Mining the draft human genome

Now that the draft human genome sequence is available, everyone wants to be able to use it. However, we have perhaps become complacent about our ability to turn new genomes into lists of genes. The higher volume of data associated with a larger genome is accompanied by a much greater increase in complexity. We need to appreciate both the scale of the challenge of vertebrate genome analysis and the limitations of current gene prediction methods and understanding.     

数据科学范式下的钙钛矿结构铁电新材料研究

 材料基因组计划倡导预测式新材料研发理念，推进高通量数据生产和利用技术，关注材料全生命周期价值。因此，材料基因组计划的执行需要在材料科学系统工程的框架下，集成统一计算、实验和理论等研究方法，以数据科学新范式为牵引、协同运用实验观测、理论建模和计算仿真研究范式，最终建立相关材料体系的性能与材料基因（原子系统的组成与结构）、工艺参数与使役条件之间的量化关系和数据库，实现新材料的按需设计和应用。本文在简单探讨科学研究范式、材料基因组计划和材料科学系统工程基本概念和方法的基础上，以钙钛矿结构氧化物铁电压电材料研究为例，探讨了数据科学范式下的新材料研究实践。结果表明，数据挖掘驱动的新材料设计确实可以降低探索时间和实验任务，加快新材料的发现和应用进程。     

The ring of life provides evidence for a genome fusion origin of eukaryotes

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.     

大肠杆菌基因组的组构

以１９９３年４月为止的ＤＮＡ序列资料为依据，讨论了一年来大肠杆菌基因的研究进展，并以日本和美国科学家分别完成的两大片段的序列资料为中心，评述了大肠杆菌基因组的组成特点及其生物学意义．     

Mapping and sequencing of structural variation from eight human genomes

Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.     

能源植物高粱基因组研究进展

 回顾了高粱基因组学研究的发展进程, 概述了初期组学数据的积累、参考基因组的破译及新一代测序技术和数据分析方法引领下的组学研究进展;介绍了高粱基因组的结构, 从比较基因组学的角度, 分析了高粱基因组的进化及其特性;探讨了高粱功能基因组的研究方法和研究进展, 总结了已经发掘的高粱关键基因和遗传位点, 对高粱组学数据资源进行了归纳。对高粱基因组学的发展方向进行了展望。     

The materials genome and CALPHAD

The mapping of the human genome is an important basis for the development of new medicals and medical treatments.Consequently,it has attracted tremendous research funding over the last decade.On June2011,the Materials Genome Initiative was announced by the US President Obama as collaboration on modeling and advanced materials databases.Unfortunately,the materials genome was given a rather vague definition in the announcement.However,the materials genome should be defined in analogy with biological genomes and one may then conclude that:at any moment,the performance of a specific material depends on its chemical composition(inherent property stored in its genome)and its environment(external interactions–processing–conditions during usage).The materials genome should thus be defined as a set of information encoded in the language of thermodynamics obtained by careful assessment of experimental data and quantum mechanical calculations from which certain conclusions about the material can be drawn.The CALPHAD databases contain the thermodynamic and kinetic properties of a materials system.Such databases allow the prediction of materials structure as well as its response to processing and usage conditions,and are major parts of integrated computational materials engineering.     

材料基因组工程专用数据库

材料数据具有多源、异构、高维等特点, 收集纷繁复杂的材料数据, 建立材料基因工程专用数据库, 是实现数据驱动的新材料研发的基础. 以材料数据的规范化表示、机器学习建模及模型跨域部署、材料数据隐私保护下的机器学习、利用知识图谱从材料数据库到知识库等材料基因专用数据库的若干核心技术为基础, 介绍了材料基因数据库平台的系统架构及实现、平台超算部署及运行. 最后以反钙钛矿负膨胀材料为例, 介绍了材料基因工程数据库平台从数据归档到机器学习建模, 再到逆向设计, 以及最终实验验证的整个流程.     

基于基因次序的基因组问距离的计算

给出了计算两个具有相同内容、不同次序的基因组之间距离的算法.给定一组内容相同、次序不同的基因组,构造一个完全图,寻找一个基因组使得它与给定的各个基因组之间距离的累加和达到最小,这个问题可以转化为偈P问题.利用最小生成树方法找到一个中心基因组,接下来构造断点图,最后利用断点图来计算集合中的每一个基因组和中心基因组之间的距离.     

A high-resolution map of human evolutionary constraint using 29 mammals

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ～4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ～60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.     

The genomic mutation rate for fitness in Drosophila.

The mutation rate per genome for local affecting fitness is crucial in theories of the evolution of sex and recombination and of outbreeding mechanisms. Mutational variation in fitness may also be important in the evolution of mate choice in animals. No information is available on the rate at which spontaneous mutations with small effects on fitness arise, although viability (probability of survival to adulthood) has been studied in Drosophila melanogaster. These experiments involved the accumulation of spontaneous mutations in the virtual absence of natural selection, in a set of independently maintained lines with a common origin. The rates of decline in mean and increase in variance among lines permit estimation of limits to the mean number of new mutations arising per generation (U) and the average homozygous effect of a new mutation of minor effect(s). For the second chromosome of D. melanogaster, the value of U is at least 0.17 (ref. 7), and (1-h)s is less than 0.02, where hs is the average decline in fitness of heterozygotes. As the second chromosome is about 40% of the genome, these data indicate a mutation rate per haploid genome of at least 0.42 for viability. Here we present similar data on the effects of homozygous spontaneous mutations on a measure of fitness in D. melanogaster.     

Malaria research in the post-genomic era

For many pathogens the availability of genome sequence, permitting genome-dependent methods of research, can partially substitute for powerful forward genetic methods (genome-independent) that have advanced model organism research for decades. In 2002 the genome sequence of Plasmodium falciparum, the parasite causing the most severe type of human malaria, was completed, eliminating many of the barriers to performing state-of-the-art molecular biological research on malaria parasites. Although new, licensed therapies may not yet have resulted from genome-dependent experiments, they have produced a wealth of new observations about the basic biology of malaria parasites, and it is likely that these will eventually lead to new therapeutic approaches. This review will focus on the basic research discoveries that have depended, in part, on the availability of the Plasmodium genome sequences.     

应用生物信息学寻找大鼠中新的microRNA分子及其实验验证

大鼠已公布的microRNA(miRNA) 数量明显少于小鼠及人miRNA的数量.本文采用同源搜索的计算方法预测大鼠新的miRNA.从miRBase数据库中下载已知动物的pre- miRNAs, 在UCSC数据库中对大鼠的全基因组序列进行了Blat分析,并根据miRNAs的筛选标准,获得45条新的大鼠miRNAs;随后随机选取其中的9条新miRNAs进行RT- PCR实验验证,发现大部分miRNAs在脑、心、肺、肾、肌肉、脾、睾丸和肝8种组织中均有表达.在此基础上,对预测的新miRNAs进行了miRNA成簇分析和miRNA基因家族分析.     

黄连基因组勘测与分析

本研究基于下一代测序技术,对黄连基因组进行了勘测,构建了两个插入片段大小分别为200bp和500bp的文库,进行了深度约30X的测序。通过测序获得了54Gb的原始数据,过滤后得到44.8G数据。通过SOAP de nove软件组装后初步获得了contig和Scaffold序列,进一步分析结果显示其基因组大小为1,116Mb左右,大约具有1.1%的杂合度,说明要完成该物种的全基因测序可能在使用鸟枪法的同时,还应该联合BAC文库测序等多种方法.对这些数据进行了初步的组装,获得了130,381条scaffold序列.     

Comparative and demographic analysis of orang-utan genomes

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000?years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.