章张

章张的个人简介

章张，中国科学院北京基因组研究所特聘研究员。

教育经历

1998－2002 宁夏大学 计算机科学 学士

2002－2004 南京理工大学 计算机科学 硕士

2004－2007 中国科学院计算技术研究所 计算机科学 博士

工作经历

2007－2009 美国耶鲁大学（Yale University） 博士后（Postdoctoral Assoicate）

2009－2011 沙特阿卜杜拉国王科技大学（King Abdullah University of Science and Technology） 研究科学家（Research Scientist）

2011－至今 中国科学院北京基因组研究所“百人计划”研究员

2016－至今 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（Executive Director）

2017－至今 中国科学院北京基因组研究所 特聘研究员（BIG Distinguished Professor）

荣誉奖项

2011年 入选中国科学院“百人计划”

2017年 中国科学院“百人计划”终期评估优秀

2018年 中国科学院-必和必拓（CAS-BHPB）导师科研奖

2019年 入选国家“万人计划”青年拔尖人才

研究方向

本项目组的主要研究方向是生物大数据整合与深度挖掘，研究内容包括：

（1）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，研发多层次组学的数据库与知识库系统，发展生物大数据生态系统理论与数据共享资源。

（2）基于机器学习的健康基因组数据深度挖掘：围绕人类脑胶质瘤等重大疾病，基于人工智能和机器学习，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。

（3）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。

科研论著

Song SH, Zhang Z:Database Resources in BIG Data Center: Submission, Archive and Integration of Big Data in Plant Science.Molecular Plant2019, in press. [PMID=30716410]Wang GY, Yin HY, Li BY, Yu CL, Wang F, Xu XJ, Cao JB, Bao YM, Wang LG, Abbasi AA, Bajic VB, Ma LN, Zhang Z:Characterization and identification of long non-coding RNAs based on feature relationship.Bioinformatics2019, in press. [PMID=30649200]Zhang Z as corresponding author in BIG Data Center Members:Database Resources of the BIG Data Center in 2019.Nucleic Acids Res2019, 47(D1):D8-D14. [PMID=30365034]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 Res2019, 47(D1):D983-D988. [PMID=30364969]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 Res2019, 47(D1):D128-D134. [PMID=30329098]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 Res2019, 47(D1):D170-D174. [PMID=30364952]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 Res2019, 47(D1):D78-D83. [PMID=30357418]Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang Y-P, Wang G-D, Zhao W:iDog: an integrated resource for domestic dogs and wild canids.Nucleic Acids Res2019, 47(D1):D793-D800. [PMID=30371881]Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang ZW, 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 Res2019, 47(D1):D163-D169. [PMID=30335176]Zhang Z authored in The RNAcentral Consortium:RNAcentral: A hub of information for non-coding RNA sequences.Nucleic Acids Res2019, 47(D1):D221-D229. [PMID=30395267]Zhang Z, Xue Y, Zhao F:Bioinformatics Commons: The Cornerstone of Life and Health Sciences.Genomics Proteomics & Bioinformatics2018, 16(4):223-225. [PMID=30268933]Yin H, Li M, Xia L, He C, Zhang Z:Computational determination of gene age and characterization of evolutionary dynamics in human.Briefings in Bioinformatics2018, doi: 10.1093/bib/bby074. [PMID=30184145]Zhang Z listed in International Society for Biocuration:Biocuration: Distilling data into knowledge.PLoS Biology2018, 16(4):e2002846. [PMID=29659566]Li RJ, Liang F, Li W, Zou D, Sun SX, Zhao YB, Zhao WM, Bao YM, Xiao JF, Zhang Z:MethBank 3.0: a database of DNA methylomes across a variety of species.Nucleic Acids Res2018, 46(D1):D288-D295. [PMID=29161430]Song SH, Tian DM, Li CP, Tang BX, Dong LL, Xiao JF, Bao YM, Zhao WM, He H, Zhang Z:Genome Variation Map: a data repository of genome variations in BIG Data Center.Nucleic Acids Res2018, 46(D1):D121-D126. [PMID=29069473]Zhang Z as corresponding author in BIG Data Center Members:Database Resources of the BIG Data Center in 2018.Nucleic Acids Res2018, 46(D1):D14-D20. [PMID=29036542]Sang J, Wang ZN,..., Hao LL, Zhang Z:ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.Nucleic Acids Res2018, 46(D1):D121-D126. [PMID=29036693]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.Molecular Biology and Evolution2017, 34(11):3006-3022. [PMID=28962009]Xia L, Zou D, Sang J, Xu XJ, Yin HY, Li MW, Wu SY, Hu SN, Hao LL, Zhang Z:Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice.Journal of Genetics and Genomics, 2017, 44(5):235-241. [PMID=28529082]Salhi A, Essack M, Alam T,..., Zhang Z, Bajic V:DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining.RNA Biology2017, 14(7):963-971.[PMID=28387604]Wang YQ, ..., Zhang Z, Zhao WM:GSA: Genome Sequence Archive.Genomics, Proteomics & Bioinformatics2017, 15(1):14-18.[PMID=28387199] [Cover Story;Preview]Xu XJ, Ji ZH,Zhang Z:CloudPhylo: a fast and scalable tool for phylogeny reconstruction.Bioinformatics2017, 33 (3):438-440.[PMID=28172557]Zhang Z authored in The RNAcentral Consortium:RNAcentral: a comprehensive database of non-coding RNA sequences.Nucleic Acids Res2017, 45(D1):D128-D134.[PMID=27794554]Zhang Z as corresponding author in BIG Data Center Members:The BIG Data Center: from deposition to integration to translation.Nucleic Acids Res2017, 45(D1):D18-D24.[PMID=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.BigDataResearch2016,2(6):43-52.(InChinese)Xue Y, ...,Zhang Z.,Huang K, Yu J:Precision Medicine: What Challenges Are We Facing?Genomics Proteomics Bioinformatics2016, 14(5):253-261.[PMID=27744061]Yin HY, Wang GY, Ma LN, Yi SV,Zhang Z:What signatures dominantly associate with gene age?Genome Biology and Evolution2016, 8(10):3083-9.[PMID=27609935]Sun SX, Xiao JF, Zhang HY*,Zhang Z:Pangenome evidence for higher codon usage bias and stronger translational selection in core genes of Escherichia coli.Frontiers in Microbiology2016, 7:1180.[PMID=27536275]Yin HY, Ma LN, Wang GY, Li MW,Zhang Z:Old genes experience stronger translational selection than young genes.Gene2016, 590(1):29-34.[PMID=27259662]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.Frontiers in Microbiology2016, 7:998.[PMID=27446038]Wang GY, Sun SX,Zhang Z:Randomness in sequence evolution increases over time.PLoS One2016,11(5): e0155935.[PMID=27224236]Zhang Z as corresponding author in IC4R Project Consortium:Information Commons for Rice (IC4R).Nucleic Acids Res2016, 44(D1):D1172-1180.[PMID=26519466]Zhang Y, Chen LL, Zhang Z:The Curation and Analysis of Rice Stress-Resistance Genes Based on RiceWiki.Hans Journal of Computational Biology2015, 5(3):29-40. (in Chinese)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 Res2015, 43(Database issue):D54-58.[PMID=25294826]Zou D, Ma L, Yu J, Zhang Z:Biological databases for human research.Genomics Proteomics Bioinformatics2015, 13(1):55-63.[PMID=25712261]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 Res2015, 43(Database issue):D187-192.[PMID=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 Res2015, 43(Database issue):D777-783.[PMID=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.Bioinformatics2014, 30(9):1297-1299.[PMID=24420766]Zhang Z, Zhu W, Luo J:Bringing biocuration to China.Genomics Proteomics Bioinformatics2014, 12(4):153-155.[PMID=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 Res2014, 42(Database issue):D1222-1228.[PMID=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 Genet2014, 46(11):1212-1219.[PMID=25240282]Wu J, Xiao J, Zhang Z, Wang X, Hu S, Yu J:Ribogenomics: the science and knowledge of RNA.Genomics Proteomics Bioinformatics2014, 12(2):57-63.[PMID=24769101]Wu H, Fang Y, Yu J, Zhang Z:The quest for a unified view of bacterial land colonization.The ISME journal2014, 8(7):1358-1369.[PMID=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 rhythms2014, 29(4):231-242.[PMID=25238853]Ma L, Cui P, Zhu J, Zhang Z, Zhang Z:Translational selection in human: more pronounced in housekeeping genes.Biol Direct2014, 9:17.[PMID=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.mBio2014, 5(6):e01867.[PMID=25425232]Zhang Z, Yu J:Does the genetic code have a eukaryotic origin?.Genomics Proteomics Bioinformatics2013, 11(1):41-55.[PMID=23402863]Zhang Z, Wong GK, Yu J:Protein coding.Encyclopedia of Life Sciences (eLS)2013.[Link]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 Sci2013, 56(10):968-974.[PMID=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).Gene2013, 523(2):187-191.[PMID=23612247]Ma L, Bajic VB, Zhang Z:On the classification of long non-coding RNAs.RNA Biol2013, 10(6):925-933.[PMID=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 One2013, 8(2):e56961.[PMID=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.Bioinformatics2013, 29(14):1837-1839.[PMID=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 One2013, 8(1):e54082.[PMID=23382867]Zhang Z, Yu J:The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids.Genomics Proteomics Bioinformatics2012, 10(4):175-180.[PMID=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 Commun2012, 419(4):779-781.[PMID=22390928]Wu H, Zhang Z, Hu S, Yu J:On the molecular mechanism of GC content variation among eubacterial genomes.Biol Direct2012, 7(1):2.[PMID=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 Bioinformatics2012, 10(4):186-196.[PMID=23084774]Dai L, Gao X, Guo Y, Xiao J, Zhang Z:Bioinformatics clouds for big data manipulation.Biol Direct2012, 7:43; discussion 43.[PMID=23190475]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 Bioinformatics2012, 10(1):4-10.[PMID=22449396]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 Bioinformatics2012, 13(1):43.[PMID=22435713]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 Bioinformatics2012, 10(2):82-93.[PMID=22768982]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.[Link]Zhang Z, Yu J:On the organizational dynamics of the genetic code.Genomics Proteomics Bioinformatics2011, 9(1-2):21-29.[PMID=21641559]Zhang Z, Yu J:Modeling compositional dynamics based on GC and purine contents of protein-coding sequences.Biol Direct2010, 5(1):63.[PMID=21059261]Zhang Z, Townsend JP:The filamentous fungal gene expression database (FFGED).Fungal Genet Biol2010, 47(3):199-204.[PMID=20025988]Zhang Z, Lopez-Giraldez F, Townsend JP:LOX: inferring Level Of eXpression from diverse methods of census sequencing.Bioinformatics2010, 26(15):1918-1919.[PMID=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 Bioinformatics2010, 8(1):77-80.[PMID=20451164]Qu H, Wu H, Zhang T, Zhang Z, Hu S, Yu J:Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes.Res Microbiol2010, 161(10):838-846.[PMID=20868744]Zhang Z, Townsend JP:Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences.PLoS Comput Biol2009, 5(6):e1000421.[PMID=19557160]Zhang Z, Cheung KH, Townsend JP:Bringing Web 2.0 to bioinformatics.Briefings in Bioinformatics2009, 10(1):1-10.[PMID=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 Evol2009, 68(4):414-423.[PMID=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 Res2007, 35(Web Server issue):W121-125.[PMID=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 Commun2007, 356(1):20-25.[PMID=17336933]Hu J, Zhao X, Zhang Z, Yu J:Compositional dynamics of guanine and cytosine content in prokaryotic genomes.Res Microbiol2007, 158(4):363-370.[PMID=17449227]Zhang Z, Yu J:Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates.Genomics Proteomics Bioinformatics2006, 4(3):173-181.[PMID=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 Bioinformatics2006, 4(4):259-263.[PMID=17531802]Zhang Z, Li J, Yu J:Computing Ka and Ks with a consideration of unequal transitional substitutions.BMC Evol Biol2006, 6:44.[PMID=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 Res2006, 34(Database issue):D572-580.[PMID=16381935]