Proceedings of the 5th International Conference on Bioinformatics and Computational Biology最新文献_第2页

Palm-print recognition algorithm based on random projection and chaotic system 基于随机投影和混沌系统的掌纹识别算法

Proceedings of the 5th International Conference on Bioinformatics and Computational Biology Pub Date : 2017-01-06 DOI: 10.1145/3035012.3035017

Jiwen Dong, Ziru Zhao, Hengjian Li, Guang Feng

引用次数: 0

An integrated approach to identify cytochrome P450 superfamilies in plant species within the malvids 植物中细胞色素P450超家族的综合鉴定方法

Proceedings of the 5th International Conference on Bioinformatics and Computational Biology Pub Date : 2017-01-06 DOI: 10.1145/3035012.3035021

Taikui Zhang, Cuiyu Liu, Hanyao Zhang, Zhaohe Yuan

{"title":"An integrated approach to identify cytochrome P450 superfamilies in plant species within the malvids","authors":"Taikui Zhang, Cuiyu Liu, Hanyao Zhang, Zhaohe Yuan","doi":"10.1145/3035012.3035021","DOIUrl":"https://doi.org/10.1145/3035012.3035021","url":null,"abstract":"The cytochrome P450 (CYP) monooxygenases present an enzyme superfamily contributing diverse biological functions and thus are crucial for survival in the plant. Although the CYP members in several plant species have been clarified, little is known about the evolutionary relationships between species within the Malvids clade, that includes cabbage (Brassica rapa), cacao (Theobroma cacao), cotton (Gossypium arboreum), eucalypts (Eucalyptus grandis), orange (Citrus sinensis), papaya (Carica papaya), pomegranate (Punica granatum), and other key species widely cultivated in agricultural. Here we de nove assembled the high-quality pomegranate transcripts with N50 of 1791bp using RNA-seq. Using an integrated HMM-search and InterProScan-verification as well as CYPED-annotation approach we identified 2350 putative CYP candidate proteins in pomegranate and the other related species within the Malvids clade. Four identified motifs were responsible for the conserved sequence structure and diverse enzyme functions. Phylogenetic analysis showed the distinct expansion of CYP families between species. Eight test species within the Malvids clade shared distinct CYP paralogs from their common ancestor. All paralogous pairs in each pomegranate CYP family showed a low ratio of Ka/Ks (<1), indicating that some replacement substitutions inner CYP family have been purified by natural selection, presumably because of their deleterious effects. Our findings provide a resource for the taxonomic and evolutionary study on plant CYP families.","PeriodicalId":130142,"journal":{"name":"Proceedings of the 5th International Conference on Bioinformatics and Computational Biology","volume":"406 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122787477","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: 1

Walsh-hadamard transform of DNA methylation profile for the classification of human cancer cells DNA甲基化谱的Walsh-hadamard转化用于人类癌细胞的分类

Proceedings of the 5th International Conference on Bioinformatics and Computational Biology Pub Date : 2017-01-06 DOI: 10.1145/3035012.3035026

Xueyuan Zhao, D. Pompili

引用次数: 3

Medical X-ray image enhancement method based on dark channel prior 基于暗通道先验的医用x射线图像增强方法

Proceedings of the 5th International Conference on Bioinformatics and Computational Biology Pub Date : 2017-01-06 DOI: 10.1145/3035012.3035020

Wang Rui, W. Guoyu

引用次数: 7

Predicting potential gene ontology from cellular response data 从细胞反应数据预测潜在的基因本体

Proceedings of the 5th International Conference on Bioinformatics and Computational Biology Pub Date : 2017-01-06 DOI: 10.1145/3035012.3035015

Hao Hong, Xiaoyao Yin, Fei Li, Naiyang Guan, Xiaochen Bo, Zhigang Luo

{"title":"Predicting potential gene ontology from cellular response data","authors":"Hao Hong, Xiaoyao Yin, Fei Li, Naiyang Guan, Xiaochen Bo, Zhigang Luo","doi":"10.1145/3035012.3035015","DOIUrl":"https://doi.org/10.1145/3035012.3035015","url":null,"abstract":"Ontologies have proven to be useful for capturing and organizing knowledge as a hierarchical set of terms and their relationships. However, curating gene ontology data by hand requires specialized knowledge of certain field, which is inefficient. Thus inferring gene ontology from the exponentially increased biological data is getting hot. Based on the Library of Integrated Network-Based Cellular Signatures (LINCS) data we came up with the hypothesis that genes participate in analogous biological processes might affect cells accordantly. By assessing cellular response after genes were knock out we built a similarity matrix with the Gene Set Enrichment Analysis (GSEA) and clustered the genes with affinity propagation algorithm. Next we mapped the cluster result to gene ontology biological process data for annotation and enrichment analysis, which confirmed our hypothesis and made it possible to predict biological processes for unannotated genes from cellular response data after genes are knock out for the first time. We further validated the rationality from the gene ontology molecular function data.1","PeriodicalId":130142,"journal":{"name":"Proceedings of the 5th International Conference on Bioinformatics and Computational Biology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129256248","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

Proceedings of the 5th International Conference on Bioinformatics and Computational Biology 第五届生物信息学与计算生物学国际会议论文集

Proceedings of the 5th International Conference on Bioinformatics and Computational Biology Pub Date : 1900-01-01 DOI: 10.1145/3035012

引用次数: 0