactions is a primary challenge in biology that computational approaches are poised to …

Cytoscape is an open source software project for integrating biomolecular interaction
networks with high-throughput expression data and other molecular states into a unified …

Motivation: Simulation and modeling is becoming a standard approach to understand
complex biochemical processes. Therefore, there is a big need for software tools that allow …

▪ Abstract Systems biology studies biological systems by systematically perturbing them
(biologically, genetically, or chemically); monitoring the gene, protein, and informational …

Metabolism is highly complex and involves thousands of different connected reactions; it is
therefore necessary to use mathematical models for holistic studies. The use of …

Background Genome-scale metabolic reconstructions under the Constraint Based
Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the …