Page 11 of 42
The chemical master equation is the fundamental equation of stochastic chemical kinetics. This differential-difference equation describes temporal evolution of the probability density function for states of a ...
High-throughput assays such as mass spectrometry have opened up the possibility for large-scale in vivo measurements of the metabolome. This data could potentially be used to estimate kinetic parameters for many ...
Compared to engineering or physics problems, dynamical models in quantitative biology typically depend on a relatively large number of parameters. Progress in developing mathematics to manipulate such multi-pa...
Isotope labeling experiments (ILEs) are increasingly used to investigate the functioning of metabolic systems. Some enzymes are subject to kinetic isotope effects (KIEs) which modulate reaction rates depending...
The spatial distribution of many genes has been visualized during the embryonic development in the starlet sea anemone Nematostella vectensis in the last decade. In situ hybridization images are available in the ...
Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as...
Time-lapse microscopy allows to monitor cell state transitions in a spatiotemporal context. Combined with single cell tracking and appropriate cell state markers, transition events can be observed within the g...
Robust statistical detection of differences in the bacterial growth rate can be challenging, particularly when dealing with small differences or noisy data. The Bayesian approach provides a consistent framewor...
Social interactions have been increasingly recognized as one of the major factors that contribute to the dynamics and function of bacterial communities. To understand their functional roles and enable the desi...
Joint modeling and analysis of phenotypic, genotypic and transcriptomic data have the potential to uncover the genetic control of gene activity and phenotypic variation, as well as shed light on the manner and...
Mycobacterium tuberculosis (MTB) is the causal agent of the disease tuberculosis (TB). Metabolic adaptations are thought to be critical to the survival of MTB during pathogenesis. Comp...
Owing to drug synergy effects, drug combinations have become a new trend in combating complex diseases like cancer, HIV and cardiovascular diseases. However, conventional synergy quantification methods often d...
The vascular endothelial growth factor (VEGF) family is central to cancer angiogenesis. However, targeting VEGF as an anti-cancer therapeutic approach has shown success for some tumor types but not others. Her...
Microbial interactions are ubiquitous in nature. Recently, many similarity-based approaches have been developed to study the interaction in microbial ecosystems. These approaches can only explain the non-direc...
The Drosophila sex determination hierarchy is a classic example of a transcriptional regulatory hierarchy, with sex-specific isoforms regulating morphology and behavior. We use a structural equation modeling appr...
Studies of cell-to-cell variation have in recent years grown in interest, due to improved bioanalytical techniques which facilitates determination of small changes with high uncertainty. Like much high-quality...
The growing ubiquity of metabolomic techniques has facilitated high frequency time-course data collection for an increasing number of applications. While the concentration trends of individual metabolites can ...
Organ segmentation is an important step in computer-aided diagnosis and pathology detection. Accurate kidney segmentation in abdominal computed tomography (CT) sequences is an essential and crucial task for su...
This article is part of a Supplement: Volume 9 Supplement 5
While the discovery of new drugs is a complex, lengthy and costly process, identifying new uses for existing drugs is a cost-effective approach to therapeutic discovery. Connectivity mapping integrates gene ex...
This article is part of a Supplement: Volume 9 Supplement 5
The protein-protein interaction plays a key role in the control of many biological functions, such as drug design and functional analysis. Determination of binding sites is widely applied in molecular biology ...
This article is part of a Supplement: Volume 9 Supplement 5
Modeling and simulation of gene-regulatory networks (GRNs) has become an important aspect of modern systems biology investigations into mechanisms underlying gene regulation. A key challenge in this area is th...
This article is part of a Supplement: Volume 9 Supplement 5
Recent biochemical advances have led to inexpensive, time-efficient production of massive volumes of raw genomic data. Traditional machine learning approaches to genome annotation typically rely on large amoun...
This article is part of a Supplement: Volume 9 Supplement 5
The original article was published in BMC Systems Biology 2013 7:S8
There are increasing efforts to bring high-throughput systems biology techniques to bear on complex animal model systems, often with a goal of learning about underlying regulatory network structures (e.g., gen...
Constraint-based analysis of genome-scale metabolic models has become a key methodology to gain insights into functions, capabilities, and properties of cellular metabolism. Since their inception, the size and...
As suggested by the origin of the word, sphingolipids are mysterious molecules with various roles in antagonistic cellular processes such as autophagy, apoptosis, proliferation and differentiation. Moreover, s...
Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistic insights into biological functions. Currently, it is possible to visualize high-thro...
Cellular decision-making is governed by molecular networks that are highly complex. An integrative understanding of these networks on a genome wide level is essential to understand cellular health and disease....
The combination of domains in multidomain proteins enhances their function and structure but lengthens the molecules and increases their cost at cellular level.
Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and tr...
The cAMP-dependent protein kinase regulatory network (PKA-RN) regulates metabolism, memory, learning, development, and response to stress. Previous models of this network considered the catalytic subunits (CS)...
The skin is largely comprised of keratinocytes within the interfollicular epidermis. Over approximately two weeks these cells differentiate and traverse the thickness of the skin. The stage of differentiation ...
The gastrointestinal peptide hormones cholecystokinin and gastrin exert their biological functions via cholecystokinin receptors CCK1R and CCK2R respectively. Gastrin, a central regulator of gastric acid secre...
Bacteria have developed a repertoire of signalling mechanisms that enable adaptive responses to fluctuating environmental conditions. The formation of biofilm, for example, allows persisting in times of extern...
Standard methods for quantifying IncuCyte ZOOM™ assays involve measurements that quantify how rapidly the initially-vacant area becomes re-colonised with cells as a function of time. Unfortunately, these measu...
Sperm-egg interaction defect is a significant cause of in-vitro fertilization failure for infertile cases. Numerous molecular interactions in the form of protein-protein interactions mediate the sperm-egg membran...
Pathological cardiac development is precipitated by dysregulation of calreticulin, an endoplasmic reticulum (ER)-resident calcium binding chaperone and critical contributor to cardiogenesis and embryonic viabi...
Understanding the underlying molecular mechanisms in human diseases is important for diagnosis and treatment of complex conditions and has traditionally been done by establishing associations between disorder-...
Qualitative reasoning frameworks, such as the Sign Consistency Model (SCM), enable modelling regulatory networks to check whether observed behaviour can be explained or if unobserved behaviour can be predicted...
Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to fac...
Most ordinary differential equation (ODE) based modeling studies in systems biology involve a hold-out validation step for model validation. In this framework a pre-determined part of the data is used as valid...
Given its recent rapid development and the central role that modeling plays in the discipline, systems biology clearly needs methods for automated modeling of dynamical systems. Process-based modeling focuses ...
Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken...
Stochastic genetic switching driven by intrinsic noise is an important process in gene expression. When the rates of gene activation/inactivation are relatively slow, fast, or medium compared with the synthesi...
Estrogen receptor alpha36 (ERalpha36), a variant of estrogen receptor alpha (ER) is expressed in about half of breast tumors, independently of the [ER+]/[ER-] status. In vitro, ERalpha36 triggers mitogenic non-ge...
Computational pharmacology can uniquely address some issues in the process of drug development by providing a macroscopic view and a deeper understanding of drug action. Specifically, network-assisted approach...
This article is part of a Supplement: Volume 9 Supplement 4
Malaria is a major health threat, affecting over 40% of the world's population. The latest report released by the World Health Organization estimated about 207 million cases of malaria infection, and about 627...
This article is part of a Supplement: Volume 9 Supplement 4
Using immune checkpoint modulators in the clinic to increase the number and activity of cytotoxic T lymphocytes that recognize tumor antigens can prolong survival for metastatic melanoma. Yet, only a fraction ...
Thousands of biological and biomedical investigators study of the functional role of single genes and their protein products in normal physiology and in disease. The findings from these studies are reported in...
Addictions to alcohol and tobacco, known risk factors for cancer, are complex heritable disorders. Addictive behaviors have a bidirectional relationship with pain. We hypothesize that the associations between ...