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Cell biology research is fundamentally limited by the number of intracellular components, particularly proteins, that can be co-measured in the same cell. Therefore, cell-to-cell heterogeneity in unmeasured pr...
Understanding the mechanisms by which hundreds of diverse cell types develop from a single mammalian zygote has been a central challenge of developmental biology. Conrad H. Waddington, in his metaphoric “epige...
Biochemical reactions are often modelled as discrete-state continuous-time stochastic processes evolving as memoryless Markov processes. However, in some cases, biochemical systems exhibit non-Markovian dynami...
This article is part of a Supplement: Volume 9 Supplement 3
A fundamental evolutionary step in the onset of living cells is thought to be the spontaneous formation of lipid vesicles (liposomes) in the pre-biotic mixture. Even though it is well known that hydrophobic fo...
This article is part of a Supplement: Volume 9 Supplement 3
The interconnection of quantitatively characterized biological devices may lead to composite systems with apparently unpredictable behaviour. Context-dependent variability of biological parts has been investig...
This article is part of a Supplement: Volume 9 Supplement 3
Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals i...
This article is part of a Supplement: Volume 9 Supplement 3
The identification of drug-target interactions (DTI) is a costly and time-consuming step in drug discovery and design. Computational methods capable of predicting reliable DTI play an important role in the fie...
This article is part of a Supplement: Volume 9 Supplement 3
Cell organization is governed and maintained via specific interactions among its constituent macromolecules. Comparison of the experimentally determined protein interaction networks in different model organism...
This article is part of a Supplement: Volume 9 Supplement 3
Recent experimental results on the effect of miRNA on the decay of its target mRNA have been analyzed against a previously hypothesized single molecule degradation pathway. According to that hypothesis, the si...
This article is part of a Supplement: Volume 9 Supplement 3
Nowadays multidisciplinary approaches combining mathematical models with experimental assays are becoming relevant for the study of biological systems. Indeed, in cancer research multidisciplinary approaches a...
This article is part of a Supplement: Volume 9 Supplement 3
Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signaling processe...
Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is...
Gene regulatory network (GRN) dynamical models are standard systems biology tools for the mechanistic understanding of developmental processes and are enabling the formalization of the epigenetic landscape (EL...
Aspergillus fumigatus is a ubiquitous airborne fungal pathogen that presents a life-threatening health risk to individuals with weakened immune systems. A. fumigatus pathogenicity depends on it...
Pre-eclampsia is the most common complication occurring during pregnancy. In the majority of cases, it is concurrent with other pathologies in a comorbid manner (frequent co-occurrences in patients), such as d...
This article is part of a Supplement: Volume 9 Supplement 2
High-throughput technologies became common tools to decipher genome-wide changes of gene expression (GE) patterns. Functional analysis of GE patterns is a daunting task as it requires often recourse to the pub...
This article is part of a Supplement: Volume 9 Supplement 2
Sufficient knowledge of molecular and genetic interactions, which comprise the entire basis of the functioning of living systems, is one of the necessary requirements for successfully answering almost any rese...
This article is part of a Supplement: Volume 9 Supplement 2
Biclustering is a popular method for identifying under which experimental conditions biological signatures are co-expressed. However, the general biclustering problem is NP-hard, offering room to focus algorit...
This article is part of a Supplement: Volume 9 Supplement 2
Flux Balance Analysis (FBA) is a widely used tool to model metabolic behavior and cellular function. Applications of FBA span a breadth of research from synthetic engineering of biofuels to understanding evolu...
The yeast Saccharomyces cerevisiae relies on the high-osmolarity glycerol (HOG) signaling pathway to respond to increases in external osmolarity. The HOG pathway is rapidly activated under conditions of elevated ...
Quantitative analysis of simple molecular networks is an important step forward understanding fundamental intracellular processes. As network motifs occurring recurrently in complex biological networks, gene a...
The exchange of metabolites and the reprogramming of metabolism in response to shifting microenvironmental conditions can drive subpopulations of cells within colonies toward divergent behaviors. Understanding...
As a result of recent advances in biotechnology, many findings related to intracellular systems have been published, e.g., transcription factor (TF) information. Although we can reproduce biological systems by in...
AMP-activated protein kinase (AMPK) is a heterotrimeric serine/threonine protein kinase that is activated by cellular perturbations associated with ATP depletion or stress. While AMPK modulates the activity of...
Organisms that need to perform multiple tasks face a fundamental tradeoff: no design can be optimal at all tasks at once. Recent theory based on Pareto optimality showed that such tradeoffs lead to a highly de...
Cerebral ischemia-reperfusion injury may simultaneously result in functional variation of multiple genes/pathways. However, most prior time-sequence studies on its pathomechanism only focused on a single gene ...
The complexity of genome-scale metabolic models makes them quite difficult for human users to read, since they contain thousands of reactions that must be included for accurate computer simulation. Interesting...
In mammalian cells protein-lipid interactions at the trans-Golgi network (TGN) determine the formation of vesicles, which transfer secretory proteins to the cellular membrane. This process is regulated by a co...
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of...
The editors of BMC Systems Biology would like to thank all our reviewers who have contributed to the journal in Volume 8 (2014).
The bacterium Pseudomonas fluorescens switches to an alginate-producing phenotype when the pleiotropic anti-sigma factor MucA is inactivated. The inactivation is accompanied by an increased biomass yield on carbo...
A substrate cycle is a set of metabolic reactions, arranged in a loop, which does not result in net consumption or production of the metabolites. The cycle operates by transforming a cofactor, e.g. oxidizing a...
microRNA (miRNA)’s direct regulation on target mRNA is affected by complex factors beyond miRNA. Therefore, at different stages during the course of carcinogenesis, miRNA may regulate different targets, which ...
DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major chal...
This article is part of a Supplement: Volume 9 Supplement 1
Rho GTPases function as molecular switches in many different signaling pathways and control a wide range of cellular processes. Rho GDP-dissociation inhibitors (RhoGDIs) regulate Rho GTPase signaling and can f...
Predicting functional properties of proteins in protein-protein interaction (PPI) networks presents a challenging problem and has important implication in computational biology. Collective classification (CC) ...
This article is part of a Supplement: Volume 9 Supplement 1
Network-based approaches have recently gained considerable popularity in high- dimensional regression settings. For example, the Cox regression model is widely used in expression analysis to predict the surviv...
This article is part of a Supplement: Volume 9 Supplement 1
Comparative network analysis can provide an effective means of analyzing large-scale biological networks and gaining novel insights into their structure and organization. Global network alignment aims to predi...
This article is part of a Supplement: Volume 9 Supplement 1
The hardware accelerators will provide solutions to computationally complex problems in bioinformatics fields. However, the effect of acceleration depends on the nature of the application, thus selection of an...
This article is part of a Supplement: Volume 9 Supplement 1
Molecular networks are the basis of biological processes. Such networks can be decomposed into smaller modules, also known as network motifs. These motifs show interesting dynamical behaviors, in which co-oper...
This article is part of a Supplement: Volume 9 Supplement 1
The ongoing cancer research has shown that malignant tumour cells have highly disrupted signalling transduction pathways. In cancer cells, signalling pathways are altered to satisfy the demands of continuous p...
This article is part of a Supplement: Volume 9 Supplement 1
High throughput techniques produce multiple functional association networks. Integrating these networks can enhance the accuracy of protein function prediction. Many algorithms have been introduced to generate...
This article is part of a Supplement: Volume 9 Supplement 1
Cell proliferation, differentiation, Gene expression, metabolism, immunization and signal transduction require the participation of ligands and targets. It is a great challenge to identify rules governing mole...
This article is part of a Supplement: Volume 9 Supplement 1
With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, a...
This article is part of a Supplement: Volume 9 Supplement 1
Initial success of inhibitors targeting oncogenes is often followed by tumor relapse due to acquired resistance. In addition to mutations in targeted oncogenes, signaling cross-talks among pathways play a vita...
Mortierella alpina is an oleaginous fungus used in the industrial scale production of arachidonic acid (ARA). In order to investigate the metabolic characteristics at a systems level and to exp...
Over the past years, tremendous efforts have been made to elucidate the molecular basis of the initiation and progression of ovarian cancer. However, most existing studies have been focused on individual genes...
Clinical trials are the main method for evaluating safety and efficacy of medical interventions and have produced many advances in improving human health. The Women’s Health Initiative overturned a half-centur...
Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this...
Metabolomic responses to extreme thermal stress have recently been investigated in Drosophila melanogaster. However, a network level understanding of metabolomic responses to longer and less drastic temperature c...