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BMC Systems Biology

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https://www.readbyqxmd.com/read/29321020/meta-analysis-of-human-gene-expression-in-response-to-mycobacterium-tuberculosis-infection-reveals-potential-therapeutic-targets
#1
Zhang Wang, Seda Arat, Michal Magid-Slav, James R Brown
BACKGROUND: With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors. RESULTS: Here we performed a statistical meta-analysis of human gene expression in response to both latent and active pulmonary tuberculosis infections from nine published datasets. We found 1655 genes that were significantly differentially expressed during active tuberculosis infection...
January 10, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29301573/dengue-virus-causes-changes-of-microrna-genes-regulatory-network-revealing-potential-targets-for-antiviral-drugs
#2
Mohamed Shahen, Zihu Guo, Akhtar Hussain Shar, Reham Ebaid, Qin Tao, Wenjuan Zhang, Ziyin Wu, Yaofei Bai, Yingxue Fu, Chunli Zheng, He Wang, Piar Ali Shar, Jianling Liu, Zhenzhong Wang, Wei Xiao, Yonghua Wan
BACKGROUND: Dengue virus (DENV) is an increasing global health threat and associated with induction of both a long-lived protective immune response and immune-suppression. So far, the potency of treatment of DENV via antiviral drugs is still under investigation. Recently, increasing evidences suggest the potential role of microRNAs (miRNAs) in regulating DENV. The present study focused on the function of miRNAs in innate insusceptible reactions and organization of various types of immune cells and inflammatory responses for DENV...
January 4, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29291750/bayesian-uncertainty-analysis-for-complex-systems-biology-models-emulation-global-parameter-searches-and-evaluation-of-gene-functions
#3
Ian Vernon, Junli Liu, Michael Goldstein, James Rowe, Jen Topping, Keith Lindsey
BACKGROUND: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs of the analysis, and need to be compared to observed data of various forms. The correct analysis of such models usually requires a global parameter search, over a high dimensional parameter space, that incorporates and respects the most important sources of uncertainty...
January 2, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29284486/use-of-transcriptomic-data-for-extending-a-model-of-the-appa-ppsr-system-in-rhodobacter-sphaeroides
#4
Rakesh Pandey, Judith P Armitage, George H Wadhams
BACKGROUND: Photosynthetic (PS) gene expression in Rhodobacter sphaeroides is regulated in response to changes in light and redox conditions mainly by PrrB/A, FnrL and AppA/PpsR systems. The PrrB/A and FnrL systems activate the expression of them under anaerobic conditions while the AppA/PpsR system represses them under aerobic conditions. Recently, two mathematical models have been developed for the AppA/PpsR system and demonstrated how the interaction between AppA and PpsR could lead to a phenotype in which PS genes are repressed under semi-aerobic conditions...
December 28, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29282071/analysis-of-the-main-active-ingredients-and-bioactivities-of-essential-oil-from-osmanthus-fragrans-var-thunbergii-using-a-complex-network-approach
#5
Le Wang, Nana Tan, Jiayao Hu, Huan Wang, Dongzhu Duan, Lin Ma, Jian Xiao, Xiaoling Wang
BACKGROUND: Osmanthus fragrans has been used as folk medicine for thousands of years. The extracts of Osmanthus fragrans flowers were reported to have various bioactivities including free radical scavenging, anti-inflammation, neuroprotection and antitumor effects. However, there is still lack of knowledge about its essential oil. METHODS: In this work, we analyzed the chemical composition of the essential oil from Osmanthus fragrans var. thunbergii by GC-MS. A complex network approach was applied to investigate the interrelationships between the ingredients, target proteins, and related pathways for the essential oil...
December 28, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29282051/microbiota-dysbiosis-in-inflammatory-bowel-diseases-in-silico-investigation-of-the-oxygen-hypothesis
#6
Michael A Henson, Poonam Phalak
BACKGROUND: Inflammatory bowel diseases (IBD), which include ulcerative colitis and Crohn's disease, cause chronic inflammation of the digestive tract in approximately 1.6 million Americans. A signature of IBD is dysbiosis of the gut microbiota marked by a significant reduction of obligate anaerobes and a sharp increase in facultative anaerobes. Numerous experimental studies have shown that IBD is strongly correlated with a decrease of Faecalibacterium prausnitzii and an increase of Escherichia coli...
December 28, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322938/mdd-carb-a-combinatorial-model-for-the-identification-of-protein-carbonylation-sites-with-substrate-motifs
#7
Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang, Tzong-Yi Lee
BACKGROUND: Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is related to a number of metabolic or aging diseases including diabetes, chronic lung disease, Parkinson's disease, and Alzheimer's disease. Due to the lack of computational methods dedicated to exploring motif signatures of protein carbonylation sites, we were motivated to exploit an iterative statistical method to characterize and identify carbonylated sites with motif signatures...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322936/investigation-on-changes-of-modularity-and-robustness-by-edge-removal-mutations-in-signaling-networks
#8
Cong-Doan Truong, Yung-Keun Kwon
BACKGROUND: Biological networks consisting of molecular components and interactions are represented by a graph model. There have been some studies based on that model to analyze a relationship between structural characteristics and dynamical behaviors in signaling network. However, little attention has been paid to changes of modularity and robustness in mutant networks. RESULTS: In this paper, we investigated the changes of modularity and robustness by edge-removal mutations in three signaling networks...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322934/computational-analysis-reveals-the-coupling-between-bistability-and-the-sign-of-a-feedback-loop-in-a-tgf-%C3%AE-1-activation-model
#9
Huipeng Li, Lakshmi Venkatraman, Balakrishnan Chakrapani Narmada, Jacob K White, Hanry Yu, Lisa Tucker-Kellogg
BACKGROUND: Bistable behaviors are prevalent in cell signaling and can be modeled by ordinary differential equations (ODEs) with kinetic parameters. A bistable switch has recently been found to regulate the activation of transforming growth factor-β1 (TGF-β1) in the context of liver fibrosis, and an ordinary differential equation (ODE) model was published showing that the net activation of TGF-β1 depends on the balance between two antagonistic sub-pathways. RESULTS: Through modeling the effects of perturbations that affect both sub-pathways, we revealed that bistability is coupled with the signs of feedback loops in the model...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322933/integrating-transcriptional-activity-in-genome-scale-models-of-metabolism
#10
Daniel Trejo Banos, Pauline Trébulle, Mohamed Elati
BACKGROUND: Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is a hot topic in systems biology. The methods developed to date focus mostly on resolving the metabolic elements and use fairly straightforward approaches to assess the impact of genome expression on the metabolic phenotype. RESULTS: We present here a method for integrating the reverse engineering of gene regulatory networks into these metabolic models...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322929/ontology-based-systematic-representation-and-analysis-of-traditional-chinese-drugs-against-rheumatism
#11
Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He
BACKGROUND: Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive information source for these drugs is still missing, and their anti-rheumatism mechanisms remain unclear. An ontology for anti-rheumatism traditional Chinese drugs would strongly support the representation, analysis, and understanding of these drugs...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322928/constraint-based-perturbation-analysis-with-cluster-newton-method-a-case-study-of-personalized-parameter-estimations-with-irinotecan-whole-body-physiologically-based-pharmacokinetic-model
#12
Shun Asami, Daisuke Kiga, Akihiko Konagaya
BACKGROUND: Drug development considering individual varieties among patients becomes crucial to improve clinical development success rates and save healthcare costs. As a useful tool to predict individual phenomena and correlations among drug characteristics and individual varieties, recently, whole-body physiologically based pharmacokinetic (WB- PBPK) models are getting more attention. WB-PBPK models generally have a lot of drug-related parameters that need to be estimated, and the estimations are difficult because the observed data are limited...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322927/cpredictor3-0-detecting-protein-complexes-from-ppi-networks-with-expression-data-and-functional-annotations
#13
Ying Xu, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan
BACKGROUND: Effectively predicting protein complexes not only helps to understand the structures and functions of proteins and their complexes, but also is useful for diagnosing disease and developing new drugs. Up to now, many methods have been developed to detect complexes by mining dense subgraphs from static protein-protein interaction (PPI) networks, while ignoring the value of other biological information and the dynamic properties of cellular systems. RESULTS: In this paper, based on our previous works CPredictor and CPredictor2...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322926/construction-and-analysis-of-gene-gene-dynamics-influence-networks-based-on-a-boolean-model
#14
Maulida Mazaya, Hung-Cuong Trinh, Yung-Keun Kwon
BACKGROUND: Identification of novel gene-gene relations is a crucial issue to understand system-level biological phenomena. To this end, many methods based on a correlation analysis of gene expressions or structural analysis of molecular interaction networks have been proposed. They have a limitation in identifying more complicated gene-gene dynamical relations, though. RESULTS: To overcome this limitation, we proposed a measure to quantify a gene-gene dynamical influence (GDI) using a Boolean network model and constructed a GDI network to indicate existence of a dynamical influence for every ordered pair of genes...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322924/detecting-causality-from-short-time-series-data-based-on-prediction-of-topologically-equivalent-attractors
#15
Ben-Gong Zhang, Weibo Li, Yazhou Shi, Xiaoping Liu, Luonan Chen
No abstract text is available yet for this article.
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322923/a-polynomial-based-model-for-cell-fate-prediction-in-human-diseases
#16
Lichun Ma, Jie Zheng
BACKGROUND: Cell fate regulation directly affects tissue homeostasis and human health. Research on cell fate decision sheds light on key regulators, facilitates understanding the mechanisms, and suggests novel strategies to treat human diseases that are related to abnormal cell development. RESULTS: In this study, we proposed a polynomial based model to predict cell fate. This model was derived from Taylor series. As a case study, gene expression data of pancreatic cells were adopted to test and verify the model...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322920/investigation-and-identification-of-functional-post-translational-modification-sites-associated-with-drug-binding-and-protein-protein-interactions
#17
Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee
BACKGROUND: Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322919/hadamard-kernel-svm-with-applications-for-breast-cancer-outcome-predictions
#18
Hao Jiang, Wai-Ki Ching, Wai-Shun Cheung, Wenpin Hou, Hong Yin
BACKGROUND: Breast cancer is one of the leading causes of deaths for women. It is of great necessity to develop effective methods for breast cancer detection and diagnosis. Recent studies have focused on gene-based signatures for outcome predictions. Kernel SVM for its discriminative power in dealing with small sample pattern recognition problems has attracted a lot attention. But how to select or construct an appropriate kernel for a specified problem still needs further investigation...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322918/a-linear-programming-computational-framework-integrates-phosphor-proteomics-and-prior-knowledge-to-predict-drug-efficacy
#19
Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi
BACKGROUND: In recent years, the integration of 'omics' technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the way of approaching drug discovery. The LINCS public data warehouse provides detailed information about cell responses with various genetic and environmental stressors. It can be greatly helpful in developing new drugs and therapeutics, as well as improving the situations of lacking effective drugs, drug resistance and relapse in cancer therapies, etc...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322917/identification-of-natural-antimicrobial-peptides-from-bacteria-through-metagenomic-and-metatranscriptomic-analysis-of-high-throughput-transcriptome-data-of-taiwanese-oolong-teas
#20
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K Robert Lai, Tzong-Yi Lee
BACKGROUND: Anti-microbial peptides (AMPs), naturally encoded by genes and generally containing 12-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria and viruses. In recent years, the widespread use of antibiotics has resulted in the rapid growth of antibiotic-resistant microorganisms that often induce critical infection and pathogenesis. Recently, the advent of high-throughput technologies has led molecular biology into a data surge in both the amount and scope of data...
December 21, 2017: BMC Systems Biology
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