Mining gene link information for survival pathway hunting
This study proposes a gene link-based method for survival time-related pathway hunting. In this method, the authors incorporate gene link information to estimate how a pathway is associated with cancer patient's survival time. Specifically, a gene link-based Cox proportional hazard model (Link-Cox) is established, in which two linked genes are considered together to represent a link variable and the association of the link with survival time is assessed using Cox proportional hazard model. On the basis of the Link-Cox model, the authors formulate a new statistic for measuring the association of a pathway with survival time...
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Understanding the aristolochic acid toxicities in rat kidneys with regulatory networks
In this study, the authors built a gene regulatory network as well as a microRNA–gene regulatory network to investigate the molecular dynamics induced by AA from a systematic perspective. With the regulatory networks, they detected some important pathways and biological processes that were affected by AA treatment, which can help explain the nephrotoxicity and carcinogenicity of AA. They found some important regulators and genes responding to AA treatment, and these genes have been reported to be related to the kidney functions, indicating their important roles in the toxicity of AA. (Source: IET Systems Biology)
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Identify asthma genes across three phases based on protein–protein interaction network
In this study, the authors present a new framework to detect asthma disease genes based on protein–protein interaction network (PPIN) and gene expression. Specifically, they construct PPINs for different stages of asthma, and detect those interactions occurred in the specific stages. By investigating the proteins in these stage-specific interactions, they find they are more likely related to asthma, and the functional enrichment analysis indicate that the pathways enriched in the differential interactions are related to the progress of asthma. Moreover, some proteins in the differential interactions have been previo...
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Identification of cancer-related genes and motifs in the human gene regulatory network
The authors investigated the regulatory network motifs and corresponding motif positions of cancer-related genes. First, they mapped disease-related genes to a transcription factor regulatory network. Next, they calculated statistically significant motifs and subsequently identified positions within these motifs that were enriched in cancer-related genes. Potential mechanisms of these motifs and positions are discussed. These results could be used to identify other disease- and cancer-related genes and could also suggest mechanisms for how these genes relate to co-occurring diseases. (Source: IET Systems Biology)
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Graphics processing unit-based alignment of protein interaction networks
In this study, the typical Hungarian-Greedy Algorithm (HGA) is used as an example for PIN alignment. The authors propose a HGA with 2-nearest neighbours (HGA-2N) and implement its graphics processing unit (GPU) acceleration. Numerical experiments demonstrate that HGA-2N can find alignments that are close to those found by HGA while dramatically reducing computing time. The GPU implementation of HGA-2N optimises the parallel pattern, computing mode and storage mode and it improves the computing time ratio between the CPU and GPU compared with HGA when large-scale networks are considered. By using HGA-2N in GPUs, conserved P...
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Revisiting topological properties and models of protein–protein interaction networks from the perspective of dataset evolution
Protein–protein interaction (PPI) networks are crucial for organisms. Many research efforts have thus been devoted to the study on the topological properties and models of PPI networks. However, existing studies did not always report consistent results on the topological properties of PPI networks. Although a number of PPI network models have been introduced, yet in the literature there is no convincing conclusion on which model is best for describing PPI networks. This situation is primarily caused by the incompleteness of current PPI datasets. To solve this problem, in this study, the authors propose to revisit th...
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer
Constructing interaction network from biomedical texts is a very important and interesting work. The authors take advantage of text mining and reinforcement learning approaches to establish protein interaction network. Considering the high computational efficiency of co-occurrence-based interaction extraction approaches and high precision of linguistic patterns approaches, the authors propose an interaction extracting algorithm where they utilise frequently used linguistic patterns to extract the interactions from texts and then find out interactions from extended unprocessed texts under the basic idea of co-occurrence app...
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Guest Editorial
(Source: IET Systems Biology)
Source: IET Systems Biology - August 11, 2015 Category: Biology Source Type: research
Global stability of infection-free state and endemic infection state of a modified human immunodeficiency virus infection model
This study proposes a modified human immunodeficiency virus (HIV) infection differential equation model with a saturated infection rate. This model has an infection-free equilibrium point and an endemic infection equilibrium point. Using Lyapunov functions and LaSalle’s invariance principle shows that if the model’s basic reproductive number R0 < 1, the infection-free equilibrium point is globally asymptotically stable, otherwise the endemic infection equilibrium point is globally asymptotically stable. It is shown that a forward bifurcation will occur when R0 = 1. The basic reproductive number R0 of the m...
Source: IET Systems Biology - June 2, 2015 Category: Biology Source Type: research
Synthesising gene clock with toggle switch and oscillator
The usefulness of a genetic clock lies in its role to stimulate a sequence of logic reactions for sequential biological circuits. A clock signal is a periodic square wave, its amplitude alternates at a steady frequency between fixed minimal and maximal levels. Transition between the minimum and the maximum is instantaneous for an ideal square wave; however, the function is unrealisable in physical bio-systems. This research develops a new genetic clock generator based on a genetic oscillator, in which, a sine wave generator is adopted as a signal oscillator. It is shown that combination of a genetic oscillator with a toggl...
Source: IET Systems Biology - June 2, 2015 Category: Biology Source Type: research
Analysis of behaviour transitions in tumour growth using a cellular automaton simulation
The authors used computational biology as an approach for analysing the emergent dynamics of tumour growth at cellular level. They applied cellular automata for modelling the behaviour of cells when the main cancer cell hallmarks are present. Their model is oriented to mimic the development of multicellular spheroids of tumour cells. In their modelling, cells have a genome associated with the different cancer hallmarks, indicating if those are acquired as a consequence of mutations. The presence of the cancer hallmarks defines cell states and cell mitotic behaviours. These hallmarks are associated with a series of paramete...
Source: IET Systems Biology - June 2, 2015 Category: Biology Source Type: research
Exploiting intrinsic fluctuations to identify model parameters
Parameterisation of kinetic models plays a central role in computational systems biology. Besides the lack of experimental data of high enough quality, some of the biggest challenges here are identification issues. Model parameters can be structurally non-identifiable because of functional relationships. Noise in measured data is usually considered to be a nuisance for parameter estimation. However, it turns out that intrinsic fluctuations in particle numbers can make parameters identifiable that were previously non-identifiable. The authors present a method to identify model parameters that are structurally non-identifiab...
Source: IET Systems Biology - March 20, 2015 Category: Biology Source Type: research
Alternative cell polarity behaviours arise from changes in G-protein spatial dynamics
Yeast cells form a single mating projection when exposed to mating pheromone, a classic example of cell polarity. Prolonged treatment with pheromone or specific mutations results in alternative cell polarity behaviours. The authors performed mathematical modelling to investigate these unusual cell morphologies from the perspective of balancing spatial amplification (i.e. positive feedback that localises components) with spatial tracking (i.e. negative feedback that allows sensing of gradient). First, they used generic models of cell polarity to explore different cell polarity behaviours that arose from changes in the model...
Source: IET Systems Biology - March 20, 2015 Category: Biology Source Type: research
Regulation of signal transduction by spatial parameters: a case in NF–κB oscillation
NF-kB is a transcription factor regulating expression of more than 500 genes, and its dysfunction leads to the autoimmune and inflammatory diseases. In malignant cancer cells, NF-kB is constitutively activated. Thus the elucidation of mechanisms for NF-kB regulation is important for the establishment of therapeutic treatment caused by incorrect NF-kB responses. Cytoplasmic NF-kB translocates to the nucleus by the application of extracellular stimuli such as cytokines. Nuclear NF-kB is known to oscillate with the cycle of 1.5–4.5 h, and it is thought that the oscillation pattern regulates the expression profiles...
Source: IET Systems Biology - March 20, 2015 Category: Biology Source Type: research
Open access notice for the paper ‘Anomalous diffusion and multi fractional Brownian motion: simulating molecular crowding and physical obstacles in systems biology’
(Source: IET Systems Biology)
Source: IET Systems Biology - January 13, 2015 Category: Biology Source Type: research
