VARIANTS

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MitoSort:Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants
《Genomics, Proteomics & Bioinformatics》2024年第5期137-150,共14页Zhongjie Tang Weixing Zhang Peiyu Shi Sijun Li Xinhui Li Yueming Li Yicong Xu Yaqing Shu Zheng Hu Jin Xu 
supported by the National Key R&D Program of China(Grant No.2021YFA1102100);the National Natural Science Foundation of China(Grant Nos.32070644,32293190,32293191)to JX,and the Guangzhou Key Research and Development Program(Grant No.2023B03J1347)to YS and JX.
Multiplexing across donors has emerged as a popular strategy to increase throughput,reduce costs,overcome technical batch effects,and improve doublet detection in single-cell genomic studies.To eliminate additional ex...
关键词：DEMULTIPLEXING Doublet detection MitoSort Mitochondrial genome variant Single-cell genomics 
Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques
《Genomics, Proteomics & Bioinformatics》2023年第5期1014-1029,共16页Tingfu Du Chunchun Gao Shuaiyao Lu Qianlan Liu Yun Yang Wenhai Yu Wenjie Li Yong Qiao Sun Cong Tang Junbin Wang Jiahong Gao Yong Zhang Fangyu Luo Ying Yang Yun-Gui Yang Xiaozhong Peng 
supported by the National Key R&D Program of China(Grant No.2021YFC0863300);the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDB0490000);the CAMS Innovation Fund for Medical Sciences(Grant No.2021-I2M-1-024);the STI2030-Major Projects(Grant No.2021ZD0200900);the Foundation for Innovative Research Groups of the National Natural Science Foundation of China(Grant No.82221004);the National Natural Science Foundation of China(Grant Nos.32121001,32200460,and 32200460);the K.C.Wong Education Foundation(Grant No.GJTD-2019-08);the Shanghai Municipal Science and Technology Major Project,China(Grant No.2017SHZDZX01);the China National Postdoctoral Program for Innovative Talents(Grant No.BX2021291).
Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)caused the persistent coronavirus disease 2019(COVID-19)pandemic,which has resulted in millions of deaths worldwide and brought an enormous public health and ...
关键词：SARS-CoV-2 Variant of concern Subgenomic RNA Rhesus macaque TRANSCRIPTOME 
RCoV19:A One-stop Hub for SARS-CoV-2 Genome Data Integration,Variant Monitoring,and Risk Pre-warning
《Genomics, Proteomics & Bioinformatics》2023年第5期1066-1079,共14页Cuiping Li Lina Ma Dong Zou Rongqin Zhang Xue Bai Lun Li Gangao Wu Tianhao Huang Wei Zhao Enhui Jin Yiming Bao Shuhui Song 
supported by grants from the National Key R&D Program of China(Grant Nos.2023YFC3041500 and 2021YFF0703703);the Key Collaborative Research Program of the Alliance of International Science Organizations(Grant No.ANSO-CR-KP-2022-09);the National Natural Science Foundation of China(Grant No.32270718);the Beijing Nova Program(Grant No.Z211100002121006);the Youth Innovation Promotion Association of the Chinese Academy of Sciences(Grant Nos.Y2021038 and 2019104),China.
The Resource for Coronavirus 2019(RCoV19)is an open-access information resource dedicated to providing valuable data on the genomes,mutations,and variants of the severe acute respiratory syndrome coronavirus 2(SARS-Co...
关键词：SARS-CoV-2 Mutation VARIANTS Surveillance Pre-warning 
Performance Comparison of Computational Methods for the Prediction of the Function and Pathogenicity of Non-coding Variants被引量：1
《Genomics, Proteomics & Bioinformatics》2023年第3期649-661,共13页Zheng Wang Guihu Zhao Bin Li Zhenghuan Fang Qian Chen Xiaomeng Wang Tengfei Luo Yijing Wang Qiao Zhou Kuokuo Li Lu Xia Yi Zhang Xun Zhou Hongxu Pan Yuwen Zhao Yige Wang Lin Wang Jifeng Guo Beisha Tang Kun Xia Jinchen Li 
supported by the National Natural Science Foundation of China(Grant No.81801133 to JL);the Young Elite Scientist Sponsorship Program by China Association for Science and Technology(Grant No.2018QNRC001 to JL);the Innovation-Driven Project of Central South University,China(Grant No.20180033040004 to JL);the Natural Science Foundation for Young Scientists of Hunan Province,China(Grant No.2019JJ50974 to GZ);the Natural Science Foundation of Hunan Province for outstanding Young Scholars,China(Grant No.2020JJ3059 to JL).
Non-coding variants in the human genome significantly influence human traits and complex diseases via their regulation and modification effects.Hence,an increasing number of computational methods are developed to pred...
关键词：Non-coding variant Pathogenicity estimation Functional prediction Performance assessment Prediction model 
Computational Assessment of the Expression-modulating Potential for Non-coding Variants
《Genomics, Proteomics & Bioinformatics》2023年第3期662-673,共12页Fang-Yuan Shi Yu Wang Dong Huang Yu Liang Nan Liang Xiao-Wei Chen Ge Gao 
supported by funds from the National Key R&D Program of China(Grant No.2016YFC0901603);the National High-tech R&D Program of China(Grant No.2015AA020108);as well as the State Key Laboratory of Protein and Plant Gene Research and the Beijing Advanced Innovation Center for Genomics(ICG)at Peking University;supported in part by the National Program for Support of Top-notch Young Professionals。
Large-scale genome-wide association studies(GWAS)and expression quantitative trait locus(eQTL)studies have identified multiple non-coding variants associated with genetic diseases by affecting gene expression.However,...
关键词：Non-coding variant Expression-modulating variant Gene regulation Algorithm Web server 
RegVar:Tissue-specific Prioritization of Non-coding Regulatory Variants
《Genomics, Proteomics & Bioinformatics》2023年第2期385-395,共11页Hao Lu Luyu Ma Cheng Quan Lei Li Yiming Lu Gangqiao Zhou Chenggang Zhang 
supported by the General Program of the National Natural Science Foundation of China(Grant No.31771397);the Beijing Nova Program(Grant No.20180059).
Non-coding genomic variants constitute the majority of trait-associated genome variations;however,the identification of functional non-coding variants is still a challenge in human genetics,and a method for systematic...
关键词：Non-coding variant Variantprioritization Expressionregulation Expressionquantitative trait locus Deep neural network 
mvPPT:A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants
《Genomics, Proteomics & Bioinformatics》2023年第2期414-426,共13页Shi-Yuan Tong Ke Fan Zai-Wei Zhou Lin-Yun Liu Shu-Qing Zhang Yinghui Fu Guang-Zhong Wang Ying Zhu Yong-Chun Yu 
supported by the National Key R&D Program of China(Grant No.2021ZD0202500);the Shanghai Natural Science Foundation,China(Grant No.20ZR1403800);the National Natural Science Foundation of China(Grant Nos.31900476,82071259,31930044,and 31725012);the Shanghai Municipal Science and Technology Major Project(Grant No.2018SHZDZX01);ZJ Lab,the Shanghai Center for Brain Science and Brain-Inspired Technology,China,the Foundation of Shanghai Municipal Education Commission,China(Grant No.2019-01-07-00-07-E00062);the Collaborative Innovation Program of Shanghai Municipal Health Commission,China(Grant No.2020CXJQ01).
Next-generation sequencing technologies both boost the discovery of variants in the human genome and exacerbate the challenges of pathogenic variant identification.In this study,we developed Pathogenicity Prediction T...
关键词：Machine learning Missensevariant GENOMICS Computational biology Pathogenicityprediction 
REVA as A Well-curated Database for Human Expressionmodulating Variants
《Genomics, Proteomics & Bioinformatics》2021年第4期590-601,共12页Yu Wang Fang-Yuan Shi Yu Liang Ge Gao 
supported by funds from the National Key R&D Program of China(Grant No.2016YFC0901603);the National High Technology Research and Development Program of China(Grant No.2015AA020108);the State Key Laboratory of Protein and Plant Gene Research and the Beijing Advanced Innovation Center for Genomics(ICG)at Peking University,China;supported in part by the National Program for Support of Top-notch Young Professionals;supported by the High-performance Computing Platform of Peking University。
More than 90%of disease-and trait-associated human variants are noncoding.By systematically screening multiple large-scale studies,we compiled REVA,a manually curated database for over 11.8 million experimentally test...
关键词：Noncoding variant Expression-modulating variant Massively parallel reporter assay DATABASE BENCHMARK 
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling被引量：4
《Genomics, Proteomics & Bioinformatics》2021年第4期602-610,共9页Yanyan Li Honghong Zhou Xiaomin Chen Yu Zheng Quan Kang Di Hao Lili Zhang Tingrui Song Huaxia Luo Yajing Hao Runsheng Chen Peng Zhang Shunmin He 
supported by the National Key R&D Program of China(Grant No.2016YFC0901702);National Natural Science Foundation of China(Grant Nos.81902519,91940306,31871294,31701117,and 31970647);the National Key R&D Program of China(Grant Nos.2017YFC0907503,2016YFC0901002,and 2018YFA0106901);the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDB38040300);the 13th Five-year Informatization Plan of Chinese Academy of Sciences(Grant No.XXH13505-05);Special Investigation on Science and Technology Basic Resources,Ministry of Science and Technology,China(Grant No.2019FY100102);the National Genomics Data Center,China。
Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome annotation.The significance of small...
关键词：Ribosome profiling Small open reading frame Upstream open reading frame VARIANTS Disease 
The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR被引量：15
《Genomics, Proteomics & Bioinformatics》2020年第6期749-759,共11页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 
This work was supported by grants from the Strategic PriorityResearch Program of Chinese Academy of Sciences(GrantNos.XDA19090116,XDA19050302,and XDB38030400)awarded to SS,ZZ,and ML;the National Key R&D Programof China(Grant Nos.2020YFC0848900,2020YFC0847000,2016YFE0206600,and 2017YFC0907502);the 13th Five-yearInformatization Plan of Chinese Academy of Sciences(GrantNo.XXH13505-05);Genomics Data Center Construction ofChinese Academy of Sciences(Grant No.XXH-13514-0202);the Open Biodiversity and Health Big Data Programme ofInternational Union of Biological Sciences,International Part-nership Program of Chinese Academy of Sciences(Grant No.153F11KYSB20160008);the Professional Association of theAlliance of International Science Organizations(Grant No.ANSO-PA-2020-07);This work was also supported by KCWong Education Foundation to ZZ;the YouthInnovation Promotion Association of Chinese Academy ofSciences(Grant Nos.2017141 and 2019104)awarded to SSand ML.
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...
关键词：2019nCoVR SARS-CoV-2 DATABASE Genomic variation HAPLOTYPE 
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