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T2T-YAO, T2T-SHUN, and more

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Genomics, Proteomics & Bioinformatics 2023年第6期21卷 1081-1082页

作者： jingfa xiao Jun Yu National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The first high-quality reference genome for Chinese populations has just been released[1],T2Y-YAO(尧yao),and it starts a first-of-its-kind series for building virtual ancestor genomes(VAGs)for Chinese population-based studies and healthcare applications[2,3].The reasons are ***,the Han people(汉人han ren)are the world’s largest ethnicity,1.5 billion in total,19%of the global population,and 91%of the Chinese ***,the Chinese population history—regardless of whether the precise time period of each nation and State has or has not been determined—and complexity are being recorded faithfully in their genome ***,the Han ethnic groups are still co-habiting with other 55 minor ethnic peoples without geopolitical and geographical barriers.

关键词： has precise record

Database Commons:A Catalog of Worldwide Biological Databases

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 1054-1058页

作者： Lina Ma Dong Zou Lin Liu Huma Shireen Amir AAbbasi Alex Bateman jingfa xiao Wenming Zhao Yiming Bao Zhang Zhang National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China National Center for Bioinformatics Programme of Comparative and Evolutionary GenomicsFaculty of Biological SciencesQuaid-i-Azam UniversityIslamabad 45320Pakistan European Molecular Biology Laboratory European Bioinformatics Institute(EMBL-EBI)HinxtonCambridge CB101SDUnited Kingdom

Biological databases serve as a global fundamental infrastructure for the worldwide scientific community,which dramatically aid the transformation of big data into knowledge discovery and drive significant innovations in a wide range of research *** the rapid data production,biological databases continue to increase in size and *** build a catalog of worldwide biological databases,we curate a total of 5825 biological databases from 8931 publications,which are geographically distributed in 72 countries/regions and developed by 1975 institutions(as of September 20,2022).We further devise a z-index,a novel index to characterize the scientific impact of a database,and rank all these biological databases as well as their hosting institutions and countries in terms of citation and ***,we present a series of statistics and trends of worldwide biological databases,yielding a global perspective to better understand their status and impact for life and health *** up-to-date catalog of worldwide biological databases,as well as their curated meta-information and derived statistics,is publicly available at Database Commons(https://***/databasecommons/).

关键词： Biological database Catalog Database Commons Citation z-index

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国家基因组科学数据中心:现状及展望

中国科学：生命科学 2024年第6期54卷 1088-1100页

作者：陈梅丽王彦青李茹姣马英克张思思张欣宋述慧肖景发赵文明章张鲍一明中国科学院北京基因组研究所(国家生物信息中心)国家基因组科学数据中心北京100101 中国科学院大学北京100049

面向我国人口健康和社会可持续发展的重大战略需求,国家基因组科学数据中心(National Genomics Data Center,NGDC)自2019年成立以来,已初步建成具有自主知识产权、安全可控、涵盖领域广的多维组学数据汇交、存储、管理和共享体系,涵盖... 详细信息

面向我国人口健康和社会可持续发展的重大战略需求,国家基因组科学数据中心(National Genomics Data Center,NGDC)自2019年成立以来,已初步建成具有自主知识产权、安全可控、涵盖领域广的多维组学数据汇交、存储、管理和共享体系,涵盖基础组学数据资源、国家人类遗传资源、重要战略生物资源、生物安全资源以及生物信息分析工具和平台等,为人口健康、公共安全、育种改良、生物多样性等相关研究提供重要资源和参考信息.截至目前,NGDC已存储和管理27.6 PB的数据量,数据编号被Springer Nature,Elsevier,Wiley,Taylor&Francis等全球主要出版集团推荐或认可.尽管NGDC已连续六年被本领域国际权威期刊《核酸研究》称为与美国NCBI、欧洲EBI齐名的国际主要生物数据中心,但与国际一流数据中心仍存在一定差距.展望未来,NGDC将重点聚焦于数据智能审编、数据融合检索、生物大数据云平台、前沿算法工具等,同时在经费争取、人才培养和国际合作方面加大工作力度,建成国际领先的基因组科学数据中心,支撑我国生命与健康科学领域的科技创新发展和自立自强.

关键词：基因组生物信息大数据多组学人类遗传资源汇交管理国家基因组科学数据中心国家生物信息中心

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Latest notable achievements in genomics

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Science China(Life Sciences) 2012年第7期55卷 645-648页

作者： WU JiaYan xiao jingfa YU Jun Key Laboratory of Genomics Science and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China

Within the past 10 years, the progress of genomics development in China exhibited a frogleap in terms of scale,quality, organization, and international collaboration.

关键词：基因组学 DNA测序技术成绩人类基因组生物信息学国际合作生命科学数据采集

A Brief Review of Software Tools for Pangenomics

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Genomics, Proteomics & Bioinformatics 2015年第1期13卷 73-76页

作者： jingfa xiao Zhewen Zhang Jiayan Wu Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline（PGAP） ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.

关键词： Pangenomics Pangenome Comparative analysis Genomic dynamics Core genes

Coevolution study of mitochondria respiratory chain proteins:Toward the understanding of protein-protein interaction

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Journal of Genetics and Genomics 2011年第5期38卷 201-207页

作者： Ming Yang Yan Ge Jiayan Wu jingfa xiao Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China College of Biology China Agricultural University Beijing 100091 China

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein-protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using ＂Mirror tree＂ method on the respiratory chain （RC） proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions （Wilcoxon test, p-value = 4.4 × 10 6）. Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein-protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study.

关键词： Coevolution Respiratory chain proteins "Mirror tree" method Supercomplex Protein--protein interaction

DNA sequencing leads to genomics progress in China

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Science China(Life Sciences) 2011年第3期54卷 290-292页

作者： WU JiaYan xiao jingfa ZHANG RuoSi YU Jun CAS Key Laboratory of Genome Science and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China

1 Science in the large-scale sequencing era Ten years ago,the first draft sequence assembly of the human genome was completed [1],bringing biomedical research one-step closer toward the goal of revolutionizing diagnosis,prevention,and treatment of human ***,journalists from the journal Nature surveyed more than 1000 life scientists regarding this laudable aim [2],obtaining substantially negative responses [3].However,almost all of those surveyed had been influenced,in one way or another,by the availability of the human genome sequence,and they also agreed with the notion that the 'sequence is the start.' The complexity of genome biology and almost every aspect of human biology is far greater than previously thought [4].

关键词：人类基因组序列 DNA测序生命科学家中国大规模测序生物医学人类疾病

The Elements of Data Sharing

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Genomics, Proteomics & Bioinformatics 2020年第1期18卷 1-4页

作者： Zhang Zhang Shuhui Song Jun Yu Wenming Zhao jingfa xiao 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 100101China

Data and their tailored characteristics are inheritable and longlived,surpassing their analyzed results and conclusions regardless if they are produced by their generators or *** from designing experiments for the new acquisition,scientific researchers always begin with a thorough synthesis of the existing data,especially those that have been demonstrated authentic and timely.

关键词： authentic passing synthesis

The integrative analysis and database construction based on cancer multi-omics data

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The integrative analysis and database construction based on ...