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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Yongbing Zhao Junhui Yang Jiayan Wu jingfa xiao CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences Graduate School of Chinese Academy of Sciences

The reducing cost of DNA sequencing and the increasing number of bacterial genome sequences have provided a chance to study the profile and evolution of microbial genome from population ***-genome,the genetic repertoire of a given species,comprises three parts including core genome,dispensable genome and strains-specific *** genome represents those genes shared by all strains,and these genes are mainly responsible for basic process of life and species major *** genome includes those genes shared by two or more,but not all strains,and strains-specific genome are genes shared by only one *** general,dispensable genes and strain-specific genes function in contribute to the species diversity and selective advantages,such as adaptation to different niche and antibiotic resistance or colonization of a new host,and sometimes strains-specific genes are related to *** the pan-genome was present in Streptococcus agalactiae genome analysis for the first time,pan-genome analysis was employed in more than forty-three bacterial species or ***,the key issue for pangenome analysis is how to select appropriate mathematical models to depict the bacterial pan-genome feature and detect homologs(gene or genome region) from multiple genome *** algorithms and pipelines were designed to identify orthologs genes and homologs regions from multiple species,such as inparanoid/multiparanoid,Mauve,PGAP and so *** pan-genome profile was indicated from the relationship between the strains number and new detected genes,strains specific genes and the whole gene pool size under various mathematical *** important aspect is to combine specific problems in biology with pan-genome *** these years,pan-genome analysis has shed a new sight into the dynamic variation of bacterial genes composition during differentiation and adaption to different niche,and facilitated the identification of strain-specific features,s

关键词： pan-genome genome dynamics adaption evolution

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The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 578-583页

作者： Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang Anke Wang Lili Dong Zhewen Zhang Caixia Yu Yanling Sun Lianjiang Chi Huanxin Chen Shuang Zhai Yubin Sun Li Lan Xin Zhang jingfa xiao Yiming Bao Yanqing Wang Zhang Zhang Wenming Zhao China National Center for Bioinformation Beijing 100101China National Genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The Genome Sequence Archive(GSA)is a data repository for archiving raw sequence data,which provides data storage and sharing services for worldwide scientific *** explosive data growth with diverse data types,here we present the GSA family by expanding into a set of resources for raw data archive with different purposes,namely,GSA(https://***/gsa/),GSA for Human(GSA-Human,https://***/gsa-human/),and Open Archive for Miscellaneous Data(OMIX,https://***/omix/).Compared with the 2017 version,GSA has been significantly updated in data model,online functionalities,and web ***-Human,as a new partner of GSA,is a data repository specialized in human genetics-related data with controlled access and ***,as a critical complement to the two resources mentioned above,is an open archive for miscellaneous ***,all these resources form a family of resources dedicated to archiving explosive data with diverse types,accepting data submissions from all over the world,and providing free open access to all publicly available data in support of worldwide research activities.

关键词： Genome Sequence Archive GSA GSA-Human OMIX

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Quantifying authors' contributions in biological knowledge wikis

Quantifying authors' contributions in biological knowledge w...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Ming Tian jingfa xiao Xumin Wang Lin Dai Zhang Zhang School of Computer Science and Technology Beijing Institute of Technology CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics.Chinese Academy of Sciences

Background:With the exponentially exploding volume of scientific literatures available, traditional expert curation becomes increasingly ineffective to keep biological knowledge upto -date,comprehensive and *** to this reason,several efforts have been devoted to building biological knowledge wikis(bio-wiki),aiming to harness collective intelligence for knowledge ***,extant bio-wikis have not achieved a substantial success,primarily due to no credit for authors’ contributions and consequently inadequate participations from the scientific community. Methods:Sufficient participations in bio-wikis arc fundamentally vital in increasing knowledge coverage,improving knowledge accuracy and keeping knowledge up-to-date. To increase authors’ participations from the scientific community and contribute knowledge by making edits in bio-wikis,we develop an algorithm,ScienceReward,to quantify authors’ contributions by factoring edit quality as well as edit *** on quantitative contributions,ScienceReward ranks all contributed authors and provides explicit authorships for any wiki page. Results:ScienceReward provides a standard practice in bio-wikis for rewarding authors’ contributions,helpful to encourage users’ participations,improve knowledge reliability and increase collaborations in knowledge *** is implemented as an extension to MediaWiki,a bunch of codes for adding customized *** is easily installed and compatible to any MediaWiki-based system,possessing a broad scope for its application and providing a consistent appearance and functionality as Wikipedia. Conclusions:When contribution is appropriately measured and explicit authorship is duly rewarded as demonstrated in ScienceReward,bio-wikis bears significant promises in fully exploiting the power of the scientific community to integrate immense biological knowledge.

关键词： wiki contribution knowledge integration ScienceReward

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遗传密码起源初探

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科学 2009年第5期62卷 32-35页

作者：肖景发于军不详中国科学院基因组科学与信息重点实验室北京基因组研究所北京100029

生物有机体的多样性首先反映了地球作为非平衡热动力学系统的复杂性，其次是种群内部的复杂系统进化过程。不管这些复杂性如何相互作用和不断变化，生命有机体所使用的遗传信息，也就是遗传密码，却高度一致，因此这个遗传密码必定起源... 详细信息

生物有机体的多样性首先反映了地球作为非平衡热动力学系统的复杂性，其次是种群内部的复杂系统进化过程。不管这些复杂性如何相互作用和不断变化，生命有机体所使用的遗传信息，也就是遗传密码，却高度一致，因此这个遗传密码必定起源于相对更早的时期，经过不断进化达到近乎完善后才固定下来。1960年代实验分子生物学领域最大的进展就是解码遗传密码。并发现它对不同的生命有机体而言基本上是统一的。但是，解释遗传密码的由来，包括为什么密码子采用了当前的分配形式，仍然是分子生物学遗留下来的几个理论上具有挑战性的问题之一。

关键词：遗传密码共进化假说立体化学假说分步进化假说氨酰tRNA 合成酶

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Precision Medicine:What Challenges Are We Facing?

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Genomics, Proteomics & Bioinformatics 2016年第5期14卷 253-261页

作者： Yu Xue Eric-Wubbo Lameijer Kai Ye Kunlin Zhang Suhua Chang xiaoyue Wang Jianmin Wu Ge Gao Fangqing Zhao Jian Li Chunsheng Han Shuhua Xu jingfa xiao Xuerui Yang xiaomin Ying Xuegong Zhang Wei-Hua Chen Yun Liu Zhang Zhang Kun Huang Jun Yu MOE Key Lahoratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Brain ScienceHuazhong University of Science and TechnologyWuhan 430074China School of Electronic and Information Engineering.Xi'an Jiaotong University.Xi'an 710049 China CAS Key Laboratory of Mental Health Institute of PsychologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of'Medical Molecular Biology Institute of Basic Medical SciencesChinese Academy of Medical SciencesPeking Union Medical CollegeBeijing 100005China MOE Beijing Key Laboratory of Carcinogenesis and Translatiooal ResearchCenter for Cancer BioinformaticsPeking University Cancer Hospital&InstituteBeijing 100142China Center for Bioinformatics State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijing 100871China Beijing Institutes of Life Science.Chinese Academy of Sciences Beijing 100101China MOE Key Lahoratory of Developnlental Genes and Human Disease Institute of Life SciencesSoutheast UniversityNanjing 210096China State Key Laboratory of Stem Cell and Reproductive Biology Institute of Zoology Chinese Academy of SciencesBeijing 100101China Max Planck Independent Research Group on Population Genomics CAS-MPG Partner Institute for Computational Biology(PICB)Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China CAS Ker Laboratory of Genome Sciences and Information Chinese Academy of Sciences.Beijing 100101China MOE Key Laboratory of Bioinformatics School of Life Sciences Center for Synthetic and Systems BiologyTsinghua UniversityBeijing 100084China Computational Omics Lahoratory Center of Computational BiologyBeijing Institute of Basic Medical SciencesBeijing 100850China Bioinformatics Division TNLIST and MOE Key Laboratory for Bioinformatics Department of AutomationTsinghua UniversityBeijing 100084China Department of Bioinformatics and Systems Biology College of LifeScience and Technol

Following the publication of the US National Research Council （N RC） report ＂ Toward PrecMon Medicine.＂ Building a Knowledge Network for Biomedical Research and a New Taxonomy of Diseases＂ in 2011 [1], several n... 详细信息

关键词： PMI Precision Medicine data We

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GSA:Genome Sequence Archive

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Genomics, Proteomics & Bioinformatics 2017年第1期15卷 14-18页

作者： Yanqing Wang Fuhai Song Junwei Zhu Sisi Zhang Yadong Yang Tingting Chen Bixia Tang Lili Dong Nan Ding Qian Zhang Zhouxian Bai Xunong Dong Huanxin Chen Mingyuan Sun Shuang Zhai Yubin Sun Lei Yu Li Lan jingfa xiao Xiangdong Fang Hongxing Lei Zhang Zhang Wenming Zhao BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Collaborative Innovation Center of Genetics and Development Fudan UniversityShanghai 200438China Center of Alzheimer's Disease Beijing Institute for Brain DisordersBeijing 100053China

With the rapid development of sequencing technologies towards higher throughput and lower cost, sequence data are generated at an unprecedentedly explosive rate. To provide an efficient and easy-to-use platform for managing huge sequence data, here we present Genome Sequence Archive （GSA; http：//***/gsa or http：//***）, a data repository for archiving raw sequence data. In compliance with data standards and structures of the International Nucleotide Sequence Database Collaboration （INSDC）, GSA adopts four data objects （BioProject, BioSample, Experiment, and Run） for data organization, accepts raw sequence reads produced by a variety of sequencing platforms, stores both sequence reads and metadata submitted from all over the world, and makes all these data publicly available to worldwide scientific communities. In the era of big data, GSA is not only an important complement to existing INSDC members by alleviating the increasing burdens of handling sequence data deluge, but also takes the significant responsibility for global big data archive and provides free unrestricted access to all publicly available data in support of research activities throughout the world.

关键词： Genome Sequence Archive GSA Big data Raw sequence data INSDC

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The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

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Genomics, Proteomics & Bioinformatics 2020年第6期18卷 749-759页

作者： Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li Jingyao Zeng Lili Hao Shuai Jiang Hua Chen Dali Han jingfa xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao China National Center for Bioinformation Beijing 100101China National Genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house *** particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global *** provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each *** change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes ***,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe ***,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with ***,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://***/ncov/.

关键词： 2019nCoVR SARS-CoV-2 Database Genomic variation Haplotype

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A Wiki-based English-to-Chinese Scientific Nomenclature Dictionary

A Wiki-based English-to-Chinese Scientific Nomenclature Dict...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Ming Tian Jian Sang Chao Xu Dong Zou Jiaya Wu jingfa xiao Xumin Wang Lin Dai Zhang Zhang School of Computer Science and Technology Beijing Institute of Technology Research Institute of Subtropical Forestry Chinese Academy of Forestry CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences

Background:Scientific nomenclature is a system of words used to name things in a particular ***,accurate translation of scientific nomenclature from English to Chinese is of critical significance,not only for effectively facilitating communications with overseas researchers,but also for efficiently disseminating knowledge among domestic people,especially students and young researchers in ***,among English nomenclature,some do not have unique or acknowledged translations in Chinese. Furthermore,a dynamically growing volume of scientific nomenclature poses additional challenges in English-to-Chinese *** is very often,for example,in life sciences that new nomenclature emerges with the rapid development of experimental technologies and the exploding number of related scientific studies. Methods:Here we develop a wiki-based English-to-Chinese Scientific Nomenclature Dictionary(ESND),aiming to exploit the power of the whole scientific community for nomenclature translation. Results:ESND provides a collaborative platform for collectively managing Englishto -Chinese scientific *** user can add a specific nomenclature when it is not *** addition,any user can make vote when there are multiple translations available for a given English nomenclature and thus most voted translations indicate wide acceptance by the scientific community. Conclusions:Based on the collective intelligence,ESND is capable of achieving accurate and comprehensive English-to-Chinese scientific nomenclature,laying a solid foundation for domestic scientific activities.

关键词： scientific nomenclature wiki English-to-Chinese ESND collective intelligence

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Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 229-247页

作者： Zhenglin Du Liang Ma Hongzhu Qu Wei Chen Bing Zhang Xi Lu Weibo Zhai Xin Sheng Yongqiao Sun Wenjie Li Meng Lei Qiuhui Qi Na Yuan Shuo Shi Jingyao Zeng Jinyue Wang Yadong Yang Qi Liu Yaqiang Hong Lili Dong Zhewen Zhang Dong Zou Yanqing Wang Shuhui Song Fan Liu Xiangdong Fang Hua Chen Xin Liu jingfa xiao Changqing Zeng Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100101China BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

To unravel the genetic mechanisms of disease and physiological traits,it requires comprehensive sequencing analysis of large sample size in Chinese ***,we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative(CASPMI)project launched by the Chinese Academy of Sciences,including the de novo assembly of a northern Han reference genome(NH1.0)and whole genome analyses of 597 healthy people coming from most areas in *** the two existing reference genomes for Han Chinese(YH and HX1)were both from the south,we constructed NH1.0,a new reference genome from a northern individual,by combining the sequencing strategies of PacBio,10×Genomics,and Bionano *** this integrated approach,we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and *** order to generate a genomic variation map of Chinese populations,we performed the whole-genome sequencing of 597 participants and identified 24.85 million(M)single nucleotide variants(SNVs),3.85 M small indels,and 106,382 structural *** the association analysis with collected phenotypes,we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han ***,significant genetic diversity in MTHFR,TCN2,FADS1,and FADS2,which associate with circulating folate,vitamin B12,or lipid metabolism,was observed between northerners and ***,for the homocysteine-increasing allele of rs1801133(MTHFR 677T),we hypothesize that there exists a “comfort”zone for a high frequency of 677T between latitudes of 35–45 degree *** together,our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine.

关键词： De novo assembly Reference genome Variation map Phenotype association Large population

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中国人群参考基因组及基因组变异图谱资源库

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遗传 2018年第11期40卷 1048-1054页

作者：宋述慧滕徐菲肖景发中国科学院北京基因组研究所中国科学院生命与健康大数据中心北京100101 中国科学院北京基因组研究所基因组科学与信息重点实验室北京100101 中国科学院大学北京100049

随着人类基因组计划和国际千人基因组计划的实施,已公开数百个中国人个体的全基因组数据。建立高精度的中国人群参考基因组序列,发现并解析中国人群特有的序列变异,是我国未来精准医学研究的基础。为满足未来精准医学研究中国人基因组... 详细信息

随着人类基因组计划和国际千人基因组计划的实施,已公开数百个中国人个体的全基因组数据。建立高精度的中国人群参考基因组序列,发现并解析中国人群特有的序列变异,是我国未来精准医学研究的基础。为满足未来精准医学研究中国人基因组数据持续增长的科学管理和深入研究的需求,中国科学院北京基因组研究所发展并建立了基于中国人群全基因组测序数据的虚拟中国人基因组数据库(Virtual Chinese Genome Database,VCGDB)和中国人群基因组变异数据库(Genome Variation Map, GVM),面向国内外用户提供数据检索、共享、下载和在线分析服务。本文重点介绍了这两个数据库的特点和功能,以及未来发展与应用前景,以期为中国人群参考基因组及基因组变异图谱资源库的推广使用、发展完善提供有益信息。

关键词：中国人群参考基因组变异图谱

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