Wenming Zhao

Professor

Email: zhaowm (AT) big.ac.cn

Tel: +86 (10) 8409-7636

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

  • Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2018 - Present

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2012 - 2018

  • Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2008 - 2012

EDUCATION

  • M.S. in Computer & Engineering, Beihang University, Beijing, China, 2008

  • B.S. in Computer Technology & Application, Xi'an Technological University, Xi'an, China, 2001

HONORS & AWARDS

  • CAS Key Technology Talent Program, 2015. (中国科学院关键技术人才)

RESEARCH INTERESTS

  • Big data and data visualization

  • Bioinformatics Databases

  • Cloud Computing and High Performance Computing

PROJECTS & RESOURCES

  • BioProjecta centralized database for archiving and publishing research projects.

  • BioSample: a database focuses on structured and indexed descriptive information on biological samples.

  • GSA: a data repository for archiving raw sequence reads.

  • GSA-Humana data repository specialized for human genetic related data derived from biomedical researches.

  • OmixOpen Archive for Miscellaneous Data.

  • iDogan integrated resource for domestic dog (Canis lupus familiaris) and wild canids.

  • iSheep: a dedicated database for Ovis aries.

  • SorgSDa comprehensive database of sorghum genomic variations.

  • ChickenSDa data container for the variation information of chicken.

  • BioCloud: an online analysis toolkit for bioinformatics big data.

  • eGPS Cloud: evolutionary Genotype-Phenotype Systems (eGPS) cloud computing platform.

  • GenBrowser: SARS-COV-2 genome browser.

  • HGDA data portal of homologous genes across multiple species.

  • TCOD: Tropical Crops Omics Database.

ACADEMIC ACTIVITIES

  • Journal Reviewer: Bioinformatics, Briefings in Bioinformatics, BMC Genomics, Frontiers in Plant Science, Chinese Bulletin of Life Sciences, PLoS ONE

PUBLICATIONS

  1. Duan G, Wu G, Chen X, Tian D, Li Z, Sun Y, Du Z, Hao L, Song S, Gao Y, Xiao J, Zhang Z, Bao Y, Tang B, Zhao W*. HGD: an integrated homologous gene database across multiple species. Nucleic Acids Res. 2022 Nov 1:gkac970. doi: 10.1093/nar/gkac970. Epub ahead of print. PMID: 36318261.

  2. Yu D, Zhu J, Yang J, Pan YH, Mu H, Cao R, Tang B, Duan G, Hao ZQ, Dai L, Zhao GP, Zhang YP, Zhao W*, Zhang G*, Li H*. Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics. Zool Res. 2022 Sep 18;43(5):871-874. doi: 10.24272/j.issn.2095-8137.2022.238. PMID: 36031769; PMCID: PMC9486523.

  3. Zhao D, Zhang Z, Wang Z, Du Z, Wu M, Zhang T, Zhou J, Zhao W*, Meng Y*. Diagnosis and Prediction of Endometrial Carcinoma Using Machine Learning and Artificial Neural Networks Based on Public Databases. Genes (Basel). 2022 May 24;13(6):935. doi: 10.3390/genes13060935. PMID: 35741697; PMCID: PMC9222484.

  4. Yu D, Yang X, Tang B, Pan YH, Yang J, Duan G, Zhu J, Hao ZQ, Mu H, Dai L, Hu W, Zhang M, Cui Y, Jin T, Li CP, Ma L; Language translation team, Su X, Zhang G, Zhao W*, Li H*. Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2. Brief Bioinform. 2022 Jan 19:bbab583. doi: 10.1093/bib/bbab583. Epub ahead of print. PMID: 35043153.

  5. Zhang S, Zhu J, Tang B, Chen H, Xiao J, Zhang Z, Bao Y, Wang Y, Zhao W. GSA-Human: Genome Sequence Archive for Human[J]. 2021. Hereditas(Beijing)doi: 10.16288/j.yczz.21-248.

  6. 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. 2021 Aug 13:S1672-0229(21)00163-7. doi: 10.1016/j.gpb.2021.08.001. Epub ahead of print. PMID: 34400360.

  7. Wang ZH, Zhu QH, Li X, Zhu JW, Tian DM, Zhang SS, Kang HL, Li CP, Dong LL, Zhao WM*, Li MH*. iSheep: an Integrated Resource for Sheep Genome, Variant and Phenotype. Front Genet. 2021 Aug 17;12:714852. doi: 10.3389/fgene.2021.714852. PMID: 34490043; PMCID: PMC8418083.

  8. Liu Y, Wang Z, Wu X, Zhu J, Luo H, Tian D, Li C, Luo J, Zhao W*, Hao H*, Jing HC. SorGSD: updating and expanding the sorghum genome science database with new contents and tools. Biotechnol Biofuels. 2021 Aug 3;14(1):165. doi: 10.1186/s13068-021-02016-7. PMID: 34344425; PMCID: PMC8336335.

  9. 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 Dec 28:S1672-0229(20)30131-5. doi: 10.1016/j.gpb.2020.09.001. PMID: 33704069.

  10. Wang K, Wang J, Zhu C, Yang L, Ren Y, Ruan J, Fan G, Hu J, Xu W, Bi X, Zhu Y, Song Y, Chen H, Ma T, Zhao R, Jiang H, Zhang B, Feng C, Yuan Y, Gan X, Li Y, Zeng H, Liu Q, Zhang Y, Shao F, Hao S, Zhang H, Xu X, Liu X, Wang D, Zhu M, Zhang G*, Zhao W*, Qiu Q*, He S*, Wang W*. African lungfish genome sheds light on the vertebrate water-to-land transition. Cell. 2021 Mar 4;184(5):1362-1376.e18. doi: 10.1016/j.cell.2021.01.047. PMID: 33545087.

  11. Xue Y*, Bao Y*, Zhang Z*, Zhao W*, Xiao J*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021Nucleic Acids Res. 2021, 49: D18-D28.

  12. 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 speciesNucleic Acids Res 2021, 49(D1):D1186-D1191. [PMID=33170268]

  13. Gong Z, Zhu J, Li C, Jiang S, Ma L, Tang B, Zou D, Chen M, Sun Y, Song S, Zhang Z, Xiao J, Xue Y, Bao Y, Du Z*, Zhao W*An online coronavirus analysis platform from the National Genomics Data CenterZoological Research. 2020, 41(6): 705-708.

  14. Liu Q, Zhao S, Shi CM, Song S, Zhu S, Su Y, Zhao W, Li M, Bao Y, Xue Y, Chen H. Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters. Genomics Proteomics Bioinformatics. 2020 Jul 12:S1672-0229(20)30062-0. doi: 10.1016/j.gpb.2020.06.001. PMID: 32663617.

  15. Zhang Z*, Song S, Yu J, Zhao W, Xiao J, Bao Y, The Elements of Data SharingGenomics, Proteomics & Bioinformatics. 2020, 18:1-4.

  16. 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]

  17. Zhang Z*, Zhao W*, Xiao J*, Bao Y*, He S*, Zhang G*, Li Y*, Zhao G*, Chen R*, in National Genomics Data Center Members and Partners, Database Resources of the National Genomics Data Center in 2020Nucleic Acids Res. 2020, 48: D24-D33.

  18. Yu D, Dong L, Yan F, Mu H, Tang B, Yang X, Zeng T, Zhou Q, Gao F, Wang Z, Hao Z, Kang H, Zheng Y, Huang H, Wei Y, Pan W, Xu Y, Zhu J, Zhao S, Wang C, Wang P, Dai L, Li M, Lan L, Wang Y, Chen H, Li YX, Fu YX, Shao Z, Bao Y, Zhao F, Chen LN, Zhang GQ*, Zhao W*, Li H*. eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses. Natl Sci Rev. 2019 Oct;6(5):867-869. doi: 10.1093/nsr/nwz079. 

  19. Wang GD, Shao XJ, Bai B, Wang J, Wang X, Cao X, Liu YH, Wang X, Yin TT, Zhang SJ, Lu Y, Wang Z, Wang L, Zhao W, Zhang B, Ruan J, Zhang YP. Structural variation during dog domestication: insights from gray wolf and dhole genomes. Natl Sci Rev. 2019 Jan;6(1):110-122. doi: 10.1093/nsr/nwy076. Epub 2018 Jul 19. PMID: 34694297; PMCID: PMC8291444.

  20. 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 Y*, Li R*, Xiao J*, NucMap: a database of genome-wide nucleosome positioning map across speciesNucleic Acids Res. 2019, 47: D163-D169.

  21. Zhang Z*, Zhao W*, Xiao J*, Bao Y*, in BIG Data Center Members, Database Resources of the BIG Data Center in 2019Nucleic Acids Res. 2019, 47: D8-D14.

  22. Tang B, Zhou Q, Dong L, Li W, Zhang X, Lan L, Zhai S, Xiao J, Zhang Z, Bao Y, Zhang Y, Wang G*, Zhao W*iDog: an integrated resource for domestic dogs and wild canidsNucleic Acids Res. 2019, 47: D793-D800. 

  23. Tang B, Li F, Li J, Zhao W*, Zhang Z*. Delta: a new web-based 3D genome visualization and analysis platform. Bioinformatics. 2018 Apr 15;34(8):1409-1410. doi: 10.1093/bioinformatics/btx805. PMID: 29253110.

  24. Li R, Liang F, Li W, 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 speciesNucleic Acids Res. 2018, 46: D288-D295.

  25. Zhang SS, Chen TT, Zhu JW, Zhou Q, Chen X, Wang YQ, Zhao WM. GSA: Genome Sequence Archive. Yi Chuan. 2018 Nov 20;40(11):1044-1047. Chinese. doi: 10.16288/j.yczz.18-178. PMID: 30465538.

  26. 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 CenterNucleic Acids Res. 2018, 46: D121-D126.  

  27. Zhang Z*, Zhao W*, Xiao J*, Bao Y*, in BIG Data Center Members, Database Resources of the BIG Data Center in 2018Nucleic Acids Res. 2018, 46: D14-D20.

  28. 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 normalizationNucleic Acids Res. 2018, 46: D121-D126.

  29. Zhang Z*, Zhao W*, Xiao J*, et al. The BIG Data Center: from deposition to integration to translationNucleic Acids Research. 2017, 45, D18-D24.

  30. 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 WGSA: Genome Sequence ArchiveGenomics, Proteomics & Bioinformatics. 2017, 15:14-18.

  31. Luo H*, Zhao W*, Wang Y*, Xia Y, Wu X, Zhang L, Tang B, Zhu J, Fang L, Du Z, Bekele WA, Tai S, Jordan DR, Godwin ID, Snowdon RJ, Mace ES, Jing HC, Luo J: SorGSD: a sorghum genome SNP databaseBiotechnol Biofuels 2016, 9:6. [PMID=26744602]

  32. 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[J]. Big Data Research, 2016, 2(6): 2016065-.

  33. Ling S, Hu Z, Yang Z, Yang F, Li Y, Lin P, Chen K, Dong L, Cao L, Tao Y, Hao L, Chen Q, Gong Q, Wu D, Li W, Zhao W, Tian X, Hao C, Hungate EA, Catenacci DV, Hudson RR, Li WH, Lu X, Wu CI. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution. Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6496-505. doi: 10.1073/pnas.1519556112. Epub 2015 Nov 11. PMID: 26561581.

  34. 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 Research 2015, 43(D1):D777-D783. [PMID=25404132]

  35. Tang B, Wang Y, Zhu J, Zhao W.  Web resources for model organism studiesGenomics, proteomics & bioinformatics 2015, 13(1):64-68. [PMID=25707592]

  36. Ding J, Zhao L, Chang Y, Zhao W, Du Z, Hao Z. Transcriptome sequencing and characterization of Japanese scallop Patinopecten yessoensis from different shell color linesPLoS One 2015,10(2):e0116406. [PMID=25680107]

  37. Li B, Zong Y, Du Z, Chen Y, Zhang Z, Qin G, Zhao W, Tian S. Genomic characterization reveals insights into patulin biosynthesis and pathogenicity in Penicillium species.Mol Plant Microbe Interact 2015,28(6):635-47. [PMID=25625822]

  38. Di R, He J, Song S, Tian D, Liu Q, Liang X, Ma Q, Sun M, Wang J, Zhao W, Cao G, Wang J, Yang Z, Ge Y, Chu M. Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding seasonBMC Genomics 2014,15:899. [PMID=25318541]

  39. Liang F, Tang B, Wang Y, Wang J, Yu C, Chen X, Zhu J, Yan J, Zhao W*, Li R*. WBSA: web service for bisulfite sequencing data analysisPloS one 2014, 9(1):e86707.[PMID=24497972]

  40. Wang GD, Zhai W, Yang HC, Fan RX, Cao X, Zhong L, Wang L, Liu F, Wu H, Cheng LG, Poyarkov AD, Poyarkov NA Jr, Tang SS, Zhao WM, Gao Y, Lv XM, Irwin DM, Savolainen P, Wu CI, Zhang YP. The genomics of selection in dogs and the parallel evolution between dogs and humansNature Communications 2013,4:1860. [PMID=23673645]

  41. Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vågbø CB, Shi Y, Wang WL, Song SH, Lu Z, Bosmans RP, Dai Q, Hao YJ, Yang X, Zhao WM, Tong WM, Wang XJ, Bogdan F, Furu K, Fu Y, Jia G, Zhao X, Liu J, Krokan HE, Klungland A, Yang YG, He C. ALKBH5 is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility.Molecular Cell 2013,49(1):18-29. [PMID=23177736]

  42. Zhao W, Liu W, Tian D, Tang B, Wang Y, Yu C, Li R, Ling Y, Wu J, Song S, Hu S. wapRNA: a web-based application for the processing of RNA sequencesBioinformatics 2011, 27(21):3076-3077. [PMID=21896507]

  43. Tao Y, Ruan J, Yeh SH, Lu X, Wang Y, Zhai W, Cai J, Ling S, Gong Q, Chong Z, Qu Z, Li Q, Liu J, Yang J, Zheng C, Zeng C, Wang HY, Zhang J, Wang SH, Hao L, Dong L, Li W, Sun M, Zou W, Yu C, Li C, Liu G, Jiang L, Xu J, Huang H, Li C, Mi S, Zhang B, Chen B, Zhao W, Hu S, Zhuang SM, Shen Y, Shi S, Brown C, White KP, Chen DS, Chen PJ, Wu CI. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome dataProc Natl Acad Sci U S A2011,108(29):12042-7. [PMID=21730188]

  44. Zhou R*, Ling S*, Zhao W*, Osada N, Chen S, Zhang M, He Z, Bao H, Zhong C, Zhang B, Lu X, Turissini D, Duke NC, Lu J, Shi S, Wu CI. Population genetics in nonmodel organisms: II. natural selection in marginal habitats revealed by deep sequencing on dual platformsMol Biol Evol 2011,28(10):2833-42. [PMID=21504891]

  45. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK, Yang H. The Genomes of Oryza sativa: a history of duplicationsPLoS Biol 2005,3(2):e38. [PMID=15685292]

  46. Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, Yang H. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphismsNature 2004,432(7018):717-22. [PMID=15592405]

  47. Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X, Zhang Y, Ni P, Zhang J, Li S, Wang J, Wong GK, Zhao H, Yu J, Yang H, Wang J. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomicsNucleic Acids Res 2004,32:D377-82. [PMID=14681438]

  48. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H. A draft sequence of the rice genome (Oryza sativa L. ssp. indica)Science 2002,296:79-92. [PMID=11935017]