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Recently, measuring phenotype similarity began to play an important role in disease diagnosis. Researchers have begun to pay attention to develop phenotype similarity measurement. However, existing methods ignore the interactions between phenotype-associated proteins, which may lead to inaccurate phenotype similarity. We proposed a network-based method PhenoNet to calculate the similarity between...
Varicella-zoster virus causes chickenpox, a very contagious disease manifested by rash, itching, tiredness, and fever. The affected individual gets stomach, back and face covered with blister-like rash that often spreads over the entire body resulting in 250 or even 500 itchy blisters. Babies, adults, and people with weakened immune systems can be seriously affected by chickenpox. As a part of this...
Healthy lifestyle is an important requirement for people, which is obtained from balanced nutrition. Imbalanced nutrition increases risk of health problems. Balanced nutrition means the difference between nutrition needed and nutrition intake must be as minimum as possible. The condition in Indonesian, many people consume food with high carbohydrate; whereas nutrition consists of protein, carbohydrate,...
There is need for modeling biological systems to accelerate drug pipelines for treating metabolic diseases. The eliglustat treatment for Gaucher disease is approved by the FDA with a companion genomic test. The Transcriptome-To-Metabolome™ biosimulation technology was used to model, in silico, a standard non-clinical eliglustat test with an in vitro canine kidney cell system over-expressing a human...
Finding gene clusters that can be shared between drugs and diseases plays an important role in drug discovery. Targeting disease causing genes directly in drug development can increase the chance of drug approval through the clinical phase. This paper introduces a new co-clustering approach on the tripartite graph of genes, drugs, and diseases. As a result of co-clustering, gene modules and their...
The early diagnosis of the Chronic Kidney Disease (CKD) is important to reduce the progression of the disease and prevent its treatment in advanced stages. Information and Communication Technologies (ICT) can assist the CKD diagnosis and the patients' referral to a nephrologist. In this context, regulatory agencies evaluate the safety and effectiveness of this type of medical system before market...
Alzheimer's disease (AD) is currently the most common form of dementia affecting the elderly, and its occurrence rate is only expected to increase over the next several decades. Though there is a vast array of knowledge about individual molecules and genetics involved with the disease, there is no clear understanding of the mechanism of pathogenesis. To help better understand the disease process,...
Oxidative stress is a consequence of normal cellular metabolism. The effective functioning of the pathway responding to oxidative stress protects the cellular DNA against oxidative damage and its failure can induce aberrant cellular behaviour leading to diseases such as neurodegenerative disorders and cancer. Thus, understanding the normal signalling present in oxidative stress response pathways and...
Oxidative stress is a consequence of normal cellular metabolism. The effective functioning of the pathway responding to oxidative stress protects the cellular DNA against oxidative damage and its failure can induce aberrant cellular behaviour leading to diseases such as neurodegenerative disorders and cancer. Thus, understanding the normal signalling present in oxidative stress response pathways and...
We investigate the molecular mechanism of inherited arrhythmias using a multiscale model. The model has numerous parameters some of which are estimated with voltage clamp data. Errors in the estimation of parameters have a dramatic effect on the investigation of the mechanism of arrhythmias. In some cases, these errors may prevent seeing the creation of a premature cardiac beat. We present an analysis...
In silico models are often constructed to aid in the understanding of disease and the production of relevant intervention strategies. Several existing models study the acute inflammatory response, which is of importance in multiple organ dysfunction syndrome and sepsis, both of which have high mortality rates. However, no current model of inflammation considers the unique secretory dynamics of cortisol...
In this paper we summarise our current work on using Process Calculi for the modelling and analysis of biological pathways in context of better understanding respiratory disease. We present and highlight key features of some of the different Process Calculi that have been used for the modelling of biological pathways. Then we make a state-of-art on asthma, severe asthma and the possible cause of corticosteroids...
The mathematical model described in this paper is based on a discovery of a phenomenon related to red blood cells. In this phenomenon, the hemolysate of red blood cells reacts with antibodies from the plasma of the same patient. Using proteomics approach to identify those hemolysate antigens and then build a database containing those antigens can help in diagnosis, prognosis, and treatment of disease...
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of insulin and leptin signaling, and is therefore a major molecular target for the treatment of type II diabetes and obesity. WPD loop is a key element in the mechanism of PTP1B catalysis. In the apo form, WPD loop is usually in an “open” conformation, whereas it closes over the active site upon substrate binding. Here, targeted molecular...
Previous studies have suggested that some graph properties of protein interaction networks might be related with gene morbidity. In particular, it has been suggested that when a polymorphism affects a gene, it is more likely to produce a disease if the node degree in the interaction network is higher than for other genes. However, these results do not take into account the possible bias introduced...
The cell functions and development are regulated by complex networks of genes, proteins and other components by means of their mutual interactions. These networks are called gene regulatory networks (GRNs). GRNs are used to reveal the fundamental gene regulatory mechanisms, to determine the reasons for many diseases and interactions between drugs and their targets. The introduction of experimental...
To evaluate cytokine network of pulmonary fibrosis. A systematic literature search of EMBASE, MEDLINE, Cochrane Library was conducted through December 2007. Then potential regulatory pathway of cytokines was analyzed with a cubic spline intepolation and a linear differential model. The cytokines of silicosis fibrosis tissue were identified by meta-analysis. The related cytokines participated pulmonary...
In order to simulate biological processes, we use multi-agents system. However, modelling cell behavior in systems biology is complex and may be based on intracellular biochemical pathway. So, we have developed in this study a Fuzzy Influence Graph to model MAPK pathway. A Fuzzy Influence Graph is also called Fuzzy Cognitive Map. This model can be integrated in agents representing cells. Results indicate...
Atherosclerosis results from chronic inflammatory processes involving a huge number of risk factor, such as lipid profile, glycated hemoglobin and oxidative stress. Signaling pathways are not enough to explain the holistic interactions. The combined use of principal component analysis and structural equation modeling is a good choice to investigate the causality between risk factors so as to complement...
HIV (human immunodeficiency virus) infection is fatal because it directly damages human's immune system by infecting CD4+ T cells. Treatment for HIV infection is a complex process that involves interactions among the virus population, the immune system and antiretroviral drugs. However, it is difficult to treat HIV infection because the high mutation rate helps HIV to escape from drug attacks. Therefore,...
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