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2011 IEEE International Conference on Systems Biology (ISB)最新文献

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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
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033148
Chang Phang, Yong Hong Wu
In this paper, we study the bifurcation of an epidemic model with sub-optimal immunity and saturated treatment/recovery rate. Different from classical models, sub-optimal models are more realistic to explain the microparasite infections disease such as Pertussis and Influenza A. By carrying out the bifurcation analysis of the model, we show that for certain values of the model parameters, Hopf bifurcation, Bogdonov-Takens bifurcation and its associated homoclinic bifurcation occur. By studying the bifurcation curves, we can predict the persistence or extinction of diseases.
本文研究了一类具有次优免疫和饱和治疗/恢复率的流行病模型的分支问题。与经典模型不同,次优模型对百日咳和甲型流感等微寄生虫感染疾病的解释更为现实。通过对模型的分岔分析,我们发现在模型参数的一定值下,会出现Hopf分岔、Bogdonov-Takens分岔及其相关的同宿分岔。通过研究分岔曲线,我们可以预测疾病的持续或灭绝。
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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
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033182
Toutai Mituyama
3,361 putative RNA secondary structure conserved regions were identified from mammalian syntenies by using leading-edge RNA sequence data analysis tools. The identified candidates are found to be concentrated in transcription factor binding sites of various genes, which infer secondary structure conserved elements play certain roles for transcription regulation.
利用先进的RNA序列数据分析工具,从哺乳动物共系中鉴定出3361个假定的RNA二级结构保守区。发现候选基因集中在不同基因的转录因子结合位点,推测二级结构保守元件在转录调控中起一定作用。
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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
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033119
Xiao-Rong Yang, Ke-Ang Fu
In this article, an efficient algorithm to detect the breakpoints in DNA copy number alterations is considered. In view of the influence of the heavy noises, the self-weighted least square estimation is adopted to downweight the covariance matrix of the wild observations (outliers), which ensure the convergence between the estimated parameters and the true values. The proposed approach makes use of the most of the data itself to reduces the complexity of the model, and presents an insightful discussion for discovery of copy number alterations.
本文研究了一种检测DNA拷贝数变化断点的有效算法。针对重噪声的影响,采用自加权最小二乘估计对野观测值(离群值)的协方差矩阵进行降权处理,保证了估计参数与真值的收敛性。所提出的方法利用了大部分数据本身来降低模型的复杂性,并对发现拷贝数变化提出了有见地的讨论。
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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
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
MicroRNAs can regulate hundreds of target genes and play a pivotal role in a broad range of biological process. However, relatively little is known about how these highly connected miRNAs-target networks are remodelled in the context of various diseases. Here we examine the dynamic alteration of context-specific miRNA regulation to determine whether modified microRNAs regulation on specific biological processes is a useful information source for predicting cancer prognosis. A new concept, Context-specific miRNA activity (CoMi activity) is introduced to describe the statistical difference between the expression level of a miRNA's target genes and non-targets genes within a given gene set (context).
microrna可以调控数百个靶基因,在广泛的生物过程中发挥关键作用。然而,对于这些高度连接的mirna靶标网络如何在各种疾病的背景下被重塑,人们知之甚少。在这里,我们研究了上下文特异性miRNA调控的动态变化,以确定修饰的microrna对特定生物过程的调控是否是预测癌症预后的有用信息源。引入了一个新概念,上下文特异性miRNA活性(CoMi活性),用于描述给定基因集(上下文)中miRNA靶基因和非靶基因表达水平之间的统计差异。
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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
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033177
Qiang Huang, Ling-Yun Wu, Jibin Qu, Xiang-Sun Zhang
More and more gene expression data are available due to the rapid development of high-throughput experimental techniques such as microarray and next generation sequencing (NGS). The gene expression data analysis is still one of the fundamental tasks in bioinformatics. In this paper, we propose a new profile-state hidden Markov model (HMM) for analyzing time-course gene expression data, which gives a new point of view to explain the variation of gene expression and regulation in different time. This model addresses the bicluster problem in time-course data efficiently and can identify the irregular shape and overlapping biclusters. The comprehensive computational experiments on simulated and real data show that the new method is effective and useful.
由于微阵列和下一代测序等高通量实验技术的快速发展,越来越多的基因表达数据可用。基因表达数据分析仍然是生物信息学的基本任务之一。本文提出了一种新的用于分析时间过程基因表达数据的谱态隐马尔可夫模型(HMM),为解释基因在不同时间的表达和调控变化提供了新的视角。该模型有效地解决了时间过程数据中的双聚类问题,能够识别不规则形状和重叠的双聚类。仿真和实际数据的综合计算实验表明了该方法的有效性和实用性。
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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
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033142
Yang Gao, Yan Zhang
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.
同源重组是一种基本的细胞过程,被细胞广泛用于基因重组和DNA双链断裂的精确修复。它可能导致形成一个称为Holliday结的关键中间物,这是一个四向DNA结,需要被分解以允许染色体分离。不同的Holliday结分解系统和酶已经从生命的所有三个领域被表征。在细菌中,RuvABC复合体是最重要的分解系统。在这项研究中,我们进行了比较基因组学研究,以鉴定一种新的dna结合蛋白YebC,它可能是RuvABC分解体的关键调节因子。另一方面,在一些缺乏RuvC的生物体中存在YebC同源物,这意味着它可能参与其他生物过程。对YebC蛋白序列的进一步系统发育分析揭示了该家族的两个功能不同的亚型:YebC_I和YebC_II。只有YebC_I亚群可能在细菌RuvABC基因表达调控中起重要作用。对真核生物中yebc样蛋白的研究表明,它们可能起源于YebC_II蛋白,并在线粒体中进化出一种特异性翻译激活剂的新功能。最后,预测了与Holliday结分辨率相关的其他门特异性基因。总之,本研究对细菌Holliday结分解和同源重组的基本机制提供了新的认识。
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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
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033127
Fuyan Hu, Xingming Zhao
Identifying dysregulation modules for complex diseases, such as B-cell lymphomas, can provide insights into the mechanisms of diseases and help to identify novel drug targets. In this work, based on molecular interaction network, we applied a network flow model to identify the dysregulation modules for three subtypes of non-Hodgkin's lymphomas, including Burkitt's lymphoma (BL), follicular lymphoma (FL), and mantle cell lymphoma (MCL). In our identified dysregulation modules, there are multiple genes that were reported in literature to be related to B-cell lymphomas, which demonstrate that our presented method is really effective for identifying dysregulation modules related to diseases.
识别复杂疾病的失调模块,如b细胞淋巴瘤,可以提供对疾病机制的见解,并有助于确定新的药物靶点。在这项工作中,我们基于分子相互作用网络,应用网络流模型来识别三种非霍奇金淋巴瘤亚型的失调模块,包括伯基特淋巴瘤(BL)、滤泡性淋巴瘤(FL)和套细胞淋巴瘤(MCL)。在我们确定的失调模块中,有多个基因被文献报道与b细胞淋巴瘤相关,这表明我们提出的方法对于识别与疾病相关的失调模块是非常有效的。
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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
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033180
Tao Zeng, Luonan Chen
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.
相变广泛存在于生物界,如细胞周期阶段的转变、细胞分化阶段的转变、肿瘤发生步骤的转变等。这些被认为是遗传系统从一种表型/基因型到另一种表型/基因型的转换。在以往的研究中,生物相变的分子机制主要关注与特定相变相关的不同基因型,而对相变过程中基因功能的级联性研究较少。然而,追踪遗传系统在特定相变或过程中的时间特征是一项基本而重要的任务,它可以为认识生命和提高生命质量提供线索。为了克服传统的时间分割和时间双聚类方法的缺陷,本文提出了一种基于因果过程模型(CPM)的生物相变系统研究方法:基于基因特异性分割的边界基因估计和基于全数据分割的时间块构建。在对合成数据进行计算验证后,利用CPM对众所周知的酵母细胞周期数据进行分析,确定了两个细胞周期中6个相的时间周期,揭示了相/周期相关的生物学过程。这些初步结果表明,CPM方法与传统方法相比是有效的,并且具有阐明更复杂相变的遗传机制的潜力。
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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
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
Microglia play a pivotal role in synaptic plasticity of chronic pain. In this study, the potential role of interleukin 1beta (IL-1β), mainly released by microglia in early stage of nerve injury, in mechanical allodynia induced by tetanic stimulation of the sciatic nerve (TSS) was examined. Mechanical allodynia was observed on both ipsilateral and contralateral sides of TSS. Moreover, the expression of the microglial marker Iba-1 and the proinflammatory cytokine IL-1β were significantly increased. Intrathecal injection of the IL-1 receptor antagonist (IL-1ra, 3.5 µg/ml, 20 µl/rat) 30 min before TSS significantly inhibited bilateral mechanical allodynia on day 3, 5 and 7 after TSS. Immunohistochemistry showed that IL-1β was colocalized with the microglial marker OX-42 in the spinal superficial dorsal horn, but not with the astrocytic marker GFAP and the neuronal marker NeuN on day 4 following TSS. The results demonstrate that microglial IL-1β participates in the hypersensitivity of pain behaviors induced by TSS.
小胶质细胞在慢性疼痛的突触可塑性中起关键作用。本研究探讨了主要由小胶质细胞在神经损伤早期释放的白细胞介素1β (IL-1β)在强直刺激坐骨神经(TSS)引起的机械性异常性痛中的潜在作用。在TSS的同侧和对侧均观察到机械异常性疼痛。此外,小胶质细胞标志物Iba-1和促炎细胞因子IL-1β的表达显著升高。TSS前30分钟鞘内注射IL-1受体拮抗剂(IL-1ra, 3.5µg/ml, 20µl/大鼠)可显著抑制TSS后第3、5、7天的双侧机械异常性痛。免疫组织化学显示,在TSS后第4天,IL-1β与脊髓浅背角的小胶质细胞标志物OX-42共定位,而与星形胶质细胞标志物GFAP和神经元标志物NeuN不共定位。结果表明,小胶质细胞IL-1β参与了TSS诱导的疼痛行为的超敏反应。
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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?
Pub Date : 2011-10-03 DOI: 10.1109/ISB.2011.6033157
Chao Xu, Jiajia Chen, Bairong Shen
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.
双向启动子结构在许多生物中都有报道,一些先前的研究也对双向排列的保护进行了研究。然而,对这种基因组结构的进化保守性的解释仍然不足。本研究在几种真核生物中进行了双向基因的大规模鉴定和通路富集分析,并对人类和小鼠的这种排列进行了比较分析,以发现这种基因组结构保存的驱动力。对人和小鼠双向基因的表达和生物学功能进行了比较分析。结果表明,该结构的选择性约束主要来自于双向基因的功能偏倚,而非配对基因之间的协同调控。我们的分析结果表明,双向基因在通路水平上是保守的,双向结构保守的潜在选择约束来自基因功能偏好,而不是成对基因表达的共同调控。
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引用次数: 2
期刊
2011 IEEE International Conference on Systems Biology (ISB)
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