2014 8th International Conference on Systems Biology (ISB)最新文献

Dynamical behaviour of a delay differential equation of Hepatitis B virus 乙型肝炎病毒时滞微分方程的动力学行为

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990425

Dayun Wu, Yongmei Su

引用次数: 1

VaccineWatch: a monitoring system of vaccine messages from social media data VaccineWatch:一个监测来自社交媒体数据的疫苗信息的系统

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990742

Somrak Numnark, S. Ingsriswang, D. Wichadakul

引用次数: 5

Dissecting the obesity disease landscape: Identifying gene-gene interactions that are highly associated with body mass index 剖析肥胖疾病景观:确定与体重指数高度相关的基因-基因相互作用

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990744

R. De, S. Verma, M. Holmes, F. Asselbergs, J. Moore, B. Keating, M. Ritchie, D. Gilbert-Diamond

{"title":"Dissecting the obesity disease landscape: Identifying gene-gene interactions that are highly associated with body mass index","authors":"R. De, S. Verma, M. Holmes, F. Asselbergs, J. Moore, B. Keating, M. Ritchie, D. Gilbert-Diamond","doi":"10.1109/ISB.2014.6990744","DOIUrl":"https://doi.org/10.1109/ISB.2014.6990744","url":null,"abstract":"Despite heritability estimates of 40-70% for obesity, less than 2% of its variation is explained by Body Mass Index (BMI) associated loci that have been identified so far. Epistasis, or gene-gene interactions are a plausible source to explain portions of the missing heritability of BMI. Using genotypic data from 18,686 individuals across five study cohorts - ARIC, CARDIA, FHS, CHS, MESA - we filtered SNPs (Single Nucleotide Polymorphisms) using two parallel approaches. SNPs were filtered either on the strength of their main effects of association with BMI, or on the number of knowledge sources supporting a specific SNP-SNP interaction in the context of obesity. Filtered SNPs were specifically analyzed for interactions that are highly associated with BMI using QMDR (Quantitative Multifactor Dimensionality Reduction). QMDR is a nonparametric, genetic model-free method that detects nonlinear interactions in the context of a quantitative trait. We identified seven novel, epistatic models with a Bonferroni corrected p-value of association <; 0.06. Prior experimental evidence helps explain the plausible biological interactions highlighted within our results and their relationship with obesity. We identified interactions between genes involved in mitochondrial dysfunction (POLG2), cholesterol metabolism (SOAT2), lipid metabolism (CYP11B2), cell adhesion (EZR), cell proliferation (MAP2K5), and insulin resistance (IGF1R). This study highlights a novel approach for discovering gene-gene interactions by combining methods such as QMDR with traditional statistics.","PeriodicalId":249103,"journal":{"name":"2014 8th International Conference on Systems Biology (ISB)","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129199331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Neural fate decisions mediated by oscillatory and sustained Hes1 振荡和持续Hes1介导的神经命运决定

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990754

Shanshan Li, Zengrong Liu, Ruiqi Wang

引用次数: 1

The correlation and regression analysis on aerosol optical depth, ice cover and cloud cover in Greenland Sea 格陵兰海气溶胶光学深度与冰盖和云量的相关与回归分析

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990753

B. Qu, A. Gabric, Peijuan Gu, Meifang Zeng

{"title":"The correlation and regression analysis on aerosol optical depth, ice cover and cloud cover in Greenland Sea","authors":"B. Qu, A. Gabric, Peijuan Gu, Meifang Zeng","doi":"10.1109/ISB.2014.6990753","DOIUrl":"https://doi.org/10.1109/ISB.2014.6990753","url":null,"abstract":"Researches on Arctic aerosol, ice cover and cloud cover have received great attention and it related to the regional even global climate changing. We here study the distributions and the coupling relationships of AOD, cloud cover (CLD) and ice cover (ICE) in the Greenland Sea (20°W-10°E, 70°N-80°N) during 2003-2012. Enhanced statistics methods, such as lag regression method and co-integration analysis method are used for correlation and regression analysis. According to the 10 years satellite data, AOD was high in spring, and low in summer. Generally, AOD was higher down south and lower up north. CLD and AOD mainly had negative correlations and ICE and AOD had positive correlations. According to the lag regression analysis by statistical software EViews, both the peaks of CLD and peaks of ICE were all 1 month earlier than the peak of AOD. The co-integration test suggested that both ICE(-1) and CLD(-1) and AOD were all zero-order integration, and there was no unit root in the residual, so there all had long-run equilibrium relationships. ICE and AOD were stationary series, and the residual had no unit root, they were good coupling. The melting of sea ice and decreasing of cloud cover would all result in the increasing of the AOD content. However, the relationship between AOD and CLD was weaker than the relationship between AOD and ICE, indicating that the aerosol in Arctic mostly came from the sea rather than from the air.","PeriodicalId":249103,"journal":{"name":"2014 8th International Conference on Systems Biology (ISB)","volume":"74 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114880860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A new approach for estimating the progression of pancreatic cancer 估计胰腺癌进展的新方法

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990743

Shuhao Sun, F. Klebaner, Tianhai Tian

{"title":"A new approach for estimating the progression of pancreatic cancer","authors":"Shuhao Sun, F. Klebaner, Tianhai Tian","doi":"10.1109/ISB.2014.6990743","DOIUrl":"https://doi.org/10.1109/ISB.2014.6990743","url":null,"abstract":"Cancer of the pancreas is a highly lethal disease and has an extremely poor prognosis. It is the fourth leading cause of death from cancer in the US and the twelfth worldwide. There are currently only few therapeutic options for patients with pancreatic cancer. Hence new insights into the pathogenesis of this lethal disease are urgently needed. In recent years, extensive biological research has been conducted to study the mechanisms that control the initiation and progression of pancreas cancer. Mathematical models have also been used to present quantitative analysis and predict reasonable time schemes for the progression of pancreatic cancer. However, in those published articles, it was assumed that the mutation rate was constant, which is not realistic. In this work, we present a new approach using non-constant mutation rate and hence reveal several important biological parameters of cancer progression, such as initial mutation rate as well as doubling time (or selective advantage coefficients) in different stages, and eventually present a better time scheme. Under more realistic assumptions regarding gene mutation and a more reasonable mutation rate, the averaged values of doubling time and selective advantage coefficient generated by our model are consistent with the predictions made by the published models.","PeriodicalId":249103,"journal":{"name":"2014 8th International Conference on Systems Biology (ISB)","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124660447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Prediction of hepatotoxicity of traditional Chinese medicine compounds by support vector machine approach 支持向量机方法预测中药化合物的肝毒性

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990426

Ludi Jiang, Yusu He, Yanling Zhang

引用次数: 7

Comparative analysis of RNA-seq data from polyA RNAs selection and ribosomal RNAs deletion protocol by strand-specific RNA sequencing technology 采用链特异性RNA测序技术对多a RNA选择和核糖体RNA删除方案的RNA-seq数据进行比较分析

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990734

Lingjie Fu, Meili Chen, Jiayan Wu, Jingfa Xiao, Zhewen Zhang

{"title":"Comparative analysis of RNA-seq data from polyA RNAs selection and ribosomal RNAs deletion protocol by strand-specific RNA sequencing technology","authors":"Lingjie Fu, Meili Chen, Jiayan Wu, Jingfa Xiao, Zhewen Zhang","doi":"10.1109/ISB.2014.6990734","DOIUrl":"https://doi.org/10.1109/ISB.2014.6990734","url":null,"abstract":"The conventional non-strand-specific RNA-seq method is widely used for many studies, but it cannot characterize which strand was the transcript originally came from. Strand-specific RNA library construction methods have been developed to overcome this drawback. Here, we compared transcriptomics data from two mainstream RNA enrichment methods (polyA RNAs selection and ribosomal RNAs deletion) by strand-specific RNA sequencing. Using paired-end strategy, we obtained 175 and 149 million high quality reads without ribosomal RNA reads by ribosomal RNAs deletion and poly(A)+ RNAs selection protocol, respectively. From these reads, rmRNA-seq had lower (53.28%) unique mapping rate than the mRNA-seq (73.89%). But, the ribosomal RNAs deletion protocol detected more known non-coding RNAs, particularly lncRNAs, pseudogenes and snoRNAs. Larger proportion (66.7%) of reads mapping to intronic and intergenic regions in ribosomal RNAs deletion method and fewer percentages (33.3%) of reads aligning to exonic regions compared with poly(A)+ RNAs selection method (35.8% and 64.2%). The ribosomal RNAs deletion protocol provides advantages over the poly(A)+ RNAs selection method in sense-antisense pairs detection. In conclusion, the comparison of these two rRNA enrichment methods provides us insight for utility of each protocol. Moreover, we believe that ribosomal RNAs deletion based strand-specific RNA sequencing show us a more comprehensive view of eukaryotic transcriptomes.","PeriodicalId":249103,"journal":{"name":"2014 8th International Conference on Systems Biology (ISB)","volume":"91 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126286521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Systematic identification of local structure binding motifs in protein-RNA recognition 蛋白质- rna识别中局部结构结合基序的系统鉴定

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990735

Zhiping Liu

引用次数: 2

A dynamic programming algorithm for nucleosome positions alignment 核小体位置对齐的动态规划算法

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990422

Yiru Zhang, Chang-Chang Cao, Hongde Liu, Xiao Sun

引用次数: 0