基于复杂网络的风险传播模型及有效算法

提出一种基于复杂网络的风险传播模型及有效算法，通过结合复杂网络中传播蔓延现象的推广模型，将风险传播模型划分为两种：主动型风险传播模型与被动型风险传播模型。并对已有风险传播算法进行改进，实验表明，该模型及算法能健全风险传播机制，提高传播速度与精确度。     

酵母基因表达调控关系的构建及其统计特性分析

[目的]从复杂网络的角度研究酵母细胞周期调控网络的统计特性。[方法]首先对酵母的细胞周期基因表达数据采用皮尔逊相关性度量,计算基因间的关联矩阵,即建立简单的基因调控网络;同时为了能够得到在宏观角度对大规模的基因调控有一个全貌的了解,进一步分析所建立调控网络的统计特性,通过计算所建立网络的统计特性：即计算网络的聚类系数、平均路径长度和网络的度分布。[结论]发现所建立的网络具有无标度和小世界特性,即所建立的酵母基因调控网络属于复杂网络,这为进一步深入研究基因调控网络的统计学和动力学特性打下了基础。     

Gene regulation in the third dimension

Analysis of the spatial organization of chromosomes reveals complex three-dimensional networks of chromosomal interactions. These interactions affect gene expression at multiple levels, including long-range control by distant enhancers and repressors, coordinated expression of genes, and modification of epigenetic states. Major challenges now include deciphering the mechanisms by which loci come together and understanding the functional consequences of these often transient associations.     

Regulatory blueprint for a chordate embryo

Ciona is an emerging model system for elucidating gene networks in development. Comprehensive in situ hybridization assays have identified 76 regulatory genes with localized expression patterns in the early embryo, at the time when na?ve blastomeres are determined to follow specific cell fates. Systematic gene disruption assays provided more than 3000 combinations of gene expression profiles in mutant backgrounds. Deduced gene circuit diagrams describing the formation of larval tissues were computationally visualized. These diagrams constitute a blueprint for the Ciona embryo and provide a foundation for understanding the evolutionary origins of the chordate body plan.     

用人工神经网络模拟土体塌陷的可行性分析

探讨了利用人工神经网络预测土体塌陷与土体参数和荷载条件之间关系的可行性。BP神经网络是最常用的神经网络之一,通过网络训练,最终确定了6个变量即输入信息、8个隐层和1个输出层的网络结构。在比较了预测值与试验值后,进一步证实了人工神经网络在评估土体塌陷方面效果明显。     

Information transduction capacity of noisy biochemical signaling networks

Molecular noise restricts the ability of an individual cell to resolve input signals of different strengths and gather information about the external environment. Transmitting information through complex signaling networks with redundancies can overcome this limitation. We developed an integrative theoretical and experimental framework, based on the formalism of information theory, to quantitatively predict and measure the amount of information transduced by molecular and cellular networks. Analyzing tumor necrosis factor (TNF) signaling revealed that individual TNF signaling pathways transduce information sufficient for accurate binary decisions, and an upstream bottleneck limits the information gained via multiple integrated pathways. Negative feedback to this bottleneck could both alleviate and enhance its limiting effect, despite decreasing noise. Bottlenecks likewise constrain information attained by networks signaling through multiple genes or cells.     

Global mapping of the yeast genetic interaction network

A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.     

木材无损检测技术中的应力波传播时延估计算法

为了准确测量应力波在木材内部的传播时间,提高木材内部缺陷识别的精度,提出了一种基于小波变换和高阶统计量的广义相关时延估计算法。该方法利用滤波算法,将采集到的应力波信号进行滤波去噪,然后输入到广义互相关时延模型,求出传播时延估计值。仿真和实际的木材检测实验结果表明:提出的算法比传统的定时器计时法时延估计精度提高81.5%,并具有较强的抗干扰能力。     

基于WGCNA的棉花子叶抗冷相关共表达模块鉴定

权重基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)是系统生物学的一种研究方法,在多样本转录组数据中挖掘与目标性状相关的基因模块应用较广泛.为深入探究棉花应对冷害胁迫的分子机制,以4℃低温处理不同时间点的2个棉花品种(新陆中16和新陆中32)幼苗...     

水稻披垂叶突变基因研究进展

水稻是重要的粮食作物,全球有超过50%的人口以稻米作为主食。同时水稻又作为一种模式生物被各大研究机构所研究。水稻披垂叶突变体是由于控制水稻中脉形成的基因发生突变,导致基因发生功能缺失,使水稻叶片中脉的形成不能正常进行,从而出现披垂叶的性状。目前已经发现2个基因位点与水稻中脉形成有关,DL和DL2基因正是这2个不同的位点。研究水稻披垂叶突变基因,对研究水稻叶中脉的形成以及水稻理想株型的选育有重要的意义。对水稻披垂叶突变基因的研究进展进行综述,以对水稻这一类特殊株型得到更好地了解。     

A gene expression map for Caenorhabditis elegans

We have assembled data from Caenorhabditis elegans DNA microarray experiments involving many growth conditions, developmental stages, and varieties of mutants. Co-regulated genes were grouped together and visualized in a three-dimensional expression map that displays correlations of gene expression profiles as distances in two dimensions and gene density in the third dimension. The gene expression map can be used as a gene discovery tool to identify genes that are co-regulated with known sets of genes (such as heat shock, growth control genes, germ line genes, and so forth) or to uncover previously unknown genetic functions (such as genomic instability in males and sperm caused by specific transposons).     

Host-parasite coevolutionary conflict between Arabidopsis and downy mildew

Plants are constantly exposed to attack by an array of diverse pathogens but lack a somatically adaptive immune system. In spite of this, natural plant populations do not often suffer destructive disease epidemics. Elucidating how allelic diversity within plant genes that function to detect pathogens (resistance genes) counteracts changing structures of pathogen genes required for host invasion (pathogenicity effectors) is critical to our understanding of the dynamics of natural plant populations. The RPP13 resistance gene is the most polymorphic gene analyzed to date in the model plant Arabidopsis thaliana. Here we report the cloning of the avirulence gene, ATR13, that triggers RPP13-mediated resistance, and we show that it too exhibits extreme levels of amino acid polymorphism. Evidence of diversifying selection visible in both components suggests that the host and pathogen may be locked in a coevolutionary conflict at these loci, where attempts to evade host resistance by the pathogen are matched by the development of new detection capabilities by the host.     

人类1号染色体可变剪接与普通剪接基因同义密码子的使用分析Ⅱ.基因表达水平和基因长度与密码子使用偏爱

进一步研究基因表达水平和基因长度与密码子使用偏爱之间的关系.多变量统计分析发现,人类1号染色体选择性剪接基因和普通剪接基因密码子使用变化都呈现单一趋势,且它们之间的密码子使用模式也非常相似,推测的高表达基因确实偏爱以 C或G结尾的密码子,基因表达水平与密码子使用偏爱之间的关联也达到显著水平.因此,人类1号染色体高表达基因密码子的使用偏爱可能主要被翻译选择所决定.此外,基因长度与密码子偏爱水平之间也存在高度相关,说明相对较短的基因具有较高的密码子使用偏爱,翻译选择可能缩短了高表达基因的长度从而提高翻译效率.     

运用布尔网络模型和贝叶斯网络模型推测基因调控网络的比较研究

基因调控网络的研究从基因之间相互作用的角度揭示复杂的生命现象,是功能基因组学研究的重要内容,也是当前生物信息学研究的前沿。布尔网络模型和贝叶斯网络模型都是研究基因调控网络的有力工具。本文分别采用布尔网络模型和贝叶斯网络模式推测基因调控网络,实验结果显示布尔网络推测出了7条正确的调控关系,而贝叶斯网络仅推测出5条正确的调控关系,在本实验中推测基因之间的调控关系正确数布尔网络模型优于贝叶斯网络模型。     

Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization

Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.