Page 28 of 42
Cervical cancer is a major mortality factor in the female population. This neoplastic is an excellent model for studying the mechanisms involved in cancer maintenance, because the Human Papilloma Virus (HPV) i...
13C metabolic flux analysis is one of the pertinent ways to compare two or more physiological states. From a more theoretical standpoint, the structural properties of metabolic networks can be analysed to explor....
Human iPS cells (hiPSCs) have attracted considerable attention for applications to drug screening and analyses of disease mechanisms, and even as next generation materials for regenerative medicine. Genetic re...
This article is part of a Supplement: Volume 5 Supplement 1
Type 2 diabetes mellitus (T2DM) is a complex systemic disease, with significant disorders of metabolism. The liver, a central energy metabolic organ, plays a critical role in the development of diabetes. Altho...
This article is part of a Supplement: Volume 5 Supplement 1
Revealing the multi-equilibrium property of a metabolic network is a fundamental and important topic in systems biology. Due to the complexity of the metabolic network, it is generally a difficult task to stud...
This article is part of a Supplement: Volume 5 Supplement 1
In this paper the dynamics of the transcription-translation system for XlnR regulon in Aspergillus niger is modeled. The model is based on Hill regulation functions and uses ordinary differential equations. The n...
This article is part of a Supplement: Volume 5 Supplement 1
The ability of living cells to respond appropriately to apoptosis signals is crucial for the proper development and homeostasis of multicellular organisms. For example, viable cells must be stable enough to ap...
This article is part of a Supplement: Volume 5 Supplement 1
Comprehensive kinetic models of microbial metabolism can enhance the understanding of system dynamics and regulatory mechanisms, which is helpful in optimizing microbial production of industrial chemicals. Clostr...
This article is part of a Supplement: Volume 5 Supplement 1
Efficient identification of drug targets is one of major challenges for drug discovery and drug development. Traditional approaches to drug target identification include literature search-based target prioriti...
This article is part of a Supplement: Volume 5 Supplement 1
Multicomponent therapeutics offer bright prospects for the control of complex diseases in a synergistic manner. However, finding ways to screen the synergistic combinations from numerous pharmacological agents...
This article is part of a Supplement: Volume 5 Supplement 1
Cellular functions depend on genetic, physical and other types of interactions. As such, derived interaction networks can be utilized to discover novel genes involved in specific biological processes. Epistati...
This article is part of a Supplement: Volume 5 Supplement 1
For understanding cellular systems and biological networks, it is important to analyze functions and interactions of proteins and domains. Many methods for predicting protein-protein interactions have been dev...
This article is part of a Supplement: Volume 5 Supplement 1
Protein-DNA interactions play an important role in many fundamental biological activities such as DNA replication, transcription and repair. Identification of amino acid residues involved in DNA binding site i...
This article is part of a Supplement: Volume 5 Supplement 1
Enzymes are known as the largest class of proteins and their functions are usually annotated by the Enzyme Commission (EC), which uses a hierarchy structure, i.e., four numbers separated by periods, to classif...
This article is part of a Supplement: Volume 5 Supplement 1
A protein binding hot spot is a cluster of residues in the interface that are energetically important for the binding of the protein with its interaction partner. Identifying protein binding hot spots can give...
This article is part of a Supplement: Volume 5 Supplement 1
Identification of gene regulatory networks is useful in understanding gene regulation in any organism. Some regulatory network information has already been determined experimentally for model organisms, but mu...
This article is part of a Supplement: Volume 5 Supplement 1
Hypoxia-inducible factors (HIFs) are transcription factors that play a crucial role in response to hypoxic stress in living organisms. The HIF pathway is activated by changes in cellular oxygen levels and has ...
This article is part of a Supplement: Volume 5 Supplement 1
Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their biological relevance and exact regulatory mechanism remain less understood. To study th...
This article is part of a Supplement: Volume 5 Supplement 1
A report of the 4nd International Conference on Computational Systems Biology, 9-11 September 2010, Suzhou, China.
This article is part of a Supplement: Volume 5 Supplement 1
Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for...
miRNAs are a class of non-coding RNA molecules that play crucial roles in the regulation of virus-host interactions. The ever-increasing data of known viral miRNAs and human protein interaction network (PIN) h...
While functional genomics, focused on gene functions and gene-gene interactions, has become a very active field of research in molecular biology, equivalent methodologies embracing the environment and gene-env...
Understanding complex systems through decomposition into simple interacting components is a pervasive paradigm throughout modern science and engineering. For cellular metabolism, complexity can be reduced by d...
Deterministic dynamic models of complex biological systems contain a large number of parameters and state variables, related through nonlinear differential equations with various types of feedback. A metamodel...
Network modeling of whole transcriptome expression data enables characterization of complex epistatic (gene-gene) interactions that underlie cellular functions. Though numerous methods have been proposed and s...
Cells constantly sense many internal and environmental signals and respond through their complex signaling network, leading to particular biological outcomes. However, a systematic characterization and optimiz...
Cells must respond to various perturbations using their limited available gene repertoires. In order to study how cells coordinate various responses, we conducted a comprehensive comparison of 1,186 gene expre...
Messenger RNA expression is regulated by a complex interplay of different regulatory proteins. Unfortunately, directly measuring the individual activity of these regulatory proteins is difficult, leaving us wi...
The image of the "epigenetic landscape", with a series of branching valleys and ridges depicting stable cellular states and the barriers between those states, has been a popular visual metaphor for cell lineag...
Every phenotypic trait can be viewed as a "system" in which a group of interconnected components function synergistically to yield a unified whole. Once a system's components and their interactions have been d...
Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in tre...
BMP6 mediated osteoblast differentiation plays a key role in skeletal development and bone disease. Unfortunately, the signaling pathways regulated by BMP6 are largely uncharacterized due to both a lack of dat...
With the advent of genomic technology, the size of metabolic networks that are subject to analysis is growing. A common task when analyzing metabolic networks is to find all possible steady state regimes. Ther...
Epistatic Miniarray Profiling(E-MAP) quantifies the net effect on growth rate of disrupting pairs of genes, often producing phenotypes that may be more (negative epistasis) or less (positive epistasis) severe ...
Protein-protein interaction networks and phenotype similarity information have been synthesized together to discover novel disease-causing genes. Genetic or phenotypic similarities are manifested as certain mo...
Caloric restriction (CR) has been shown to keep organisms in a relatively youthful and healthy state compared to ad libitum fed counterparts, as well as to extend the lifespan of a diverse set of organisms. Se...
The carotenoids are pure isoprenoids that are essential components of the photosynthetic apparatus and are coordinately synthesized with chlorophylls in chloroplasts. However, little is known about the mechani...
Network reconstructions at the cell level are a major development in Systems Biology. However, we are far from fully exploiting its potentialities. Often, the incremental complexity of the pursued systems over...
Yeast is considered to be a workhorse of the biotechnology industry for the production of many value-added chemicals, alcoholic beverages and biofuels. Optimization of the fermentation is a challenging task th...
The molecular circuitry of living organisms performs remarkably robust regulatory tasks, despite the often intrinsic variability of its components. A large body of research has in fact highlighted that robustn...
Synthetic lethal genetic interactions among proteins have been widely used to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interac...
The quantification of experimentally-induced alterations in biological pathways remains a major challenge in systems biology. One example of this is the quantitative characterization of alterations in defined,...
In this paper we apply a novel agent-based simulation method in order to model intracellular reactions in detail. The simulations are performed within a virtual cytoskeleton enriched with further crowding elem...
Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the so...
Bacteria have evolved a rich set of mechanisms for sensing and adapting to adverse conditions in their environment. These are crucial for their survival, which requires them to react to extracellular stresses ...
Staphylococcus aureus is a major human pathogen and strains resistant to existing treatments continue to emerge. Development of novel treatments is therefore important. Antimicrobial peptides represent a source o...
Estrogens regulate diverse physiological processes in various tissues through genomic and non-genomic mechanisms that result in activation or repression of gene expression. Transcription regulation upon estrog...
The individual character of pharmacokinetics is of great importance in the risk assessment of new drug leads in pharmacological research. Amongst others, it is severely influenced by the properties and inter-i...
Large-scale RNAi-based screens are playing a critical role in defining sets of genes that regulate specific cellular processes. Numerous screens have been completed and in some cases more than one screen has e...
The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. C...