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BMC Systems Biology

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https://www.readbyqxmd.com/read/29769129/a-powerful-nonparametric-method-for-detecting-differentially-co-expressed-genes-distance-correlation-screening-and-edge-count-test
#1
Qingyang Zhang
BACKGROUND: Differential co-expression analysis, as a complement of differential expression analysis, offers significant insights into the changes in molecular mechanism of different phenotypes. A prevailing approach to detecting differentially co-expressed genes is to compare Pearson's correlation coefficients in two phenotypes. However, due to the limitations of Pearson's correlation measure, this approach lacks the power to detect nonlinear changes in gene co-expression which is common in gene regulatory networks...
May 16, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29699591/new-perspectives-systems-medicine-in-cardiovascular-disease
#2
Frank Kramer, Steffen Just, Tanja Zeller
BACKGROUND: Cardiovascular diseases (CVD) represent one of the most important causes of morbidity and mortality worldwide. Innovative approaches to increase the understanding of the underpinnings of CVD promise to enhance CVD risk assessment and might pave the way to tailored therapies. Within the last years, systems medicine has emerged as a novel tool to study the genetic, molecular and physiological interactions. CONCLUSION: In this review, we provide an overview of the current molecular-experimental, epidemiological and bioinformatical tools applied in systems medicine in the cardiovascular field...
April 25, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745860/modeling-biological-systems-with-uncertain-kinetic-data-using-fuzzy-continuous-petri-nets
#3
Fei Liu, Siyuan Chen, Monika Heiner, Hengjie Song
BACKGROUND: Uncertainties exist in many biological systems, which can be classified as random uncertainties and fuzzy uncertainties. The former can usually be dealt with using stochastic methods, while the latter have to be handled with such approaches as fuzzy methods. RESULTS: In this paper, we focus on a special type of biological systems that can be described using ordinary differential equations or continuous Petri nets (CPNs), but some kinetic parameters are missing or inaccurate...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745859/detecting-complexes-from-edge-weighted-ppi-networks-via-genes-expression-analysis
#4
Zehua Zhang, Jian Song, Jijun Tang, Xinying Xu, Fei Guo
BACKGROUND: Identifying complexes from PPI networks has become a key problem to elucidate protein functions and identify signal and biological processes in a cell. Proteins binding as complexes are important roles of life activity. Accurate determination of complexes in PPI networks is crucial for understanding principles of cellular organization. RESULTS: We propose a novel method to identify complexes on PPI networks, based on different co-expression information...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745858/kf-finder-identification-of-key-factors-from-host-microbial-networks-in-cervical-cancer
#5
Jialu Hu, Yiqun Gao, Yan Zheng, Xuequn Shang
BACKGROUND: The human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can also cause many diseases by interfering the regular metabolism and immune system. Recent studies have demonstrated that the microbial community is closely associated with various types of cell carcinoma. The search for key factors, which also refer to cancer causing agents, can provide an important clue in understanding the regulatory mechanism of microbiota in uterine cervix cancer...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745857/identification-of-novel-drug-targets-for-diamond-blackfan-anemia-based-on-rps19-gene-mutation-using-protein-protein-interaction-network
#6
Abbas Khan, Arif Ali, Muhammad Junaid, Chang Liu, Aman Chandra Kaushik, William C S Cho, Dong-Qing Wei
BACKGROUND: Diamond-Blackfan anemia (DBA) is a congenital erythroid aplasia that usually presents in infancy. In order to explore the molecular mechanisms of wild and mutated samples from DBA patients were exposed to bioinformatics investigation. Biological network of differentially expressed genes was constructed. This study aimed to identify novel therapeutic signatures in DBA and uncovered their mechanisms. The gene expression dataset of GSE14335 was used, which consists of 6 normal and 4 diseased cases...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745856/70propred-a-predictor-for-discovering-sigma70-promoters-based-on-combining-multiple-features
#7
Wenying He, Cangzhi Jia, Yucong Duan, Quan Zou
BACKGROUND: Promoter is an important sequence regulation element, which is in charge of gene transcription initiation. In prokaryotes, σ70 promoters regulate the transcription of most genes. The promoter recognition has been a crucial part of gene structure recognition. It's also the core issue of constructing gene transcriptional regulation network. With the successfully completion of genome sequencing from an increasing number of microbe species, the accurate identification of σ70 promoter regions in DNA sequence is not easy...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745852/transcriptomic-and-metabolic-flux-analyses-reveal-shift-of-metabolic-patterns-during-rice-grain-development
#8
Fangzhou Shen, Xueting Wu, Luoxi Shi, Hang Zhang, Yangmin Chen, Xiaoquan Qi, Zhuo Wang, Xuan Li
BACKGROUND: Rice (Oryza sativa) is one of the most important grain crops, which serves as food source for nearly half of the world population. The study of rice development process as well as related strategies for production has made significant progress. However, the comprehensive study on development of different rice tissues at both transcriptomic and metabolic flux level across different stages was lacked. RESULTS: In this study, we performed RNA-Seq and characterized the expression profiles of differentiated tissues from Oryza sativa Zhonghua 11, including leaves, sheath, stamen, pistil, lemma and palea of the booting stage, and embryo, endosperm, lemma and palea of the mature grain stage...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745850/feedback-regulation-in-a-stem-cell-model-with-acute-myeloid-leukaemia
#9
Jianfeng Jiao, Min Luo, Ruiqi Wang
BACKGROUND: The haematopoietic lineages with leukaemia lineages are considered in this paper. In particular, we mainly consider that haematopoietic lineages are tightly controlled by negative feedback inhibition of end-product. Actually, leukemia has been found 100 years ago. Up to now, the exact mechanism is still unknown, and many factors are thought to be associated with the pathogenesis of leukemia. Nevertheless, it is very necessary to continue the profound study of the pathogenesis of leukemia...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745845/ppi-network-analyses-of-human-wd40-protein-family-systematically-reveal-their-tendency-to-assemble-complexes-and-facilitate-the-complex-predictions
#10
Xu-Dong Zou, Ke An, Yun-Dong Wu, Zhi-Qiang Ye
BACKGROUND: WD40 repeat proteins constitute one of the largest families in eukaryotes, and widely participate in various fundamental cellular processes by interacting with other molecules. Based on individual WD40 proteins, previous work has demonstrated that their structural characteristics should confer great potential of interaction and complex formation, and has speculated that they may serve as hubs in the protein-protein interaction (PPI) network. However, what roles the whole family plays in organizing the PPI network, and whether this information can be utilized in complex prediction remain unclear...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745842/functional-enrichment-analysis-based-on-long-noncoding-rna-associations
#11
Kuo-Sheng Hung, Chung-Chi Hsiao, Tun-Wen Pai, Chin-Hwa Hu, Wen-Shyong Tzou, Wen-Der Wang, Yet-Ran Chen
BACKGROUND: Differential gene expression analysis using RNA-seq data is a popular approach for discovering specific regulation mechanisms under certain environmental settings. Both gene ontology (GO) and KEGG pathway enrichment analysis are major processes for investigating gene groups that participate in common biological responses or possess related functions. However, traditional approaches based on differentially expressed genes only detect a few significant GO terms and pathways, which are frequently insufficient to explain all-inclusive gene regulation mechanisms...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745841/fixation-probability-of-a-beneficial-mutation-conferring-decreased-generation-time-in-changing-environments
#12
Fangshu Cui, Bo Yuan
BACKGROUND: One central building block of population genetics is the fixation probability. It is a probabilistic understanding of the eventual fate of new mutations. Moreover, the fixation probability of new beneficial mutations plays an important effect on the adaptation of populations to environmental challenges. Great progress has been made in the study of the beneficial mutations that increases offspring number. However, the fixation probability of beneficial mutations with a shorter generation time under various genetic and ecological conditions has not been explored...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745840/hierarchical-combinatorial-deep-learning-architecture-for-pancreas-segmentation-of-medical-computed-tomography-cancer-images
#13
Min Fu, Wenming Wu, Xiafei Hong, Qiuhua Liu, Jialin Jiang, Yaobin Ou, Yupei Zhao, Xinqi Gong
BACKGROUND: Efficient computational recognition and segmentation of target organ from medical images are foundational in diagnosis and treatment, especially about pancreas cancer. In practice, the diversity in appearance of pancreas and organs in abdomen, makes detailed texture information of objects important in segmentation algorithm. According to our observations, however, the structures of previous networks, such as the Richer Feature Convolutional Network (RCF), are too coarse to segment the object (pancreas) accurately, especially the edge...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745839/multi-target-drug-repositioning-by-bipartite-block-wise-sparse-multi-task-learning
#14
Limin Li, Xiao He, Karsten Borgwardt
BACKGROUND: Finding potential drug targets is a crucial step in drug discovery and development. Recently, resources such as the Library of Integrated Network-Based Cellular Signatures (LINCS) L1000 database provide gene expression profiles induced by various chemical and genetic perturbations and thereby make it possible to analyze the relationship between compounds and gene targets at a genome-wide scale. Current approaches for comparing the expression profiles are based on pairwise connectivity mapping analysis...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745838/improved-flower-pollination-algorithm-for-identifying-essential-proteins
#15
Xiujuan Lei, Ming Fang, Fang-Xiang Wu, Luonan Chen
BACKGROUND: Essential proteins are necessary for the survival and development of cells. The identification of essential proteins can help to understand the minimal requirements for cellular life and it also plays an important role in the disease genes study and drug design. With the development of high-throughput techniques, a large amount of protein-protein interactions data is available to predict essential proteins at the network level. Hitherto, even though a number of essential protein discovery methods have been proposed, the prediction precision still needs to be improved...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745833/differential-networking-meta-analysis-of-gastric-cancer-across-asian-and-american-racial-groups
#16
Wentao Dai, Quanxue Li, Bing-Ya Liu, Yi-Xue Li, Yuan-Yuan Li
BACKGROUND: Gastric Carcinoma is one of the most lethal cancer around the world, and is also the most common cancers in Eastern Asia. A lot of differentially expressed genes have been detected as being associated with Gastric Carcinoma (GC) progression, however, little is known about the underlying dysfunctional regulation mechanisms. To address this problem, we previously developed a differential networking approach that is characterized by involving differential coexpression analysis (DCEA), stage-specific gene regulatory network (GRN) modelling and differential regulation networking (DRN) analysis...
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29745831/integrating-data-and-model-driven-strategies-in-systems-biology
#17
EDITORIAL
Yong Wang, Xiang-Sun Zhang, Luonan Chen
A report of the 11th International Conference on Systems Biology (ISB2017), 18-21 August, Shenzhen, China.
April 24, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29650016/evolution-of-computational-models-in-biomodels-database-and-the-physiome-model-repository
#18
Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath
BACKGROUND: A useful model is one that is being (re)used. The development of a successful model does not finish with its publication. During reuse, models are being modified, i.e. expanded, corrected, and refined. Even small changes in the encoding of a model can, however, significantly affect its interpretation. Our motivation for the present study is to identify changes in models and make them transparent and traceable. METHODS: We analysed 13734 models from BioModels Database and the Physiome Model Repository...
April 12, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29671405/ncrna-disease-association-prediction-based-on-sequence-information-and-tripartite-network
#19
Takuya Mori, Hayliang Ngouv, Morihiro Hayashida, Tatsuya Akutsu, Jose C Nacher
BACKGROUND: Current technology has demonstrated that mutation and deregulation of non-coding RNAs (ncRNAs) are associated with diverse human diseases and important biological processes. Therefore, developing a novel computational method for predicting potential ncRNA-disease associations could benefit pathologists in understanding the correlation between ncRNAs and disease diagnosis, treatment, and prevention. However, only a few studies have investigated these associations in pathogenesis...
April 11, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29671404/regulation-of-dual-specificity-phosphatases-in-breast-cancer-during-initial-treatment-with-herceptin-a-boolean-model-analysis
#20
Petronela Buiga, Ari Elson, Lydia Tabernero, Jean-Marc Schwartz
BACKGROUND: 25% of breast cancer patients suffer from aggressive HER2-positive tumours that are characterised by overexpression of the HER2 protein or by its increased tyrosine kinase activity. Herceptin is a major drug used to treat HER2 positive breast cancer. Understanding the molecular events that occur when breast cancer cells are exposed to Herceptin is therefore of significant importance. Dual specificity phosphatases (DUSPs) are central regulators of cell signalling that function downstream of HER2, but their role in the cellular response to Herceptin is mostly unknown...
April 11, 2018: BMC Systems Biology
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