Professor
Email: zhangzhang (AT) big.ac.cn
Tel: +86 (10) 8409-7261
Email: zhangzhang (AT) big.ac.cn
Tel: +86 (10) 8409-7261
Associate Director of National Genomics Data Center (NGDC), Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (CNCB), China, 2020 - Present
BIG Distinguished Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2017 - Present
Associate Director of BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2016 - 2020
Professor, University of Chinese Academy of Sciences, China, 2015 - Present
Professor in the CAS 100-Talent Program, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2011 - Present
Research Scientist, King Abdullah University of Science and Technology, Kingdom of Saudi Arabia, 2009 - 2011
Postdoctoral Associate, Yale University, United States of America, 2007 - 2009
PhD in Computer Science, Institute of Computing Technology, Chinese Academy of Sciences, China, 2007
MS in Computer Science, Nanjing University of Science and Technology, China, 2004
BS in Computer Science, Ningxia University, China, 2002
2021年中国科学院大学-BHPB导师科研奖(UCAS-BHPB Excellent Supervisor Award, November 2021)
2020年中国科学院大学“领雁金奖”引航奖(UCAS Lingyan Golden Award, September 2020)
2019年国家“万人计划”青年拔尖人才(National Ten Thousand Talent Program for Young Top-notch Talent, February 2019)
2018年中国科学院大学-BHPB导师科研奖(UCAS-BHPB Excellent Supervisor Award, September 2018)
2017年中国科学院北京基因组研究所特聘研究员(BIG Distinguished Professor, September 2017)
2017年中国科学院“百人计划”终期评估优秀奖(Excellence Award in the Final Evaluation of the CAS 100-Talent Program, August 2017)
2021年中国科学院-必和必拓BHPB奖 - 滕徐菲
2021年博士研究生国家奖学金 - 李昭
2021年硕士研究生国家奖学金 - 朱彤彤
2021年北京市普通高等学校优秀毕业生 - 刘琳
2020年博士研究生国家奖学金 - 刘琳
2020年硕士研究生国家奖学金 - 张源笙
2020年第二届精准医学前沿研究生学术论坛论文荣誉奖 - 刘琳
2020年第二届精准医学前沿研究生学术论坛最佳论文三等奖 - 滕徐菲
2019年第四届国际生命与健康大数据论坛最佳报告奖 - 滕徐菲
2019年北京市普通高等学校优秀毕业生 - 王佩
2019年硕士研究生国家奖学金 - 王佩
2019年北京市普通高等学校优秀毕业生 - 桑健
2018年博士研究生国家奖学金 - 桑健
2018年硕士研究生国家奖学金 - 曹佳宝
2018年中国科学院-必和必拓BHPB奖 - 桑健
2017年地奥奖学金 - 徐行健
Big Data Integration and Curation: construction of multi-omics databases and knowledgebases by big data integration and curation and development of new theory for biological big data commons and ecosystem, with particular focuses on public health and national strategic important species.
生物大数据整合审编与数据库系统研发:面向我国人口健康和重要战略生物资源,建立海量多组学数据资源体系,研发多层次组学数据库、信息库与知识库系统,发展生物大数据公共资源生态系统理论。
Computational Health Genomics: development of new methods and algorithms by associating omics data with health data and conducting integrative data analysis and deep mining via artificial intelligence and machine learning, with the aim to provide more effective ways for precision health and medical treatment for brain tumors, like glioma.
健康基因组数据智能深度挖掘:围绕人类脑胶质瘤等重大疾病,基于人工智能、机器学习、统计学习等多学科前沿交叉技术,研发面向精准医学的肿瘤多组学数据与健康数据的整合分析和深度挖掘的新方法与新技术。
Computational Molecular Evolution: establishment of molecular evolutionary models and theories at the nucleotide and codon levels and development of new methods and tools for detecting national selection pressure.
计算分子进化与自然选择压力检测:发展分子序列在核苷酸和密码子水平上的演化新模型和新理论,研发自然选择压力检测新方法与新技术。
Introduction to Omics (for graduates; in English)
Bioinformatics, Genomics, Big Data (for graduates; in Chinese)
Genomics (for undergraduates; in Chinese)
BrainBase: a curated knowledgebase for brain diseases
Editome Disease Knowledgebase: a knowledgebase of editome-disease associations
Plant Editosome Database: a curated database of RNA editosome in plant
LncBook + LncRNAWiki: a expert + community curated resource for human long non-coding RNAs
Database Commons: a catalog of global biological databases
KaKs_Calculator: a toolkit for estimating nonsynonymous and synonymous substitution rates (v1: >700 citations; v2: >510 citations, as of July 2021; Google Scholar)
Academic Degree Committee Memeber: Beijing Institute of Genomics, CAS (2015—)
Associate Editor: Bioinformatics Advances (2021—)
Asian Associate Editor: Briefings in Bioinformatics (2017—)
Associate Editor-in-Chief: Genomics, Proteomics & Bioinformatics (2012—)
Peer Reviewer Publons: https://publons.com/author/388485
Grant Referee: NSFC, MOST, UK BBSRC
Executive Committee Member: International Society for Biocuration (2015—2018)
Membership: Genetics Society of China, International Society for Computational Biology
Zhang 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-34990803
李茹姣, 张欣, 宋述慧, 王彦青, 邹东, 肖景发, 赵文明, 章张, 鲍一明: 基因组科学数据的安全管理与应用. 大数据 2022, 8(1):37-45.
Zhang 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-34591957
Xiong 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-34718752
Liu 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-34718720
Liu 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-34751395
Jiang 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-34718745
Jia 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-34643715
CNCB-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-34718731
Chen 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-34400360
Chen 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-34175476
Zhang SS, Chen X, Chen TT, Zhu JW, Tang BX, Wang AK, Dong LL, Zhang ZW, Sun YL, Yu CX, Zhai S, Sun YB, Chen HX, Du ZL, Xiao JF, Zhang Z, Bao YM, Wang YQ, Zhao WM: GSA-Human: Genome Sequence Archive for Human. Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji 2021, 43(10):988-993. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-34702711
The 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-33106848
Liu 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-33718187
Li 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-33045751
Li 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-33170268
CNCB-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-33175170
Zhao 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-32102777
Zhang 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-32360769
Yan 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-32619768
Xiong 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-31584095
Tian 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-31566222
Teng 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-33581339
Song 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-33704069
Sang 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-32683045
National 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-31702008
Miao 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-34557722
Liu 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-32539851
Li 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-31599330
Li 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-32756901
Gong 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-33045776
Zhao 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-30335176
Zhang 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:000518438500001
Yin 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-30184145
Wang 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-30649200
The 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-30395267
Tang 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-30371881
Song 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-30716410
Pervaiz 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-31221090
Niu 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-30357418
Ma 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-31524988
Ma 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-30329098
Li 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-30364969
Li 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-30364952
BIG 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-30365034
Zhang 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-30268933
Song 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-30771506
Song 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-29069473
Sang 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-29036693
Li 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-29161430
International Society for Biocuration: Biocuration: Distilling data into knowledge. PLOS Biology 2018, 16(4):e2002846. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-29659566
BIG 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-29036542
Zhao 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-28962009
Xu 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-28172557
Xia 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-28529082
Wang 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-28387199
The 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 S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME: RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 2017, 45(D1):D128-D134. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-27794554
Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB: DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biol 2017, 14(7):963-971. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-28387604
BIG Data Center Members: The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017, 45(D1):D18-D24. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-27899658
Zhao W, Zhang S, Tang B, Chen T, Hao L, Sang J, Li R, Xiao J, Zhang Z: Constructing the international database management system for omics big data. Big Data Research 2016, 2(6):43-52.
Yin HY, Ma LN, Wang GY, Li MW, Zhang Z: Old genes experience stronger translational selection than young genes. Gene 2016, 590(1):29-34. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-WOS:000381539800004
Yin H, Wang G, Ma L, Yi SV, Zhang Z: What Signatures Dominantly Associate with Gene Age? Genome Biol Evol 2016, 8(10):3083-3089. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-27609935
Xue Y, Lameijer EW, Ye K, Zhang K, Chang S, Wang X, Wu J, Gao G, Zhao F, Li J, Han C, Xu S, Xiao J, Yang X, Ying X, Zhang X, Chen WH, Liu Y, Zhang Z, Huang K, Yu J: Precision Medicine: What Challenges Are We Facing? Genomics Proteomics Bioinformatics 2016, 14(5):253-261. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-27744061
Wang G, Sun S, Zhang Z: Randomness in Sequence Evolution Increases over Time. PLoS One 2016, 11(5):e0155935. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-27224236
Tian X, Zhang Z, Yang T, Chen M, Li J, Chen F, Yang J, Li W, Zhang B, Zhang Z, Wu J, Zhang C, Long L, Xiao J: Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level. Front Microbiol 2016, 7:998. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-27446038
Sun S, Xiao J, Zhang H, Zhang Z: Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli. Front Microbiol 2016, 7:1180. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-27536275
Consortium IRP, Hao L, Zhang H, Zhang Z, Hu S, Xue Y: Information Commons for Rice (IC4R). Nucleic Acids Res 2016, 44(D1):D1172-1180. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-26519466
Zou D, Sun S, Li R, Liu J, Zhang J, Zhang Z: MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data. Nucleic Acids Res 2015, 43(Database issue):D54-58. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25294826
Zou D, Ma L, Yu J, Zhang Z: Biological databases for human research. Genomics Proteomics Bioinformatics 2015, 13(1):55-63. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25712261
Zhang Y, Chen L, Zhang Z: The Curation and Analysis of Rice Stress-Resistance Genes Based on RiceWiki. Hans Journal of Computational Biology 2015, 5(3):29-40.
Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z: LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res 2015, 43(Database issue):D187-192. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25399417
Bai B, Zhao WM, Tang BX, Wang YQ, Wang L, Zhang Z, Yang HC, Liu YH, Zhu JW, Irwin DM, Wang GD, Zhang YP: DoGSD: the dog and wolf genome SNP database. Nucleic Acids Res 2015, 43(Database issue):D777-783. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25404132
Zhao Y, Jia X, Yang J, Ling Y, Zhang Z, Yu J, Wu J, Xiao J: PanGP: a tool for quickly analyzing bacterial pan-genome profile. Bioinformatics 2014, 30(9):1297-1299. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-24420766
Zhang Z, Zhu W, Luo J: Bringing biocuration to China. Genomics Proteomics Bioinformatics 2014, 12(4):153-155. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25042682
Zhang Z, Sang J, Ma L, Wu G, Wu H, Huang D, Zou D, Liu S, Li A, Hao L, Tian M, Xu C, Wang X, Wu J, Xiao J, Dai L, Chen LL, Hu S, Yu J: RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Res 2014, 42(Database issue):D1222-1228. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-24136999
Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y, Xu J, Zheng X, Ren L, Wang G, Zhang Y, Huo L, Zhao Z, Cao D, Lu C, Li C, Zhou Y, Liu Z, Fan Z, Shan G, Li X, Wu S, Song L, Hou G, Jiang Y, Jeney Z, Yu D, Wang L, Shao C, Song L, Sun J, Ji P, Wang J, Li Q, Xu L, Sun F, Feng J, Wang C, Wang S, Wang B, Li Y, Zhu Y, Xue W, Zhao L, Wang J, Gu Y, Lv W, Wu K, Xiao J, Wu J, Zhang Z, Yu J, Sun X: Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet 2014, 46(11):1212-1219. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25240282
Wu J, Xiao J, Zhang Z, Wang X, Hu S, Yu J: Ribogenomics: the science and knowledge of RNA. Genomics Proteomics Bioinformatics 2014, 12(2):57-63. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-24769101
Wu H, Fang Y, Yu J, Zhang Z: The quest for a unified view of bacterial land colonization. The ISME journal 2014, 8(7):1358-1369. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-24451209
Wu G, Zhu J, Yu J, Zhou L, Huang JZ, Zhang Z: Evaluation of five methods for genome-wide circadian gene identification. Journal of biological rhythms 2014, 29(4):231-242. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25238853
Ma L, Cui P, Zhu J, Zhang Z, Zhang Z: Translational selection in human: more pronounced in housekeeping genes. Biol Direct 2014, 9:17. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25011537
Kang Y, Gu C, Yuan L, Wang Y, Zhu Y, Li X, Luo Q, Xiao J, Jiang D, Qian M, Ahmed Khan A, Chen F, Zhang Z, Yu J: Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks. mBio 2014, 5(6):e01867. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-25425232
Zhang Z, Yu J: Does the genetic code have a eukaryotic origin? Genomics Proteomics Bioinformatics 2013, 11(1):41-55. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23402863
Wu J, Xiao J, Wang L, Zhong J, Yin H, Wu S, Zhang Z, Yu J: Systematic analysis of intron size and abundance parameters in diverse lineages. Sci China Life Sci 2013, 56(10):968-974. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-24022126
Tong X, Yang Y, Wang W, Bai Z, Ma L, Zheng X, Sun H, Zhang Z, Zhao M, Yu J, Ge RL: Expression profiling of abundant genes in pulmonary and cardiac muscle tissues of Tibetan Antelope (Pantholops hodgsonii). Gene 2013, 523(2):187-191. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23612247
Ma L, Bajic VB, Zhang Z: On the classification of long non-coding RNAs. RNA Biol 2013, 10(6):925-933. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23696037
Dai L, Xu C, Tian M, Sang J, Zou D, Li A, Liu G, Chen F, Wu J, Xiao J, Wang X, Yu J, Zhang Z: Community intelligence in knowledge curation: an application to managing scientific nomenclature. PLoS One 2013, 8(2):e56961. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23451119
Dai L, Tian M, Wu J, Xiao J, Wang X, Townsend JP, Zhang Z: AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification. Bioinformatics 2013, 29(14):1837-1839. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23732274
Chen M, Xiao J, Zhang Z, Liu J, Wu J, Yu J: Identification of human HK genes and gene expression regulation study in cancer from transcriptomics data analysis. PLoS One 2013, 8(1):e54082. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23382867
Zhang Z, Yu J: The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids. Genomics Proteomics Bioinformatics 2012, 10(4):175-180. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23084772
Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L: ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. Biochem Biophys Res Commun 2012, 419(4):779-781. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-22390928
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J: Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 2012, 13(1):43. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-22435713
Wu H, Zhang Z, Hu S, Yu J: On the molecular mechanism of GC content variation among eubacterial genomes. Biol Direct 2012, 7(1):2. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-22230424
Wu H, Qu H, Wan N, Zhang Z, Hu S, Yu J: Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition. Genomics Proteomics Bioinformatics 2012, 10(4):186-196. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23084774
Dai L, Gao X, Guo Y, Xiao J, Zhang Z: Bioinformatics clouds for big data manipulation. Biol Direct 2012, 7:43; discussion 43. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-23190475
Cui P, Liu W, Zhao Y, Lin Q, Zhang D, Ding F, Xin C, Zhang Z, Song S, Sun F, Yu J, Hu S: Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis. Genomics Proteomics Bioinformatics 2012, 10(2):82-93. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-22768982
Cui P, Ding F, Lin Q, Zhang L, Li A, Zhang Z, Hu S, Yu J: Distinct contributions of replication and transcription to mutation rate variation of human genomes. Genomics Proteomics Bioinformatics 2012, 10(1):4-10. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-22449396
Zhang Z, Yu J: On the organizational dynamics of the genetic code. Genomics Proteomics Bioinformatics 2011, 9(1-2):21-29. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-21641559
Zhang Z, Bajic VB, Yu J, Cheung K-H, Townsend JP: Data Integration in Bioinformatics: Current Efforts and Challenges. In: Bioinformatics - Trends and Methodologies. Edited by Mahdavi MA, vol. 1. Rijeka, Croatia: InTech; 2011: 41-56.
Zhang Z, Yu J: Modeling compositional dynamics based on GC and purine contents of protein-coding sequences. Biol Direct 2010, 5:63. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-21059261
Zhang Z, Townsend JP: The filamentous fungal gene expression database (FFGED). Fungal Genet Biol 2010, 47(3):199-204. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-20025988
Zhang Z, Lopez-Giraldez F, Townsend JP: LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics 2010, 26(15):1918-1919. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-20538728
Wang D, Zhang Y, Zhang Z, Zhu J, Yu J: KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics 2010, 8(1):77-80. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-20451164
Qu HZ, Wu H, Zhang TW, Zhang Z, Hu SN, Yu J: Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Research in Microbiology 2010, 161(10):838-846. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-WOS:000286156800006
Zhang Z, Townsend JP: Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Comput Biol 2009, 5(6):e1000421. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-19557160
Zhang Z, Cheung KH, Townsend JP: Bringing Web 2.0 to bioinformatics. Brief Bioinform 2009, 10(1):1-10. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-18842678
Li J, Zhang Z, Vang S, Yu J, Wong GK, Wang J: Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J Mol Evol 2009, 68(4):414-423. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-19308632
Zheng H, Shi J, Fang X, Li Y, Vang S, Fan W, Wang J, Zhang Z, Wang W, Kristiansen K, Wang J: FGF: a web tool for Fishing Gene Family in a whole genome database. Nucleic Acids Res 2007, 35(Web Server issue):W121-125. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-17584790
Zhao X, Zhang Z, Yan J, Yu J: GC content variability of eubacteria is governed by the pol III alpha subunit. Biochem Biophys Res Commun 2007, 356(1):20-25. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-17336933
Hu J, Zhao X, Zhang Z, Yu J: Compositional dynamics of guanine and cytosine content in prokaryotic genomes. Res Microbiol 2007, 158(4):363-370. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-17449227
Zhang Z, Yu J: Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates. Genomics Proteomics Bioinformatics 2006, 4(3):173-181. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-17127215
Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J: KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 2006, 4(4):259-263. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-17531802
Zhang Z, Li J, Yu J: Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol Biol 2006, 6:44. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-16740169
Li H, Coghlan A, Ruan J, Coin LJ, Heriche JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R: TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res 2006, 34(Database issue):D572-580. https://ngdc.cncb.ac.cn/openlb/publication/OLB-PM-16381935
Biological Big Data Deposition, Public Sharing and Database Resources. The 10th
National Conference on Bioinformatics and System Biology of China, Chengdu, October 25-29, 2021.
Database Resources of the National Genomics Data Center. The 9th National Conference on Bioinformatics and System Biology of China, Shanghai, September 26-29, 2020.
Computational genomics of brain tumors: glioma biomarker identification and characterization through multi-omics integrative molecular profiling. KAUST Research Conference Digital Health 2020, Thuwal, Saudi Arabia, January 20-22, 2020.
Building a big data ecosystem for bioinformatics. The 4th Annual European Bioinformatics Core Community Workshop, Basel, Switzerland, 26 July 2019.
生命组学大数据管理与资源体系建设, 中国科学院青年创新促进会第一届青年生命科学论坛, 乌鲁木齐, 2019年7月12-16日.
生命组学数据资源体系建设, 第六届全国计算生物学与生物信息学学术会议, 成都, 2019年3月30-31日.
Database Resources of the BIG Data Center in 2018. International Conference on Precision Medicine, Bangkok, Thailand, 19-20 July 2018.
基因大数据汇交共享与多组学数据资源体系建设, 北京生物信息学系列论坛, 北京大学, 2018年1月19日
The BIG Data Center: from deposition to integration to translation. The Sino-ASEAN Conference on Precision Medicine, Burapha University, Thailand, 17-18 June 2017.
The BIG Data Center’s database resources: towards precision medicine . The 10th International Biocuration Conference, Stanford University, United States, 26-29 March 2017.
The BIG Data Center: from deposition to integration to translation. The 4th Youth Forum for Computer & Life Sciences Interdisciplinary Research (第四届数学、计算机与生命科学交叉研究青年学者论坛), Beijing, China, May 21-22, 2016.
The BIG Data Center for Life and Health Sciences. The Phoenix City Forum for Genome Informatics (基因组信息学凤凰城论坛), Tangshan, China, May 13-15, 2016.
The BIG Data Center: from deposition to integration to translation. The 9th International Biocuration Conference, Geneva, Switzerland, April 10-14, 2016.
Big Data integration: scalability and sustainability. KAUST Research Conference on Computational and Experimental Interfaces of Big Data and Biotechnology, Thuwal, Saudi Arabia, Jan. 25-27, 2016.
Toward Sustainability and Scalability for Big Data Integration. 2015 Functional Genomics Summit II, Beijing, China, Nov. 11-12, 2015.
Community integration of big data. The 2015 International Conference of Genomics, Xi'an, China, Oct. 22-25, 2015.
Bringing biocuration to China. The 1st International Coastal Biology Congress, Yantai, China, Sept. 26-30, 2014.
Big data integration, curation, and analysis. The 3rd Young Bioinformatics PI Workshop, Guangzhou, China, Sept. 19-21, 2014.
Biocuration in the era of big data. The Workshop on Statistical and Computational Theory and Methodology for Big Data Analysis, Banff, Canada, Feb. 9-14, 2014.
Community curation in biological knowledge wikis. The 6th International Biocuration Conference, Churchill College, Cambridge, United Kingdom, April 7-10, 2013.
Rewarding community-curated contributions in biological knowledge wikis. The High-throughput Sequencing Data Analysis and Approaches Workshop, Beijing, China, Dec. 5-7, 2012.
Next-Generation Bioinformatics: harnessing collective resources for large-scale data manipulation, in workshop “Challenges and future of Bioinformatics: sharing insights from the Dutch and Chinese perspective”, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China, March 19, 2012.