2014 8th International Conference on Systems Biology (ISB)最新文献_第4页

Evolution analysis for HA gene of human influenza A H3N2 virus (1990 – 2013) 人甲型流感H3N2病毒HA基因1990 - 2013年进化分析

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990736

Su-Li Li, Meng-Zhe Jin, Zhao-Hui Qi

引用次数: 0

Reversal DNA methylation patterns for cancer diagnosis 逆转DNA甲基化模式用于癌症诊断

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-12-18 DOI: 10.1109/ISB.2014.6990740

Hongdong Li, G. Hong, Zheng Guo

{"title":"Reversal DNA methylation patterns for cancer diagnosis","authors":"Hongdong Li, G. Hong, Zheng Guo","doi":"10.1109/ISB.2014.6990740","DOIUrl":"https://doi.org/10.1109/ISB.2014.6990740","url":null,"abstract":"Detecting aberrant DNA methylation as diagnostic or prognostic biomarkers for cancer has been a topic of considerable interest recently. However, current classifiers based on absolute methylation values detected from a cohort of samples are typically difficult to be transferable to other cohorts of samples. Here, we employed a modified rank-based method to extract pairs of CpG sites with reversal relative DNA methylation levels in disease samples to those in normal controls for five cancer types respectively. The reversal pairs showed excellent prediction performance with the accuracy above 95% for each type of cancer. Furthermore, the reversal pairs identified for a cancer type could distinguish samples with different subtypes and different malignant stages including early stage of this cancer from normal controls and were also specific to this cancer. In conclusion, the reversal pairs detected by the rank-based method are accurate and transferable to independent cohorts of samples, which are also applicable to early cancer diagnosis. They could also be used to detect common molecular alterations in cancer, which can shed light on the other follow-up studies.","PeriodicalId":249103,"journal":{"name":"2014 8th International Conference on Systems Biology (ISB)","volume":"45 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":"126225028","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: 2

Mining correlation patterns of taxa, pathways and environmental factors with an improved weighted network community detection algorithm 利用改进的加权网络群落检测算法挖掘分类群、路径和环境因子的关联模式

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-10-01 DOI: 10.1109/ISB.2014.6990746

Xiao-Ying Yan, Shaowu Zhang, Ze-Gang Wei, Wei-feng Guo

{"title":"Mining correlation patterns of taxa, pathways and environmental factors with an improved weighted network community detection algorithm","authors":"Xiao-Ying Yan, Shaowu Zhang, Ze-Gang Wei, Wei-feng Guo","doi":"10.1109/ISB.2014.6990746","DOIUrl":"https://doi.org/10.1109/ISB.2014.6990746","url":null,"abstract":"With the development of high-throughput and low-cost sequencing technology, a large amount of marine microbial sequences is generated. So, it is possible to research more uncultivated marine microbes. Generally, the functional capability and taxa structure are highly related with environment factors in microbial communities, which are hidden in these large amount sequences. However, most works used the canonical correlation analysis (CCA) method to research the correlative relationship among taxa, pathways and environmental factors. CCA is difficult to find which environmental factors are the major determinants of some special taxa and pathway. In this paper, we integrated 14 ocean metagenomes with geographical, meteorological and geophysicochemical data to construct the correlative weighted networks with Spearman correlation. By using an improved weighted network community detection algorithm, named as IWNCD, we find some special correlation patterns among taxa, pathways and environmental factors. Analysis of these patterns shows that the climatic factors such as temperature, sunlight, and correlated CO2, and the nutrients such as chlorophyII and primary production are the main determining factors of the functional community composition; The growth and development of some special taxa are dependent on some main environmental factors such as sunlight, temperature, CO2, primary production, dissolved oxygen, dissolved silicate; In addition, sampling sites more similar in geographic location have a greater tendency to be closer together based on their metabolic pathways.","PeriodicalId":249103,"journal":{"name":"2014 8th International Conference on Systems Biology (ISB)","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132995965","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

Detection of SNP-SNP interaction based on the generalized particle swarm optimization algorithm 基于广义粒子群优化算法的SNP-SNP相互作用检测

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-10-01 DOI: 10.1109/ISB.2014.6990748

Changyi Ma, J. Shang, Shengjun Li, Y. Sun

引用次数: 5

Predicting Golgi-resident proteins in plants by incorporating N-terminal transmembrane domain information in the general form of Chou's pseudoamino acid compositions 利用周氏假氨基酸组成一般形式的n端跨膜结构域信息预测植物中的高尔基蛋白

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-10-01 DOI: 10.1109/ISB.2014.6990759

Yasen Jiao, Pufeng Du, Xiaoquan Su

引用次数: 3

Evidence based disease network construction towards drug repositioning 面向药物重新定位的循证疾病网络构建

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-10-01 DOI: 10.1109/ISB.2014.6990758

Liwei Wang, Jiabei Wang, Qian Zhu

引用次数: 2

An Entropy-based Statistical Workflow Provides Noise-Minimizing Biological Annotation for 基于熵的统计工作流提供了噪声最小化的生物注释

2014 8th International Conference on Systems Biology (ISB) Pub Date : 2014-10-01 DOI: 10.1109/ISB.2014.6990749

Muscular Aging, Theodoros Koutsandreas, I. Valavanis, E. Pilalis, A. Chatziioannou

{"title":"An Entropy-based Statistical Workflow Provides Noise-Minimizing Biological Annotation for","authors":"Muscular Aging, Theodoros Koutsandreas, I. Valavanis, E. Pilalis, A. Chatziioannou","doi":"10.1109/ISB.2014.6990749","DOIUrl":"https://doi.org/10.1109/ISB.2014.6990749","url":null,"abstract":"This study aims to expand the efficiency of the interpretation concerning the aging process, by exploring a broad gene set, derived from the analysis of an integrative transcriptomic microarray dataset. The dataset comprises human skeletal muscle samples, obtained from healthy males and females, that were used to derive a gene signature of a high informative content, with respect to its functional association with the aging phenotype. Towards this end, a multilayered computational workflow integrating advanced statistical methodologies for the derivation of reliable confidence measures, distribution-based entropy calculations to examine the informational content of the dataset, enrichment analysis, graph-theoretic methods and intuitive visualization was applied. Specifically, statistical testing revealed differentially expressed genes, while an uncertainty calculation algorithm, exploiting Gene Ontology (GO) terms annotations, extended the list of significant genes from 254 to 2791, namely p-value threshold was increased from 0.0005 to 0.103, while keeping simultaneously noise measurements legitimately low. This rich gene set associated functionally the macroscopic phenotype of muscular aging with highly informative, stably correlated with each other, molecular annotations in the GO database. Finally, a set of 57 reliable genes was identified that comprise a gender-independent aging signature, after incorporating crucial information about genes pivotal regulatory role as inferred by the GO tree. The biological interpretation was highly assisted by the illustration of the functional mappings between genes, cellular location and biological processes through circle packing graphs.","PeriodicalId":249103,"journal":{"name":"2014 8th International Conference on Systems Biology (ISB)","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133867145","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