Page 16 of 42
mRNA translation involves simultaneous movement of multiple ribosomes on the mRNA and is also subject to regulatory mechanisms at different stages. Translation can be described by various codon-based models, i...
Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and hori...
Mathematical modeling is often used to formalize hypotheses on how a biochemical network operates by discriminating between competing models. Bayesian model selection offers a way to determine the amount of ev...
The miRNAs are small non-coding RNAs of roughly 22 nucleotides in length, which can bind with and inhibit protein coding mRNAs through complementary base pairing. By degrading mRNAs and repressing proteins, mi...
Resistance to stress is often heterogeneous among individuals within a population, which helps protect against intermittent stress (bet hedging). This is also the case for heat shock resistance in the budding ...
Data-driven studies on the dynamics of reconstructed protein-protein interaction (PPI) networks facilitate investigation and identification of proteins important for particular processes or diseases and reduce...
Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level....
Several dynamic models of a gene regulatory network of the light-induced floral transition process in Arabidopsis have been developed to capture the behavior of gene transcription and infer predictions based on e...
Protein-protein interaction (PPI) is one of the most important functional components of a living cell. Recently, researchers have been interested in investigating the correlation between PPI and microRNA, whic...
Accurate estimation of parameters of biochemical models is required to characterize the dynamics of molecular processes. This problem is intimately linked to identifying the most informative experiments for ac...
The editors of BMC Systems Biology would like to thank all our reviewers who have contributed to the journal in Volume 7 (2013).
The demand for novel molecularly targeted drugs will continue to rise as we move forward toward the goal of personalizing cancer treatment to the molecular signature of individual tumors. However, the identifi...
Muscle development and remodelling, mitochondrial physiology and inflammation are thought to be inter-related and to have implications for metabolism in both health and disease. However, our understanding of t...
MADS domain proteins are transcription factors that coordinate several important developmental processes in plants. These proteins interact with other MADS domain proteins to form dimers, and it has been propo...
Constraint-based reconstruction and analysis (COBRA) is used for modeling genome-scale metabolic networks (MNs). In a COBRA model, extreme pathways (ExPas) are the edges of its conical solution space, which is...
This article is part of a Supplement: Volume 8 Supplement 1
Biological networks obtained by high-throughput profiling or human curation are typically noisy. For functional module identification, single network clustering algorithms may not yield accurate and robust res...
This article is part of a Supplement: Volume 8 Supplement 1
Hematopoiesis is a highly orchestrated developmental process that comprises various developmental stages of the hematopoietic stem cells (HSCs). During development, the decision to leave the self-renewing stat...
This article is part of a Supplement: Volume 8 Supplement 1
Boolean network (BN) is a mathematical model for genetic network and control of genetic networks has become an important issue owing to their potential application in the field of drug discovery and treatment ...
This article is part of a Supplement: Volume 8 Supplement 1
Genome-wide association studies have identified many individual genes associated with complex traits. However, pathway and network information have not been fully exploited in searches for genetic determinants...
This article is part of a Supplement: Volume 8 Supplement 1
Type 2 diabetes (T2D) is one of the most common chronic metabolic diseases characterized by insulin resistance and the decrease of insulin secretion. Genetic variation can only explain part of the heritability...
This article is part of a Supplement: Volume 8 Supplement 1
Aberrant DNA methylation is often associated with cancers. Thus, screening genes with cancer-associated aberrant DNA methylation is a useful method to identify candidate cancer-causing genes. Aberrant DNA meth...
This article is part of a Supplement: Volume 8 Supplement 1
Recent global genomic analyses identified 69 gene sets and 12 core signaling pathways genetically altered in pancreatic cancer, which is a highly malignant disease. A comprehensive understanding of the genetic...
This article is part of a Supplement: Volume 8 Supplement 1
The detection of associations between protein complexes and human inherited diseases is of great importance in understanding mechanisms of diseases. Dysfunctions of a protein complex are usually defined by its...
This article is part of a Supplement: Volume 8 Supplement 1
Living cells are realized by complex gene expression programs that are moderated by regulatory proteins called transcription factors (TFs). The TFs control the differential expression of target genes in the co...
This article is part of a Supplement: Volume 8 Supplement 1
When studying metabolism at the organ level, a major challenge is to understand the matter exchanges between the input and output components of the system. For example, in nutrition, biochemical models have be...
Genome-wide microarrays have been useful for predicting chemical-genetic interactions at the gene level. However, interpreting genome-wide microarray results can be overwhelming due to the vast output of gene ...
In the post-genomic era, a central and overarching question in the analysis of protein-protein interaction networks continues to be whether biological characteristics and functions of proteins such as lethalit...
To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure inste...
A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to add...
During embryogenesis, signaling molecules produced by one cell population direct gene regulatory changes in neighboring cells and influence their developmental fates and spatial organization. One of the earlie...
Identifying permissible limits of intracellular parameters such as protein expression provides important information for examining robustness. In this study, we used the TEV protease-mediated induction of prot...
During the last decade, a number of authors have shown that the genetic regulation of metabolic networks may follow optimality principles. Optimal control theory has been succesfully used to compute optimal en...
Lag phase is a period of time with no growth that occurs when stationary phase bacteria are transferred to a fresh medium. Bacteria in lag phase seem inert: their biomass does not increase. The low number of c...
Cyanobacteria are photoautotrophic prokaryotes that exhibit robust growth under diverse environmental conditions with minimal nutritional requirements. They can use solar energy to convert CO2 and other reduced c...
Epigenetics refers to the reversible functional modifications of the genome that do not correlate to changes in the DNA sequence. The aim of this study is to understand DNA methylation patterns across differen...
Cellular differentiation and reprogramming are processes that are carefully orchestrated by the activation and repression of specific sets of genes. An increasing amount of experimental results show that despi...
To uncover molecular functions and networks in biological cellular systems, it is important to dissect interactions between proteins and RNAs. Many studies have been performed to investigate and analyze intera...
This article is part of a Supplement: Volume 7 Supplement 2
Discovering transcription factor binding sites (TFBS) is one of primary challenges to decipher complex gene regulatory networks encrypted in a genome. A set of short DNA sequences identified by a transcription...
This article is part of a Supplement: Volume 7 Supplement 2
Metabolism is a vital cellular process, and its malfunction can be a major contributor to many human diseases. Metabolites can serve as a metabolic disease biomarker. An detection of such biomarkers plays a si...
This article is part of a Supplement: Volume 7 Supplement 2
Recent reports indicate that a subgroup of tumor cells named cancer stem cells (CSCs) or tumor initiating cells (TICs) are responsible for tumor initiation, growth and drug resistance. This subgroup of tumor c...
This article is part of a Supplement: Volume 7 Supplement 2
In dynamic biological processes, genes, transcription factors(TF) and microRNAs(miRNAs) play vital regulation roles. Many researchers have focused on the transcription factors or miRNAs in transcriptional or p...
This article is part of a Supplement: Volume 7 Supplement 2
RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire muc...
This article is part of a Supplement: Volume 7 Supplement 2
With recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extreme...
This article is part of a Supplement: Volume 7 Supplement 2
Transcriptional regulation in multi-cellular organisms is a complex process involving multiple modular regulatory elements for each gene. Building whole-genome models of transcriptional networks requires mappi...
This article is part of a Supplement: Volume 7 Supplement 6
Missing values commonly occur in the microarray data, which usually contain more than 5% missing values with up to 90% of genes affected. Inaccurate missing value estimation results in reducing the power of do...
This article is part of a Supplement: Volume 7 Supplement 6
Tumor biomarkers are potentially useful in several ways such as the identification of individuals at increased risk of developing cancer, in screening for early malignancies and in aiding cancer diagnoses; tum...
This article is part of a Supplement: Volume 7 Supplement 6
Structural variations (SVs), such as insertions, deletions, inversions, and duplications, are a common feature in human genomes, and a number of studies have reported that such SVs are associated with human di...
This article is part of a Supplement: Volume 7 Supplement 6
One of the most important projects in the post-genome-era is the systemic identification of biological network. The almost of studies for network identification focused on the improvement of computational effi...
This article is part of a Supplement: Volume 7 Supplement 6
Glycogen and glucose are two sugar sources available during the lag phase of E. coli, but the mechanism that regulates their utilization is still unclear.
This article is part of a Supplement: Volume 7 Supplement 6
This article is part of a Supplement: Volume 7 Supplement 6