2011 IEEE International Conference on Systems Biology (ISB)最新文献_第4页

Bifurcation of an epidemic model with sub-optimal immunity and saturated recovery rate 具有次优免疫和饱和恢复率的流行病模型的分岔

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033148

Chang Phang, Yong Hong Wu

引用次数: 0

An identification of secondary structure conserved elements in mammalian syntenic regions 哺乳动物同属区二级结构保守元件的鉴定

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033182

Toutai Mituyama

引用次数: 0

Copy number detection using self-weighted least square regression 使用自加权最小二乘回归的拷贝数检测

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033119

Xiao-Rong Yang, Ke-Ang Fu

引用次数: 0

Context-specific miRNA regulation network predicts cancer prognosis 情境特异性miRNA调控网络预测癌症预后

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033159

Xionghui Zhou, Juan Liu, Changning Liu, S. Rayner, Fengji Liang, J. Ju, Yinghui Li, Shanguang Chen, J. Xiong

引用次数: 6

Analyzing time-course gene expression data using profile-state hidden Markov model 利用谱态隐马尔可夫模型分析时间过程基因表达数据

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033177

Qiang Huang, Ling-Yun Wu, Jibin Qu, Xiang-Sun Zhang

引用次数: 6

Comparative genomics revealed a novel DNA-binding regulatory protein involved in homologous recombination in bacteria 比较基因组学揭示了一种新的参与细菌同源重组的dna结合调控蛋白

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033142

Yang Gao, Yan Zhang

{"title":"Comparative genomics revealed a novel DNA-binding regulatory protein involved in homologous recombination in bacteria","authors":"Yang Gao, Yan Zhang","doi":"10.1109/ISB.2011.6033142","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033142","url":null,"abstract":"Homologous recombination is a fundamental cellular process that is most widely used by cells to rearrange genes and accurately repair DNA double-strand breaks. It may result in the formation of a critical intermediate named Holliday junction, which is a four-way DNA junction and needs to be resolved to allow chromosome segregation. Different Holliday junction resolution systems and enzymes have been characterized from all three domains of life. In bacteria, the RuvABC complex is the most important resolution system. In this study, we conducted comparative genomics studies to identify a novel DNA-binding protein, YebC, which may serve as a key regulator of RuvABC resolvasome. On the other hand, the presence of YebC orthologs in some organisms lacking RuvC implied that it might participate in other biological processes. Further phylogenetic analysis of YebC protein sequences revealed two functionally different subtypes of this family: YebC_I and YebC_II. Only YebC_I subgroup may play an important role in regulating RuvABC gene expression in bacteria. Investigation of YebC-like proteins in eukaryotes suggested that they may have originated from YebC_II proteins and evolved a new function as a specific translational activator in mitochondria. Finally, additional phylum-specific genes associated with Holliday junction resolution were predicted. Overall, this study provides new insight into the basic mechanism of Holliday junction resolution and homologous recombination in bacteria.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130921445","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

Detecting B-cell lymphomas dysregulation modules based on molecular interaction network 基于分子相互作用网络的b细胞淋巴瘤失调模块检测

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033127

Fuyan Hu, Xingming Zhao

引用次数: 0

Identifying temporal trace of biological process during phase transition 识别相变过程中生物过程的时间轨迹

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033180

Tao Zeng, Luonan Chen

{"title":"Identifying temporal trace of biological process during phase transition","authors":"Tao Zeng, Luonan Chen","doi":"10.1109/ISB.2011.6033180","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033180","url":null,"abstract":"Phase transition widely exists in the biological world, such as the transformation of cell cycle phases, cell differentiation stages, cancer development steps, and so on. These are considered as the conversions of a genetic system from one phenotype/genotype to another. In previous studies, the molecular mechanisms of biological phase transition have attracted much attention, in particular, on the different genotypes related to specific phase but less of focus on the cascade of genes' functions during the phase change. However, it is a fundamental but important mission to track the temporal characteristics of a genetic system during specific phase transition or process, which can offer clues for understanding life and advancing its quality. By overcoming the hurdles of traditional time segmentation and temporal biclustering methods, a causal process model (CPM) in the present work is proposed to study the biological phase transition in a systematic way: boundary gene estimation for gene-specific segmentation and temporal block construction for whole data division. After the computational validation on synthetic data, CPM was used to analyze the well-known Yeast cell cycle data to identify the time periods of six phases in two cell cycles, and revealed phase/cycle related biological processes. These primary results demonstrate that CPM is efficient comparing to traditional methods, and has potential to elucidate the genetic mechanism with more complicated phase transitions.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127170050","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

Antiallodynic effects of microglial interleukin-1β inhibition in the spinal cord 脊髓小胶质细胞白介素-1β抑制的抗异动作用

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033144

Yu-Xia Chu, Min Wang, M. Yao, Xin-mei Zhou, Xia-Ying Du, Xiao Wan, Zi-Fang Li, Mengyin Zhu, Xiao Chen

引用次数: 0

The preservation of bidirectional promoter architecture in Eukaryotes - Functional or co-regulation constraint? 真核生物中双向启动子结构的保存——功能约束还是共调控约束?

2011 IEEE International Conference on Systems Biology (ISB) Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033157

Chao Xu, Jiajia Chen, Bairong Shen

{"title":"The preservation of bidirectional promoter architecture in Eukaryotes - Functional or co-regulation constraint?","authors":"Chao Xu, Jiajia Chen, Bairong Shen","doi":"10.1109/ISB.2011.6033157","DOIUrl":"https://doi.org/10.1109/ISB.2011.6033157","url":null,"abstract":"The bidirectional promoter architecture has been reported in many organisms, and the conservation of bidirectional arrangement has also been studied in several former researches. However, the explanation for the evolutionary conservation about this genomic structure is still insufficient. In this study the large scale identification and pathway enrichment analysis for bidirectional genes were performed in several eukaryotes, and the comparative analysis of this arrangement between human and mouse were dissected for the purpose of discovering the drive force of the preservation of this genomic structure. The comparative analysis about the gene expression and biological functions between human and mouse bidirectional genes were performed. It was observed that the selective constraint of this architecture mainly derives from the function bias of bidirectional genes rather than the co-regulation between paired genes. The results of our analyses indicated that the bidirectional genes are conserved in pathway level and the potential selective constraints of bidirectional architecture conservation comes from the gene function preference rather than the co-regulation of paired genes' expression.","PeriodicalId":355056,"journal":{"name":"2011 IEEE International Conference on Systems Biology (ISB)","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128153192","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