National Genomics Data Center

Zhang Zhang

Professor

Email: zhangzhang (AT) big.ac.cn

Tel: +86 (10) 8409-7261

Chinese Name: 章张  CV-EN-ZZ.pdf


PROFESSIONAL EXPERIENCE

  • 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 CenterBeijing Institute of Genomics, Chinese Academy of Sciences, China, 2016 - 2020

  • Professor, University of Chinese Academy of Sciences, China, 2016 - 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

EDUCATION

  • 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

HONORS & AWARDS

  • National Ten Thousand Talent Program for Young Top-notch Talent, February 2019

  • UCAS-BHPB Excellent Supervisor Award, September 2018

  • Professor Rank Promotion to 3rd-level (under Four Levels Academic Rank System in CAS), April 2018

  • BIG Distinguished Professor, September 2017

  • Excellence Award in the Evaluation of the CAS 100-Talent Program, August 2017

RESEARCH INTERESTS

  • Big Data Integration and Curation: construction of multi-omics databases and knowledgebases by big data integration and curation and development of new theory as well as data commons for biological big data 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。

  • 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.

    基于人工智能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、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。

TEACHING

  • Introduction to Omics (for graduates; in English)

  • Bioinformatics, Genomics, Big Data (for graduates; in Chinese)

  • Genomics (undergraduates; in Chinese)

FEATURED PROJECTS & RESOURCES

ACADEMIC ACTIVITIES

PUBLICATIONS

  1. Li QP, Li Z, Feng CR, Jiang S, Zhang Z, Ma LN: Multi-omics annotation of human long non-coding RNAs. Biochemical Society Transactions 2020, accepted. [PMID=32756901]

  2. Yan J, Zou D, Li C, Zhang Z, Song SH, Wang XF: SR4R: an integrative SNP resource for genomic breeding and population research in rice. Genomics, Proteomics & Bioinformatics 2020, accepted. [PMID=32619768]

  3. Liu L, Wang GY, Wang LG, Yu CL, Li MW, Song SH, Hao LL, Ma LN, Zhang Z: Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biology Direct 2020, 15(1):10. [PMID=32539851]

  4. Zhang Z, Song SH, Yu J, Zhao WM, Xiao JF, Bao YM: The elements of data sharing. Genomics, Proteomics & Bioinformatics 2020, 18(1):1-4. [PMID=32360769]

  5. 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 resourceYi Chuan 2020, 42(2):212-221. [PMID=32102777]

  6. National Genomics Data Center Members and Partners: Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 2020, 48(D1):D24-D33. [PMID=31702008]

  7. 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. [PMID=31566222]

  8. 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. [PMID=31584095]

  9. Li Z, Zhang Y, Zou D, Zhao Y, Wang H, 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. [PMID=31599330]

  10. Sang J, Zou D, Wang ZN, Wang F, Zhang YS, Xia L, Li ZH, Ma LN, Li MW, Xu BX, Liu XN, Wu SY, Liu L, Niu GY, Li M, Luo YF, Hu SN, Hao LL, Zhang Z: Rice Genome Reannotation Using Massive RNA-Seq Data in IC4R. Genomics Proteomics & Bioinformatics 2020, in press. [PMID=32683045]

  11. Yin H, Li M, Xia L, He C, Zhang Z: Computational determination of gene age and characterization of evolutionary dynamics in human. Briefings in Bioinformatics, 2019, 20(6):2141-2149. [PMID=30184145]

  12. 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. [PMID=31837468]

  13. 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. [PMID=31221090]

  14. Ma LN, Cao J, Liu L, Li Z, Shireen H, Pervaiz N, Batool F, Raza R, Zou D, Bao YM, Abbasi AA, Zhang Z: Community curation and expert curation of human long non-coding RNAs. Current Protocols in Bioinformatics 2019, 67(1):e82.

  15. Song SH, Zhang Z: Database Resources in BIG Data Center: Submission, Archive and Integration of Big Data in Plant Science. Molecular Plant 2019, 12(3):279-281.[PMID=30716410]

  16. 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. Bioinformatics 2019, 35(17):2949-2956. [PMID=30649200]

  17. Zhang Z as corresponding author in BIG Data Center Members: Database Resources of the BIG Data Center in 2019. Nucleic Acids Res 2019, 47(D1):D8-D14. [PMID=30365034]

  18. 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. [PMID=30364969]

  19. 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. [PMID=30329098]

  20. 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. [PMID=30364952]

  21. 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. [PMID=30357418]

  22. 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 Res 2019, 47(D1):D793-D800. [PMID=30371881]

  23. 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 Res 2019, 47(D1):D163-D169. [PMID=30335176]

  24. Zhang Z authored in The RNAcentral Consortium: RNAcentral: A hub of information for non-coding RNA sequences. Nucleic Acids Res 2019, 47(D1):D221-D229. [PMID=30395267]

  25. Song SH, Tian DM, Zhang Z, Hu SN, Yu, J: Rice Genomics: Over the Past Two Decades and Into the Future. Genomics Proteomics Bioinformatics 2018, 16(6):397-404. [PMID=30771506]

  26. Zhang Z, Xue Y, Zhao F: Bioinformatics Commons: The Cornerstone of Life and Health Sciences. Genomics Proteomics & Bioinformatics 2018, 16(4):223-225. [PMID=30268933]

  27. Zhang Z listed in International Society for Biocuration: Biocuration: Distilling data into knowledge. PLoS Biology 2018, 16(4):e2002846. [PMID=29659566]

  28. 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 Res 2018, 46(D1):D288-D295. [PMID=29161430]

  29. 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 Res 2018, 46(D1):D121-D126.  [PMID=29069473]

  30. Zhang Z as corresponding author in BIG Data Center Members: Database Resources of the BIG Data Center in 2018. Nucleic Acids Res 2018, 46(D1):D14-D20. [PMID=29036542]

  31. Sang J, Wang ZN,..., Hao LL, Zhang Z: ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Res 2018, 46(D1):D121-D126. [PMID=29036693]

  32. 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 Evolution 2017, 34(11):3006-3022. [PMID=28962009]

  33. 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]

  34. 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 Biology 2017, 14(7):963-971.[PMID=28387604]

  35. Wang YQ, ..., Zhang Z, Zhao WM: GSA: Genome Sequence Archive. Genomics, Proteomics & Bioinformatics 2017, 15(1):14-18. [PMID=28387199]  [Cover Story; Preview]

  36. Xu XJ, Ji ZH, Zhang Z: CloudPhylo: a fast and scalable tool for phylogeny reconstruction. Bioinformatics 2017, 33 (3):438-440. [PMID=28172557]

  37. Zhang Z authored in The RNAcentral Consortium: RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 2017, 45(D1):D128-D134. [PMID=27794554]

  38. Zhang Z as corresponding author in BIG Data Center Members: The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017, 45(D1):D18-D24. [PMID=27899658]

  39. 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. (In Chinese)

  40. Xue Y, ..., Zhang Z., Huang K, Yu J: Precision Medicine: What Challenges Are We Facing? Genomics Proteomics Bioinformatics 2016, 14(5):253-261. [PMID=27744061]

  41. Yin HY, Wang GY, Ma LN, Yi SV, Zhang Z: What signatures dominantly associate with gene age? Genome Biology and Evolution 2016, 8(10):3083-9. [PMID=27609935]

  42. 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 Microbiology 2016, 7:1180. [PMID=27536275]

  43. 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. [PMID=27259662]

  44. 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 Microbiology 2016, 7:998. [PMID=27446038]

  45. Wang GY, Sun SX, Zhang Z: Randomness in sequence evolution increases over time. PLoS One 201611(5): e0155935. [PMID=27224236]

  46. Zhang Z as corresponding author in IC4R Project Consortium: Information Commons for Rice (IC4R)Nucleic Acids Res 2016, 44(D1):D1172-1180. [PMID=26519466]

  47. Zhang Y, Chen LL, Zhang Z: The Curation and Analysis of Rice Stress-Resistance Genes Based on RiceWiki. Hans Journal of Computational Biology 2015, 5(3):29-40. (in Chinese)

  48. 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. [PMID=25294826]

  49. Zou D, Ma L, Yu J, Zhang Z: Biological databases for human researchGenomics Proteomics Bioinformatics 2015, 13(1):55-63. [PMID=25712261]

  50. 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 RNAsNucleic Acids Res 2015, 43(Database issue):D187-192. [PMID=25399417]

  51. 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 databaseNucleic Acids Res 2015, 43(Database issue):D777-783. [PMID=25404132]

  52. 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 profileBioinformatics 2014, 30(9):1297-1299.[PMID=24420766]

  53. Zhang Z, Zhu W, Luo J: Bringing biocuration to ChinaGenomics Proteomics Bioinformatics 2014, 12(4):153-155. [PMID=25042682]

  54. 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 genesNucleic Acids Res 2014, 42(Database issue):D1222-1228. [PMID=24136999]

  55. 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 carpioNat Genet 2014, 46(11):1212-1219. [PMID=25240282]

  56. Wu J, Xiao J, Zhang Z, Wang X, Hu S, Yu J: Ribogenomics: the science and knowledge of RNAGenomics Proteomics Bioinformatics 2014, 12(2):57-63. [PMID=24769101]

  57. Wu H, Fang Y, Yu J, Zhang Z: The quest for a unified view of bacterial land colonizationThe ISME journal 2014, 8(7):1358-1369. [PMID=24451209]

  58. Wu G, Zhu J, Yu J, Zhou L, Huang JZ, Zhang Z: Evaluation of five methods for genome-wide circadian gene identificationJournal of biological rhythms 2014, 29(4):231-242.[PMID=25238853]

  59. Ma L, Cui P, Zhu J, Zhang Z, Zhang Z: Translational selection in human: more pronounced in housekeeping genesBiol Direct 2014, 9:17. [PMID=25011537]

  60. 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 frameworksmBio 2014, 5(6):e01867. [PMID=25425232]

  61. Zhang Z, Yu J: Does the genetic code have a eukaryotic origin?Genomics Proteomics Bioinformatics 2013, 11(1):41-55. [PMID=23402863]

  62. Zhang Z, Wong GK, Yu J: Protein codingEncyclopedia of Life Sciences (eLS) 2013. [Link]

  63. 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 lineagesSci China Life Sci 2013, 56(10):968-974. [PMID=24022126]

  64. 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. [PMID=23612247]

  65. Ma L, Bajic VB, Zhang Z: On the classification of long non-coding RNAsRNA Biol 2013, 10(6):925-933. [PMID=23696037]

  66. 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 nomenclaturePLoS One 2013, 8(2):e56961. [PMID=23451119]

  67. 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 quantificationBioinformatics 2013, 29(14):1837-1839. [PMID=23732274]

  68. 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 analysisPLoS One 2013, 8(1):e54082. [PMID=23382867]

  69. Zhang Z, Yu J: The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acidsGenomics Proteomics Bioinformatics 2012, 10(4):175-180. [PMID=23084772]

  70. Zhang Z, Xiao J, Wu J, Zhang H, Liu G, Wang X, Dai L: ParaAT: a parallel tool for constructing multiple protein-coding DNA alignmentsBiochem Biophys Res Commun 2012, 419(4):779-781. [PMID=22390928]

  71. Wu H, Zhang Z, Hu S, Yu J: On the molecular mechanism of GC content variation among eubacterial genomesBiol Direct 2012, 7(1):2. [PMID=22230424]

  72. 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. [PMID=23084774]

  73. Dai L, Gao X, Guo Y, Xiao J, Zhang Z: Bioinformatics clouds for big data manipulationBiol Direct 2012, 7:43; discussion 43. [PMID=23190475]

  74. 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 genomesGenomics Proteomics Bioinformatics 2012, 10(1):4-10.[PMID=22449396]

  75. 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 significanceBMC Bioinformatics 2012, 13(1):43. [PMID=22435713]

  76. 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 testisGenomics Proteomics Bioinformatics 2012, 10(2):82-93. [PMID=22768982]

  77. 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]

  78. Zhang Z, Yu J: On the organizational dynamics of the genetic codeGenomics Proteomics Bioinformatics 2011, 9(1-2):21-29. [PMID=21641559]

  79. Zhang Z, Yu J: Modeling compositional dynamics based on GC and purine contents of protein-coding sequencesBiol Direct 2010, 5(1):63. [PMID=21059261]

  80. Zhang Z, Townsend JP: The filamentous fungal gene expression database (FFGED)Fungal Genet Biol 2010, 47(3):199-204. [PMID=20025988]

  81. Zhang Z, Lopez-Giraldez F, Townsend JP: LOX: inferring Level Of eXpression from diverse methods of census sequencingBioinformatics 2010, 26(15):1918-1919.[PMID=20538728]

  82. Wang D, Zhang Y, Zhang Z, Zhu J, Yu J: KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategiesGenomics Proteomics Bioinformatics 2010, 8(1):77-80. [PMID=20451164]

  83. Qu H, Wu H, Zhang T, Zhang Z, Hu S, Yu J: Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomesRes Microbiol 2010, 161(10):838-846. [PMID=20868744]

  84. Zhang Z, Townsend JP: Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequencesPLoS Comput Biol 2009, 5(6):e1000421.[PMID=19557160]

  85. Zhang Z, Cheung KH, Townsend JP: Bringing Web 2.0 to bioinformaticsBriefings in Bioinformatics 2009, 10(1):1-10. [PMID=18842678]

  86. 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 lineageJ Mol Evol 2009, 68(4):414-423.[PMID=19308632]

  87. 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 databaseNucleic Acids Res 2007, 35(Web Server issue):W121-125. [PMID=17584790]

  88. Zhao X, Zhang Z, Yan J, Yu J: GC content variability of eubacteria is governed by the pol III alpha subunitBiochem Biophys Res Commun 2007, 356(1):20-25.[PMID=17336933]

  89. Hu J, Zhao X, Zhang Z, Yu J: Compositional dynamics of guanine and cytosine content in prokaryotic genomesRes Microbiol 2007, 158(4):363-370. [PMID=17449227]

  90. Zhang Z, Yu J: Evaluation of six methods for estimating synonymous and nonsynonymous substitution ratesGenomics Proteomics Bioinformatics 2006, 4(3):173-181.[PMID=17127215]

  91. Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J: KaKs_Calculator: calculating Ka and Ks through model selection and model averagingGenomics Proteomics Bioinformatics 2006, 4(4):259-263. [PMID=17531802]

  92. Zhang Z, Li J, Yu J: Computing Ka and Ks with a consideration of unequal transitional substitutionsBMC Evol Biol 2006, 6:44. [PMID=16740169]

  93. 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 familiesNucleic Acids Res 2006, 34(Database issue):D572-580. [PMID=16381935]

SELECTED INVITED TALKS

  1. 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.

  2. Building a big data ecosystem for bioinformatics. The 4th Annual European Bioinformatics Core Community Workshop, Basel, Switzerland, 26 July 2019.

  3. 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.

  4. 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.

  5. Database Resources of the BIG Data Center in 2018. International Conference on Precision Medicine, Bangkok, Thailand, 19-20 July 2018.

  6. 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

  7. The BIG Data Center: from deposition to integration to translation. The Sino-ASEAN Conference on Precision Medicine, Burapha University, Thailand, 17-18 June 2017.

  8. The BIG Data Center’s database resources: towards precision medicine . The 10th International Biocuration Conference, Stanford University, United States, 26-29 March 2017.

  9. 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.

  10. 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.

  11. The BIG Data Center: from deposition to integration to translation. The 9th International Biocuration Conference, Geneva, Switzerland, April 10-14, 2016.

  12. 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.

  13. Toward Sustainability and Scalability for Big Data Integration. 2015 Functional Genomics Summit II, Beijing, China, Nov. 11-12, 2015.

  14. Community integration of big data. The 2015 International Conference of Genomics, Xi'an, China, Oct. 22-25, 2015.

  15. Bringing biocuration to China. The 1st International Coastal Biology Congress, Yantai, China, Sept. 26-30, 2014.

  16. Big data integration, curation, and analysis. The 3rd Young Bioinformatics PI Workshop, Guangzhou, China, Sept. 19-21, 2014.

  17. 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.

  18. Community curation in biological knowledge wikis. The 6th International Biocuration Conference, Churchill College, Cambridge, United Kingdom, April 7-10, 2013.

  19. Rewarding community-curated contributions in biological knowledge wikis. The High-throughput Sequencing Data Analysis and Approaches Workshop, Beijing, China, Dec. 5-7, 2012.

  20. 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.