It is now clear that a detailed picture of cell regulation requires a comprehensive understanding of the abundant short protein motifs through which signaling is channeled. The current body of knowledge has slowly accumulated through piecemeal experimental investigation of individual motifs in signaling. Computational methods contributed little to this process. A new generation of bioinformatic...

Systems biology aims for building quantitative models to address unresolved issues in molecular biology. In order to describe the behavior of biological cells adequately, gene regulatory networks (GRNs) are intensively investigated. As the validity of models built for GRNs depends crucially on the kinetic rates, various methods have been developed to estimate these parameters from experimental ...

Introduction: Extensive use of diagnostic radiology is the largest contributor to total population radiation doses. Thus, appropriate equipment and safe practice are necessary for good-quality images with optimal doses. This study aimed to perform quality control (QC) audit for radiography and fluoroscopy devices owned by private sector in Syria (2005-2013) to verify compliance of performance o...

background & aim: investigation of suspension cell culture and callus production in catharanthus roseus. catharanthus roseus is an herbaceous perennial plant belongs to the family apocynaceae. c. roseus is important as commercial medicinal plant because of its alkaloidal content. whole plant contains about 130 alkaloids those are classified as vinca alkaloids. vincristine and vinblastine; t...

How to design a robust gene network to tolerate more intrinsic kinetic parameter variations and to attenuate more extrinsic environmental noises to achieve a desired filtering level will be an important topic for systems biology and synthetic biology. At present, there is no good systematic design method to achieve robust gene network design. In this study, a gene network suffering from intrins...

The reverse engineering of gene regulatory network (GRN) is an important problem in systems biology. While gene expression data provide a main source of insights, other types of data are needed to elucidate the structure and dynamics of gene regulation. Epigenetic data (e.g., histone modification) show promise to provide more insights into gene regulation and on epigenetic implication in biolog...

An important problem in systems biology is to reconstruct gene regulatory networks (GRNs) from experimental data and other a priori information. The DREAM project offers some types of experimental data, such as knockout data, knockdown data, time series data, etc. Among them, multifactorial perturbation data are easier and less expensive to obtain than other types of experimental data and are t...

In Systems Biology, modelers develop more and more reaction-based models to describe the mechanistic biochemical reactions underlying cell processes. They may also work, however, with a simpler formalism of influence graphs, to merely describe the positive and negative influences between molecular species. The first approach is promoted by reaction model exchange formats such as SBML, and tools...

The paper presents the use of signal regulatory networks, a biologically-inspired model based on gene regulatory networks. Signal regulatory networks are a way of understanding a class of self-organising IT systems, signal regulated systems. The paper builds on the theory of signal regulated systems and introduces some formalisms to clarify the discussion. An exemplar signal regulated system th...

Living organisms consist of interacting objects such as organs, cells, and genes. Therefore, they can be considered complex systems and we have applied a complex systems simulation methodology to a living organism, focussing on the relationship between interacting genes and phenotype. Different levels can be distinguished in a complex system, from the level with the most fine-grained entities, ...