Proceedings of the ... Asia-Pacific bioinformatics conference最新文献_第8页

System Identification and Robustness Analysis of the Circadian Regulatory Network via Microarray Data in Arabidopsis Thaliana 基于微阵列数据的拟南芥昼夜节律调节网络系统识别和稳健性分析

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0006

C. Li, W. Chang, B. S. Chen

{"title":"System Identification and Robustness Analysis of the Circadian Regulatory Network via Microarray Data in Arabidopsis Thaliana","authors":"C. Li, W. Chang, B. S. Chen","doi":"10.1142/9781860947292_0006","DOIUrl":"https://doi.org/10.1142/9781860947292_0006","url":null,"abstract":"The circadian regulatory network is one of the main topics of plant investigations. The intracellular interactions among genes in response to the environmental stimuli of light are related to the foundation of functional genomics in plant. However, the sensitivity analysis of the circadian system has not analyzed by perturbed stochastic dynamic model via microarray data in plant. In this study, the circadian network is constructed for Arabidopsis thaliana using a stochastic dynamic model with sigmoid interaction, activation delay, and regulation of input light taken into consideration. The describing function method in nonlinear control theory about nonlinear limit cycle (oscillation) is employed to interpret the oscillations of the circadian regulatory networks from the viewpoint that nonlinear network will continue to oscillate if its feedback loop gain is equal to 1 to support the oscillation of circadian network. Based on the dynamic model via microarray data, the system sensitivity analysis is performed to assess the robustness of circadian regulatory network via biological perturbations. We found that the circadian network is more sensitive to the perturbation of the trans-expression threshold, is more sensitive to the activation level of steady state, rather than the trans-sensitivity rate.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2005-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80584103","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

Identification of MicroRNA Precursors via SVM 基于支持向量机的MicroRNA前体鉴定

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0030

L. Yang, W. Hsu, M. Lee, L. Wong

引用次数: 4

Automating the Search for Lateral Gene Transfer 自动搜索横向基因转移

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0002

M. Ragan

{"title":"Automating the Search for Lateral Gene Transfer","authors":"M. Ragan","doi":"10.1142/9781860947292_0002","DOIUrl":"https://doi.org/10.1142/9781860947292_0002","url":null,"abstract":"Most genes have attained their observed distribution among ge omes by transmission from parent to offspring through time. In prokaryotes (bacteria and archa ea), however, some genes are where they are as the result of transfer from an unrelated lineage. To el ucidate the biological origins and functional consequences of lateral gene transfer (LGT), we have constructed an automated computational pipeline to recognise protein families among prokaryotic g enomes, generate high-quality multiple sequence alignments of orthologs, infer statistically sound phylogenetic trees, and find topologically incongruent subtrees (prima facie instances of LGT). This pip eline requires that we automate workflows, design and optimize algorithms, mobilise high-performanc e computing resources, and efficiently manage federated data. I will summarise results from the automa ted comparison of 422971 proteins in 22437 families across 144 sequenced prokaryotic genomes, i nclud ng the nature and extent of LGT among these lineages, major donors and recipients, the bioc hemi al pathways and physiological functions most affected, and implications for the role of LGT in e volution of biochemical pathways.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2005-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80408853","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

Property-Dependent Analysis of Aligned Proteins from Two Or More Populations 来自两个或多个群体的对齐蛋白的特性依赖分析

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0020

Steinar Thorvaldsen, E. Ytterstad, T. Flå

引用次数: 6

Consequences of Mutation, Selection, and Physico-Chemical Properties of Encoded Proteins on Synonymous Codon Usage in Adenoviruses 腺病毒中编码蛋白的突变、选择和理化性质对同义密码子使用的影响

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0018

Sandip Paul, Sabyasachi Das, C. Dutta

{"title":"Consequences of Mutation, Selection, and Physico-Chemical Properties of Encoded Proteins on Synonymous Codon Usage in Adenoviruses","authors":"Sandip Paul, Sabyasachi Das, C. Dutta","doi":"10.1142/9781860947292_0018","DOIUrl":"https://doi.org/10.1142/9781860947292_0018","url":null,"abstract":"Trends in synonymous codon usage in adenoviruses have been examined through the multivariate statistical analysis on the annotated protein-coding regions of 22 adenoviral species, for which complete genome sequences are available. One of the major determinants of such trends is the G + C content at third codon positions of the genes, the average value of which varied from one viral genome to other depending on the overall mutational bias of the species. G3S and C3S interacted synergistically along the first principal axis of Correspondence analysis on the Relative Synonymous Codon Usage of adenoviral genes, but antagonistically along the second principal axis. Other major determinants of the trends are the natural selection, putatively operative at the level of translation and quite interestingly, hydropathy of the encoded proteins. The trends in codon usage, though characterized by distinct virus-specific mutational bias, do not exhibit any sign of host-specificity. Significant variations are observed in synonymous codon choice in structural and nonstructural genes of adenoviruses.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2005-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82581336","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

Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes 鉴定共表达基因组中转录因子结合位点的过度代表组合

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0028

S. Huang, Debra L. Fulton, David J. Arenillas, P. Perco, S. Sui, J. Mortimer, W. Wasserman

{"title":"Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes","authors":"S. Huang, Debra L. Fulton, David J. Arenillas, P. Perco, S. Sui, J. Mortimer, W. Wasserman","doi":"10.1142/9781860947292_0028","DOIUrl":"https://doi.org/10.1142/9781860947292_0028","url":null,"abstract":"Transcription regulation is mediated by combinatorial interactions between diverse trans-acting proteins and arrays of cis-regulatory sequences. Revealing this complex interplay between transcription factors and binding sites remains a fundamental problem for understanding the flow of genetic information. The oPOSSUM analysis system facilitates the interpretation of gene expression data through the analysis of transcription factor binding sites shared by sets of co-expressed genes. The system is based on cross-species sequence comparisons for phylogenetic footprinting and motif models for binding site prediction. We introduce a new set of analysis algorithms for the study of the combinatorial properties of transcription factor binding sites shared by sets of co-expressed genes. The new methods circumvent computational challenges through an applied focus on families of transcription factors with similar binding properties. The algorithm accurately identifies combinations of binding sites over-represented in reference collections and clarifies the results obtained by existing methods for the study of isolated binding sites.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2005-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75677973","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: 11

Genome Wide Computational Analysis of Small Nuclear RNA Genes for Oryza Sativa (Indica and Japonica) 水稻(籼稻和粳稻)核小RNA基因全基因组计算分析

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0031

M. Shashikanth, A. Snethalatharani, S. Mubarak, K. Ulaganathan

{"title":"Genome Wide Computational Analysis of Small Nuclear RNA Genes for Oryza Sativa (Indica and Japonica)","authors":"M. Shashikanth, A. Snethalatharani, S. Mubarak, K. Ulaganathan","doi":"10.1142/9781860947292_0031","DOIUrl":"https://doi.org/10.1142/9781860947292_0031","url":null,"abstract":"Genome-wide computational analysis for small nuclear RNA (snRNA) genes resulted in identification of 76 and 73 putative snRNA genes from indica and japonica rice genomes, respectively. We used the basic criteria of a minimum of 70 % sequence identity to the plant snRNA gene used for genome search, presence of conserved promoter elements: TATA box, USE motif and monocot promoter specific elements (MSPs) and extensive sequence alignment to rice / plant expressed sequence tags to denote predicted sequence as snRNA genes. Comparative sequence analysis with snRNA genes from other organisms and predicted secondary structures showed that there is overall conservation of snRNA sequence and structure with plant specific features (presence of TATA box in both polymerase II and III transcribed genes, location of USE motif upstream to the TATA box at fixed but different distance in polymerase II and polymerase III transcribed snRNA genes) and the presence of multiple monocot specific MSPs upstream to the USE motif. Detailed analysis results including all multiple sequence alignments, sequence logos, secondary structures, sequences etc are available at http://kulab.org","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2005-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91443933","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

EDAM: An Efficient Clique Discovery Algorithm with Frequency Transformation for Finding Motifs 基于频率变换的高效团块发现算法

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0015

Yifei Ma, Guoren Wang, Yongguang Li, Yuhai Zhao

引用次数: 0

Gene Expression Data Clustering Based on Local Similarity Combination 基于局部相似组合的基因表达数据聚类

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0038

De Pan, Fei Wang

引用次数: 0

A Recursive Method for Solving Haplotype Frequencies in Multiple Loci Linkage Analysis 多位点连锁分析中单倍型频率的递归求解方法

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2005-12-01 DOI: 10.1142/9781860947292_0016

M. Ng

引用次数: 0