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章张-中国科学院大学-UCAS

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章张-中国科学院大学-UCAS
[中文]
[English]
研究领域
招生信息
教育背景
教授课程
科研活动
指导学生
工作经历
发表论著
基本信息
章张男博导中国科学院北京基因组研究所（国家生物信息中心）电子邮件： zhangzhang@big.ac.cn通信地址：北京市朝阳区北辰西路1号院中国科学院北京基因组研究所邮政编码： 100101
研究领域
生物信息学/计算生物学
招生信息
欢迎生物信息学、计算机科学、数学、物理等专业背景学生报考。
招生专业
0710J3-生物信息学
招生方向
生物大数据整合挖掘计算健康基因组学
教育背景
2004-09--2007-07 中国科学院计算技术研究所计算机科学博士2002-09--2004-07 南京理工大学计算机科学硕士1998-09--2002-07 宁夏大学计算机科学学士
教授课程
基因组学概述生命组学基因组学大数据科学基因组技术与健康大数据健康数据与基因组技术生物信息学前沿讲座基因组学前沿
科研活动
Associate Editor: Bioinformatics Advances (2021—)Asian Associate Editor: Briefings in Bioinformatics (2017—)Associate Editor-in-Chief: Genomics, Proteomics & Bioinformatics (2012—)
科研项目
（ 1 ）&nbsp生物信息技术共享、转化研究平台建设, 参与, 国家任务, 2012-01--2016-12（ 2 ）&nbsp****（择优）, 负责人, 中国科学院计划, 2014-01--2017-12（ 3 ）&nbsp动物复杂性状的进化解析与调控—动物复杂性状多组学数据的存储与访问平台建设, 负责人, 中国科学院计划, 2014-01--2019-12（ 4 ）&nbsp分子模块组学数据整合与辞海系统建设, 负责人, 中国科学院计划, 2016-01--2017-12（ 5 ）&nbsp中国人群全基因组测序与系统分析, 负责人, 国家任务, 2017-07--2020-12（ 6 ）&nbsp生物多样性组学数据平台和数据库系统, 负责人, 中国科学院计划, 2018-01--2022-12（ 7 ）&nbsp基于多层次微进化特征的自然选择压力检测研究, 负责人, 国家任务, 2019-01--2022-12（ 8 ）&nbsp生物大数据知识挖掘理论及应用, 负责人, 国家任务, 2021-01--2025-12
参与会议
（1）Biological Big Data Deposition, Public Sharing and Database Resources 2021-10-25（2）RiceWiki: a wiki-based database for community curation of rice genes. Zhang Zhang 2014-04-06（3）Big biological data integration and curation 2014中国科学数据大会—科研大数据和数据科学 Zhang Zhang 2014-02-24（4）Biocuration in the era of big data. Zhang Zhang 2014-02-09（5）Biological databases: wikify or die. Zhang Zhang 2013-10-28（6）Community curation in biological knowledge wikis Zhang Zhang 2013-04-07（7）Next-Generation Bioinformatics: harnessing collective resources for large-scale data manipulation Zhang Zhang 2012-03-19（8）Estimating codon usage bias and its statistical significance by accounting for background nucleotide composition Zhang Zhang 2011-10-22
指导学生
已指导学生孙世翔博士研究生 0710J3-生物信息学殷红彦博士研究生 0710J3-生物信息学于春蕾硕士研究生 0710J3-生物信息学徐行健博士研究生 0710J3-生物信息学王光煜博士研究生 0710J3-生物信息学夏琳博士研究生 0710J3-生物信息学李漫硕士研究生 0710J3-生物信息学曹佳宝硕士研究生 085238-生物工程桑健博士研究生 0710J3-生物信息学王佩硕士研究生 0710J3-生物信息学连明硕士研究生 0710Z1-基因组学张阳硕士研究生 085211-计算机技术刘琳博士研究生 0710J3-生物信息学高纯纯博士研究生 0710J3-生物信息学张源笙硕士研究生 085238-生物工程陈茹茹硕士研究生 0710J3-生物信息学程远硕士研究生 0710J3-生物信息学杜强硕士研究生 0710J3-生物信息学冯昶瑞硕士研究生 0710J3-生物信息学滕徐菲博士研究生 0710J3-生物信息学现指导学生刘晓楠博士研究生 0710J3-生物信息学牛广艺博士研究生 0710J3-生物信息学朱彤彤博士研究生 0710J3-生物信息学李乾鹏博士研究生 0710J3-生物信息学陈铭博士研究生 0710J3-生物信息学刘畅硕士研究生 0710Z1-基因组学张阳博士研究生 0710J3-生物信息学李昭博士研究生 0710J3-生物信息学潘榕硕士研究生 0710J3-生物信息学荆蔚硕士研究生 0710J3-生物信息学罗思成硕士研究生 0710J3-生物信息学
工作经历
2020至今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副主任2016—2020 中国科学院北京基因组研究所生命与健康大数据中心执行主任2011至今中国科学院大学教授2011至今中国科学院北京基因组研究所研究员，博士生导师2009—2011 沙特阿卜杜拉国王理工大学（King Abdullah University of Science and Technology）研究科学家2007—2009 美国耶鲁大学（Yale University）博士后
发表论著
https://ngdc.cncb.ac.cn/people/zhang-zhangZhang Z: KaKs_Calculator 3.0: Calculating selective pressure on coding and non-coding sequences. Genomics Proteomics Bioinformatics 2022. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34990803Zhang Y, Zou D, Zhu T, Xu T, Chen M, Niu G, Zong W, Pan R, Jing W, Sang
J, Liu C, Xiong Y, Sun Y, Zhai S, Chen H, Zhao W, Xiao J, Bao Y, Hao L,
Zhang Z: Gene Expression Nebulas (GEN): a comprehensive data portal
integrating transcriptomic profiles across multiple species at both bulk
and single-cell levels. Nucleic Acids Res 2022, 50(D1):D1016-D1024. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34591957Xiong Z, Yang F, Li M, Ma Y, Zhao W, Wang G, Li Z, Zheng X, Zou D, Zong W, Kang H, Jia Y, Li R, Zhang Z, Bao Y: EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. Nucleic Acids Res 2022, 50(D1):D1004-D1009. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34718752Liu L, Zhang Y, Niu G, Li Q, Li Z, Zhu T, Feng C, Liu X, Zhang Y, Xu T, Chen R, Teng X, Zhang R, Zou D, Ma L, Zhang Z: BrainBase: a curated knowledgebase for brain diseases. Nucleic Acids Res 2022, 50(D1):D1131-D1138. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34718720Liu L, Li Z, Liu C, Zou D, Li Q, Feng C, Jing W, Luo S, Zhang Z, Ma L: LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. Nucleic Acids Res 2022, 50(D1):D190-D195. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34751395Jiang S, Du Q, Feng C, Ma L, Zhang Z: CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. Nucleic Acids Res 2022, 50(D1):D962-D969. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34718745Jia L, Li Y, Huang F, Jiang Y, Li H, Wang Z, Chen T, Li J, Zhang Z, Yao W: LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes. Nucleic Acids Res 2022, 50(D1):D174-D182. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34643715CNCB-NGDC Members & Partners: Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Res 2022, 50(D1):D27-D38. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34718731Chen T, Chen X, Zhang S, Zhu J, Tang B, Wang A, Dong L, Zhang Z, Yu C,
Sun Y, Chi L, Chen H, Zhai S, Sun Y, Lan L, Zhang X, Xiao J, Bao Y, Wang
Y, Zhang Z, Zhao W: The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types. Genomics Proteomics Bioinformatics 2022:doi: 10.1016/j.gpb.2021.1008.1001. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34400360Chen M, Ma Y, Wu S, Zheng X, Kang H, Sang J, Xu X, Hao L, Li Z, Gong Z, Xiao J, Zhang Z, Zhao W, Bao Y: Genome Warehouse: A Public Repository Housing Genome-scale Data. Genomics Proteomics Bioinformatics 2022:doi: 10.1016/j.gpb.2021.1004.1001. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34175476The RNAcentral Consortium: RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res 2021, 49(D1):D212-D220. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33106848Liu X, Wang P, Teng X, Zhang Z, Song S: Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers. Front Oncol 2021, 11:624395. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33718187Li Z, Liu L, Jiang S, Li Q, Feng C, Du Q, Zou D, Xiao J, Zhang Z, Ma L: LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Res 2021, 49(D1):D962-D968. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33045751Li C, Tian D, Tang B, Liu X, Teng X, Zhao W, Zhang Z, Song S: Genome Variation Map: a worldwide collection of genome variations across multiple species. Nucleic Acids Res 2021, 49(D1):D1186-D1191. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33170268CNCB-NGDC Members & Partners: Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res 2021, 49(D1):D18-D28. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33175170Zhao WM, Song SH, Chen ML, Zou D, Ma LN, Ma YK, Li RJ, Hao LL, Li CP,
Tian DM, Tang BX, Wang YQ, Zhu JW, Chen HX, Zhang Z, Xue YB, Bao YM: The 2019 novel coronavirus resource. Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji 2020, 42(2):212-221. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-32102777Zhang Z, Song S, Yu J, Zhao W, Xiao J, Bao Y: The Elements of Data Sharing. Genomics Proteomics Bioinformatics 2020, 18(1):1-4. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-32360769Yan J, Zou D, Li C, Zhang Z, Song S, Wang X: SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice. Genomics Proteomics Bioinformatics 2020, 18(2):173-185. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-32619768Xiong Z, Li M, Yang F, Ma Y, Sang J, Li R, Li Z, Zhang Z, Bao Y: EWAS Data Hub: a resource of DNA methylation array data and metadata. Nucleic Acids Res 2020, 48(D1):D890-D895. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-31584095Tian D, Wang P, Tang B, Teng X, Li C, Liu X, Zou D, Song S, Zhang Z: GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res 2020, 48(D1):D927-D932. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-31566222Teng X, Li Q, Li Z, Zhang Y, Niu G, Xiao J, Yu J, Zhang Z, Song S: Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. Genomics Proteomics Bioinformatics 2020, 18(6):648-663. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33581339Song S, Ma L, Zou D, Tian D, Li C, Zhu J, Chen M, Wang A, Ma Y, Li M,
Teng X, Cui Y, Duan G, Zhang M, Jin T, Shi C, Du Z, Zhang Y, Liu C, Li
R, Zeng J, Hao L, Jiang S, Chen H, Han D, Xiao J, Zhang Z, Zhao W, Xue
Y, Bao Y: The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR. Genomics Proteomics Bioinformatics 2020, 18(6):749-759. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33704069Sang J, Zou D, Wang Z, Wang F, Zhang Y, Xia L, Li Z, Ma L, Li M, Xu B,
Liu X, Wu S, Liu L, Niu G, Li M, Luo Y, Hu S, Hao L, Zhang Z: IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. Genomics Proteomics Bioinformatics 2020, 18(2):161-172. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-32683045National Genomics Data Center Members & Partners: Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 2020, 48(D1):D24-D33. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-31702008Miao W, Song L, Ba S, Zhang L, Guan G, Zhang Z, Ning K: Protist 10,000 Genomes Project. Innovation (N Y) 2020, 1(3):100058. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34557722Liu L, Wang G, Wang L, Yu C, Li M, Song S, Hao L, Ma L, Zhang Z: Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biol Direct 2020, 15(1):10. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-32539851Li Z, Zhang Y, Zou D, Zhao Y, Wang HL, Zhang Y, Xia X, Luo J, Guo H, Zhang Z: LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Res 2020, 48(D1):D1069-D1075. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-31599330Li Q, Li Z, Feng C, Jiang S, Zhang Z, Ma L: Multi-omics annotation of human long non-coding RNAs. Biochem Soc Trans 2020, 48(4):1545-1556. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-32756901Gong Z, Zhu JW, Li CP, Jiang S, Ma LN, Tang BX, Zou D, Chen ML, Sun YB,
Song SH, Zhang Z, Xiao JF, Xue YB, Bao YM, Du ZL, Zhao WM: An online coronavirus analysis platform from the National Genomics Data Center. Zool Res 2020, 41(6):705-708. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-33045776Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann YW, Li R, Xiao J: NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Res 2019, 47(D1):D163-D169. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30335176Zhang Z, Yu J, Eisenhaber F, Gao X, Gojobori T: In Memory of Vladimir B. Bajic (1952-2019). Genomics Proteomics & Bioinformatics 2019, 17(5):473-474. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-WOS:000518438500001Yin H, Li M, Xia L, He C, Zhang Z: Computational determination of gene age and characterization of evolutionary dynamics in human. Brief Bioinform 2019, 20(6):2141-2149. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30184145Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA, Bajic VB, Ma L, Zhang Z: Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics 2019, 35(17):2949-2956. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30649200The RNAcentral Consortium: RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res 2019, 47(D1):D221-D229. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30395267Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang YP, Wang GD, Zhao W: iDog: an integrated resource for domestic dogs and wild canids. Nucleic Acids Res 2019, 47(D1):D793-D800. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30371881Song S, Zhang Z: Database Resources in BIG Data Center: Submission, Archiving, and Integration of Big Data in Plant Science. Molecular plant 2019, 12(3):279-281. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30716410Pervaiz N, Shakeel N, Qasim A, Zehra R, Anwar S, Rana N, Xue Y, Zhang Z, Bao Y, Abbasi AA: Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals. BMC Evol Biol 2019, 19(1):128. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-31221090Niu G, Zou D, Li M, Zhang Y, Sang J, Xia L, Li M, Liu L, Cao J, Zhang Y, Wang P, Hu S, Hao L, Zhang Z: Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human. Nucleic Acids Res 2019, 47(D1):D78-D83. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30357418Ma L, Cao J, Liu L, Li Z, Shireen H, Pervaiz N, Batool F, Raza RZ, Zou D, Bao Y, Abbasi AA, Zhang Z: Community Curation and Expert Curation of Human Long Noncoding RNAs with LncRNAWiki and LncBook. Curr Protoc Bioinformatics 2019, 67(1):e82. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-31524988Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z: LncBook: a curated knowledgebase of human long non-coding RNAs. Nucleic Acids Res 2019, 47(D1):D128-D134. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30329098Li M, Zou D, Li Z, Gao R, Sang J, Zhang Y, Li R, Xia L, Zhang T, Niu G, Bao Y, Zhang Z: EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. Nucleic Acids Res 2019, 47(D1):D983-D988. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30364969Li M, Xia L, Zhang Y, Niu G, Li M, Wang P, Zhang Y, Sang J, Zou D, Hu S, Hao L, Zhang Z: Plant editosome database: a curated database of RNA editosome in plants. Nucleic Acids Res 2019, 47(D1):D170-D174. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30364952BIG Data Center Members: Database Resources of the BIG Data Center in 2019. Nucleic Acids Res 2019, 47(D1):D8-D14. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30365034Zhang Z, Xue Y, Zhao F: Bioinformatics Commons: The Cornerstone of Life and Health Sciences. Genomics Proteomics Bioinformatics 2018, 16(4):223-225. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30268933Song S, Tian D, Zhang Z, Hu S, Yu J: Rice Genomics: over the Past Two Decades and into the Future. Genomics Proteomics Bioinformatics 2018, 16(6):397-404. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-30771506Song S, Tian D, Li C, Tang B, Dong L, Xiao J, Bao Y, Zhao W, He H, Zhang Z: Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids Res 2018, 46(D1):D944-D949. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-29069473Sang J, Wang Z, Li M, Cao J, Niu G, Xia L, Zou D, Wang F, Xu X, Han X,
Fan J, Yang Y, Zuo W, Zhang Y, Zhao W, Bao Y, Xiao J, Hu S, Hao L, Zhang
Z: ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Res 2018, 46(D1):D121-D126. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-29036693Li R, Liang F, Li M, Zou D, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z: MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res 2018, 46(D1):D288-D295. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-29161430International Society for Biocuration: Biocuration: Distilling data into knowledge. PLOS Biology 2018, 16(4):e2002846. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-29659566BIG Data Center Members: Database Resources of the BIG Data Center in 2018. Nucleic Acids Research 2018, 46(D1):D14-D20. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-29036542Zhao ZM, Campbell MC, Li N, Lee DSW, Zhang Z, Townsend JP: Detection
of Regional Variation in Selection Intensity within Protein-Coding Genes
Using DNA Sequence Polymorphism and Divergence. Mol Biol Evol 2017, 34(11):3006-3022. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-28962009Xu X, Ji Z, Zhang Z: CloudPhylo: a fast and scalable tool for phylogeny reconstruction. Bioinformatics 2017, 33(3):438-440. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-28172557Xia L, Zou D, Sang J, Xu X, Yin H, Li M, Wu S, Hu S, Hao L, Zhang Z: Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice. J Genet Genomics 2017, 44(5):235-241. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-28529082Wang Y, Song F, Zhu J, Zhang S, Yang Y, Chen T, Tang B, Dong L, Ding N,
Zhang Q, Bai Z, Dong X, Chen H, Sun M, Zhai S, Sun Y, Yu L, Lan L, Xiao
J, Fang X, Lei H, Zhang Z, Zhao W: GSA: Genome Sequence Archive. Genomics Proteomics Bioinformatics 2017, 15(1):14-18. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-28387199The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray
KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A,
Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP,
Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M,
Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E,
Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS,
Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu
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2013 中国科学院大学，网络信息中心.