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Database Commons:A Catalog of Worldwide Biological Databases

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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Genomic Epidemiology of SARS-CoV-2 in Pakistan

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Genomics, Proteomics & Bioinformatics 2021年第5期19卷 727-740页

作者： Shuhui Song Cuiping Li Lu Kang Dongmei Tian Nazish Badar Wentai Ma Shilei Zhao Xuan Jiang Chun Wang Yongqiao Sun Wenjie Li Meng Lei Shuangli Li Qiuhui Qi Aamer Ikram Muhammad Salman Massab Umair huma shireen Fatima Batool Bing Zhang Hua Chen Yun-Gui Yang Amir Ali Abbasi Mingkun Li 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 Department of Virology and Immunology National Institute of HealthIslamabad 45500Pakistan National Center for Bioinformatics Programme of Comparative and Evolutionary GenomicsFaculty of Biological SciencesQuaid-i-Azam UniversityIslamabad 45320Pakistan Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyThe Innovation Academy of Seed DesignChinese Academy of SciencesBeijing 100101China

COVID-19 has swept globally and Pakistan is no *** investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,*** identified a total of 347 mutated positions,31 of which were over-represented in ***,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or *** of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying *** genomic epidemiology revealed five distinctive spreading *** largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this ***,28 putative international introductions were identified,several of which are consistent with the epidemiological *** all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.

关键词： SARS-CoV-2 Virus Molecular evolution Haplotype network Pakistan

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