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Transcription factors (TFs) and miRNAs are essential for the regulation of gene expression; however, the global view of human gene regulatory networks remains poorly understood. For example, how is the express...
Acute kidney injury (AKI) is a frequent condition in hospitalised patients undergoing major surgery or the critically ill and is associated with increased mortality. Based on the volume of the published litera...
Synthetic genetic transistors are vital for signal amplification and switching in genetic circuits. However, it is still problematic to efficiently select the adequate promoters, Ribosome Binding Sides (RBSs) ...
Organisms have evolved ways of regulating transcription to better adapt to varying environments. Could the current functional genomics data and models support the possibility of engineering a genome with compl...
Metabolomics has become increasingly popular in the study of disease phenotypes and molecular pathophysiology. One branch of metabolomics that encompasses the high-throughput screening of cellular metabolism i...
A fundamental issue in systems biology is how to design simplified mathematical models for describing the dynamics of complex biochemical reaction systems. Among them, a key question is how to use simplified r...
This article is part of a Supplement: Volume 7 Supplement 4
The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the ...
This article is part of a Supplement: Volume 7 Supplement 4
Identifying protein complexes is crucial to understanding principles of cellular organization and functional mechanisms. As many evidences have indicated that the subgraphs with high density or with high modul...
This article is part of a Supplement: Volume 7 Supplement 4
Advances in biotechnology have changed the manner of characterizing large populations of microbial communities that are ubiquitous across several environments."Metagenome" sequencing involves decoding the DNA ...
This article is part of a Supplement: Volume 7 Supplement 4
Sets of genes that are known to be associated with each other can be used to interpret microarray data. This gene set approach to microarray data analysis can illustrate patterns of gene expression which may b...
This article is part of a Supplement: Volume 7 Supplement 4
The TNM staging system is based on three anatomic prognostic factors: Tumor, Lymph Node and Metastasis. However, cancer is no longer considered an anatomic disease. Therefore, the TNM should be expanded to acc...
This article is part of a Supplement: Volume 7 Supplement 4
The figures included in many of the biomedical publications play an important role in understanding the biological experiments and facts described within. Recent studies have shown that it is possible to integ...
This article is part of a Supplement: Volume 7 Supplement 4
Pattern mining for biological sequences is an important problem in bioinformatics and computational biology. Biological data mining yield impact in diverse biological fields, such as discovery of co-occurring ...
This article is part of a Supplement: Volume 7 Supplement 4
High-throughput genomic and proteomic data have important applications in medicine including prevention, diagnosis, treatment, and prognosis of diseases, and molecular biology, for example pathway identificati...
This article is part of a Supplement: Volume 7 Supplement 4
Multicolour Fluorescence In-Situ Hybridization (M-FISH) images are employed for detecting chromosomal abnormalities such as chromosomal translocations, deletions, duplication and inversions. This technique uses m...
This article is part of a Supplement: Volume 7 Supplement 4
MicroRNAs (miRNAs) are a large class of non-coding RNAs with important functions wide spread in animals, plants and viruses. Studies showed that an RNase III family member called Drosha recognizes most miRNAs,...
This article is part of a Supplement: Volume 7 Supplement 4
Study of biological networks is an essential first step to understand the complex functions they govern in different organisms. The topology of interactions that define how biological networks operate is often...
This article is part of a Supplement: Volume 7 Supplement 4
Biomarker discovery holds the promise for advancing personalized medicine as the biomarkers can help match patients to optimal treatment to improve patient outcomes. However, serious concerns have been raised ...
This article is part of a Supplement: Volume 7 Supplement 4
High-throughput technologies, such as DNA microarray, have significantly advanced biological and biomedical research by enabling researchers to carry out genome-wide screens. One critical task in analyzing gen...
This article is part of a Supplement: Volume 7 Supplement 4
The regulation of gene expression by transcription factors is a key determinant of cellular phenotypes. Deciphering genome-wide networks that capture which transcription factors regulate which genes is one of ...
Influenza A virus (IAV) infection-induced inflammatory regulatory networks (IRNs) are extremely complex and dynamic. Specific biological experiments for investigating the interactions between individual inflam...
Biliary atresia is a fibroinflammatory obstruction of extrahepatic bile duct that leads to end-stage liver disease in children. Despite advances in understanding the pathogenesis of biliary atresia, very littl...
Mammalian genomes are extensively transcribed producing thousands of long non-protein-coding RNAs (lncRNAs). The biological significance and function of the vast majority of lncRNAs remain unclear. Recent stud...
This article is part of a Supplement: Volume 7 Supplement 3
The understanding of the mechanisms of transcriptional regulation remains a challenge for molecular biologists in the post-genome era. It is hypothesized that the regulatory regions of genes expressed in the s...
This article is part of a Supplement: Volume 7 Supplement 3
The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of me...
This article is part of a Supplement: Volume 7 Supplement 3
In computational biology, a novel knowledge has been obtained mostly by identifying 'intra-relation,' the relation between entities on a specific biological level such as from gene expression or from microRNA ...
This article is part of a Supplement: Volume 7 Supplement 3
In the yeast Saccharomyces cerevisiae, genes containing UASINO sequences are regulated by the Ino2/Ino4 and Opi1 transcription factors, and this regulation controls lipid biosynthesis. The expression level of INO...
This article is part of a Supplement: Volume 7 Supplement 3
MicroRNAs (miRNAs) are potential regulators that contribute to the pathogenesis of cancer. Microarray technologies have been widely used to characterize aberrant miRNA expression patterns in cancer. Neverthele...
This article is part of a Supplement: Volume 7 Supplement 3
Recent cancer studies revealed, the interaction between pancreatic cancer cells and pancreatic stellate cells is of importance in the cancer progression. The activation of stellate cells is mediated by some gr...
This article is part of a Supplement: Volume 7 Supplement 3
More attention has been being paid to combinatorial effects of drugs to treat complex diseases or to avoid adverse combinations of drug cocktail. Although drug interaction information has been increasingly acc...
This article is part of a Supplement: Volume 7 Supplement 3
To facilitate new drug development, physiologically-based pharmacokinetic (PBPK) modeling methods receive growing attention as a tool to fully understand and predict complex pharmacokinetic phenomena. As the n...
This article is part of a Supplement: Volume 7 Supplement 3
Biological pathways are central to many biomedical studies and are frequently discussed in the literature. Several curated databases have been established to collate the knowledge of molecular processes consti...
This article is part of a Supplement: Volume 7 Supplement 3
Protein-protein interactions (PPIs) are crucial in cellular processes. Since the current biological experimental techniques are time-consuming and expensive, and the results suffer from the problems of incompl...
This article is part of a Supplement: Volume 7 Supplement 2
The Erratum to this article has been published in BMC Systems Biology 2015 9:50
We are witnessing rapid progress in the development of methodologies for building the combinatorial gene regulatory networks involving both TFs (Transcription Factors) and miRNAs (microRNAs). There are a few t...
This article is part of a Supplement: Volume 7 Supplement 2
In the last decade, plenty of biological networks are built from the large scale experimental data produced by the rapidly developing high-throughput techniques as well as literature and other sources. But the...
This article is part of a Supplement: Volume 7 Supplement 2
The naked mole rats (NMRs) are small-sized underground rodents with plenty of unusual traits. Their life expectancy can be up to thirty years, more than seven times longer than laboratory rat. Furthermore, the...
This article is part of a Supplement: Volume 7 Supplement 2
Understanding the molecular mechanisms underlying cancer is an important step for the effective diagnosis and treatment of cancer patients. With the huge volume of data from the large-scale cancer genomics pro...
This article is part of a Supplement: Volume 7 Supplement 2
While it has been suggested that host microRNAs (miRNAs) may downregulate viral gene expression as an antiviral defense mechanism, such a mechanism has not been explored in the influenza virus for human flu st...
This article is part of a Supplement: Volume 7 Supplement 2
Many problems in biomedical research can be posed as a comparison between related samples (healthy vs. disease, subtypes of the same disease, longitudinal data representing the progression of a disease, etc). ...
This article is part of a Supplement: Volume 7 Supplement 2
A report of the 6th IEEE International Conference on Systems Biology (IEEE ISB2012), 18-20 August, Xi'an, China.
This article is part of a Supplement: Volume 7 Supplement 2
The energetics of cerebral activity critically relies on the functional and metabolic interactions between neurons and astrocytes. Important open questions include the relation between neuronal versus astrocyt...
The growing discipline of structural systems pharmacology is applied prospectively in this study to predict pharmacological outcomes of antibacterial compounds in Escherichia coli K12. This work builds upon previ...
MicroRNAs (miRNAs) are important post-transcriptional regulators that have been demonstrated to play an important role in human diseases. Elucidating the associations between miRNAs and diseases at the systema...
Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular ...
Enzymes belonging to mechanistically diverse superfamilies often display similar catalytic mechanisms. We previously observed such an association in the case of the cyclic amidohydrolase superfamily whose memb...
Flux Balance Analysis is a theoretically elegant, computationally efficient, genome-scale approach to predicting biochemical reaction fluxes. Yet FBA models exhibit persistent mathematical degeneracy that gene...
Influenza is a common infectious disease caused by influenza viruses. Annual epidemics cause severe illnesses, deaths, and economic loss around the world. To better defend against influenza viral infection, it...
Understanding the topology and dynamics of the human protein-protein interaction (PPI) network will significantly contribute to biomedical research, therefore its systematic reconstruction is required. Several...
The complexity and multiscale nature of the mammalian immune response provides an excellent test bed for the potential of mathematical modeling and simulation to facilitate mechanistic understanding. Historica...
Cell-to-cell variability in mRNA and proteins has been observed in many biological systems, including the human innate immune response to viral infection. Most of these studies have focused on variability that...