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- 1From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Reverse engineering of gene regulatory networks can be used to predict regulatory interactions of an organism faced with environmental changes, but can prove problematic, especially when focusing on...
- 2From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground The success of anti-TNF biologics for the treatment of rheumatoid arthritis has highlighted the importance of understanding the intracellular pathways that regulate TNF production in the quest for an...
- 3From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Gene duplication, a major evolutionary path to genomic innovation, can occur at the scale of an entire genome. One such "whole-genome duplication" (WGD) event among the Ascomycota fungi gave rise to genes...
- 4From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Biological networks are highly dynamic in response to environmental and physiological cues. This variability is in contrast to conventional analyses of biological networks, which have overwhelmingly...
- 5From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Interpreting proteomic and genomic data is a major challenge in predictive ecotoxicology that can be addressed by a systems biology approach. Mathematical modeling provides an organizational platform to...
- 6From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge...
- 7From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or...
- 8From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground The integration of protein-protein interaction networks derived from high-throughput screening approaches and complementary sources is a key topic in systems biology. Although integration of protein...
- 9From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground There is general agreement amongst biologists about the need for good pathway diagrams and a need to formalize the way biological pathways are depicted. However, implementing and agreeing how best to do...
- 10From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground In vitro cultivated stem cell populations are in general heterogeneous with respect to their expression of differentiation markers. In hematopoietic progenitor populations, this heterogeneity has been...
- 11From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Fluorescent and luminescent reporter genes have become popular tools for the real-time monitoring of gene expression in living cells. However, mathematical models are necessary for extracting biologically...
- 12From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Biological systems process the genetic information and environmental signals through pathways. How to map the pathways systematically and efficiently from high-throughput genomic and proteomic data is a...
- 13From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Networks are widely recognized as key determinants of structure and function in systems that span the biological, physical, and social sciences. They are static pictures of the interactions among the...
- 14From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Biological networks, such as protein-protein interactions, metabolic, signalling, transcription-regulatory networks and neural synapses, are representations of large-scale dynamic systems. The relationship...
- 15From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Many details in cell culture-derived influenza vaccine production are still poorly understood and approaches for process optimization mainly remain empirical. More insights on mammalian cell metabolism...
- 16From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground An exciting application of genetic network is to predict phenotypic consequences for environmental cues or genetic perturbations. However, de novo prediction for quantitative phenotypes based on network...
- 17From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass...
- 18From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Cancer cells simultaneously exhibit glycolysis with lactate secretion and mitochondrial respiration even in the presence of oxygen, a phenomenon known as the Warburg effect. The maintenance of this mixed...
- 19From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Recent years have seen an explosion in plant genomics, as the difficulties inherent in sequencing and functionally analyzing these biologically and economically significant organisms have been overcome....
- 20From: BMC Systems Biology. (Vol. 4) Peer-ReviewedBackground Autosomal dominant (AD) diseases result when a single mutant or non-functioning gene is present on an autosomal chromosome. These diseases often do not emerge at birth. There are presently two prevailing...