基本信息
陈华  男  博导  中国科学院北京基因组研究所(国家生物信息中心)
电子邮件: chenh@big.ac.cn
通信地址: 北京市朝阳区北辰西路1号院104号楼
邮政编码: 100101

研究领域

群体遗传学;计算基因组学;医学遗传学;法医遗传学

招生信息

   
招生专业
0710J3-生物信息学
0710Z1-基因组学
1001Z1-精准医学
招生方向
计算基因组学
统计与数量遗传学
复杂疾病的基因组学研究

教育背景

2003-09--2007-12   University of California, Berkeley   博士
学历
2003-09--2007-12   University of California, Berkeley   博士

工作经历

2015.2 - 至今,中国科学院北京基因组研究所(国家生物信息中心),研究员

2015.7 - 至今,科学院大学未来技术学院,岗位教授

2018.1 - 至今,中科院动物进化与遗传前沿交叉卓越创新中心,骨干


教授课程

统计基因组学与网络生物学
群体遗传与分子进化
数量与统计遗传学
医学遗传学与基因组学
健康数据与基因组技术
医学遗传学与人类基因组学
群体遗传学

科研活动

科研项目:

( 1 ) ****启动经费, 主持, 市地级, 2015-02--2018-12
( 2 ) "****“择优支持, 主持, 部委级, 2016-01--2018-12
( 3 ) 面向基因组大数据的群体遗传学分析方法研究, 主持, 国家级, 2016-01--2019-12
( 4 ) 微进化机制中群体基因组数据分析的新方法研究, 主持, 国家级, 2017-01--2018-12
( 5 ) 微量、降解生物物证分析关键技术在XX领域的应用研究, 参与, 部委级, 2016-01--2018-12
( 6 ) 肿瘤发生、发展和治疗过程中细胞进化模式及机制研究, 参与, 国家级, 2018-01--2019-12
( 7 ) 家犬人工选择下复杂性状的eGPS解析, 参与, 部委级, 2018-07--2019-06
( 8 ) 高质量企鹅参考基因组图谱绘制和适应性进化的基因组学基础, 主持, 国家级, 2018-08--2021-12
( 9 ) "国际人类表型组计划(一期)"--维吾尔族人群体质人类学和代谢表型的微进化机制研究, 主持, 省级, 2019-01--2021-12
( 10 ) 法医混合DNA图谱鉴定的方法与分析体系, 主持, 市地级, 2019-10--2021-10
( 11 ) 新冠病毒基因组进化规律与动态演变研究技术体系创建与应用--疫情发展规律的模型构建与解析预测, 主持, 国家级, 2020-04--2021-12

指导学生

已指导学生

刘永铭  硕士研究生  0710Z1-基因组学  

吴福泉  硕士研究生  0710Z1-基因组学  

袁午舟  博士研究生  0710Z1-基因组学  

黄莹  硕士研究生  0710J3-生物信息学  

吴昊  博士研究生  0710J3-生物信息学  

陈昕彤  硕士研究生  0710J3-生物信息学  

苏衍凯  硕士研究生  0710J3-生物信息学  

周振钓  硕士研究生  0710J3-生物信息学  

季现超  博士研究生  0710J3-生物信息学  

刘琪  博士研究生  0710Z1-基因组学  

叶思成  硕士研究生  0710J3-生物信息学  

王慈然  硕士研究生  0710J3-生物信息学  

张小龙  博士研究生  0710J3-生物信息学  

赵石磊  博士研究生  0710J3-生物信息学  

郭璐  硕士研究生  0710Z1-基因组学  

现指导学生

杨随缘  博士研究生  0710J3-生物信息学  

张爱巷  硕士研究生  1001Z1-精准医学  

杨淳  硕士研究生  1001Z1-精准医学  

王瑞珍  博士研究生  1001Z1-精准医学  

吴江  硕士研究生  0710Z1-基因组学  

羊阳  博士研究生  0710Z1-基因组学  

沙童  博士研究生  0710J3-生物信息学  

董毅  博士研究生  1001Z1-精准医学  

鹿文卓  硕士研究生  0710Z1-基因组学  

傅敏聪  博士研究生  0710J3-生物信息学  

陈剑超  硕士研究生  0710J3-生物信息学  

曹馨友  硕士研究生  0710J3-生物信息学  

刘馨凝  硕士研究生  0710J3-生物信息学  

陈琬琳  硕士研究生  0710J3-生物信息学  

论文

1.         Zhao S#, Chi L#, Chen H*. CEGA: a method for inferring natural selection by comparative population genomic analysis across species. Genome Biology. 2023. 24, 219. https://doi.org/10.1186/s13059-023-03068-8

2.         Luo H#, Zhang P#, Zhang W, Zheng Y, Hao D, Si Y, Niu Y, Song T, Li T, Zhao S, Chen H*, Xu T*, He S*. Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population. Science Bulletin. 2023. 68(2023): 2391-2404. doi:10.1016/j.scib.2023.08.027.

3.         Jia H#, Sha T#, Zhao S#, Su W#, Liu P#, Zhen R#, Li P, Zhou L, Xu Y, Wen Y, Chi L, Di B, Li P*Chen H*, Qin Z*. Genomic and epidemiological perspectives on the first local sporadic cases of Mpox in China. Emerg Microbes Infect. 2023. 12(2): 2245932. doi: 10.1080/22221751.2023. 2245932. 

4.         Chi L#, Zhang X#, Xue Y*, Chen H*. FastHaN: a fast and scalable program for constructing haplotype network. Molecular Ecology Resources. 2023. 00, 1– 5. https://doi.org/10.1111/1755-0998.13829.

5.         Zhao S#, Sha T#, Xue Y*, Chen H*. Flattening the curve: Imperative when China eases the severe COVID-19 control policy. Journal of Infection. 2023. 86(2023): e75-e77. doi.org/10.1016/j.jinf.2022.12.022.

6.         Liu H, Wu L, Liu B, Xu K, Lei W, Deng J, Rong X, Du P, Wang L, Wang D, Zhang X, Su C, Bi Y, Chen H, Liu WJ, Qi J, Cui Q, Ai S, Fan R, Jang J#, Wu G#, Gao GF#, Wang Q#. Two pan-SRAS-CoV-2 nanobodies and their multivalent derivatives effectively prevent Omicron infections in mice. Cell Reports Medicine. 2023.

2022

7.         Hou Y#, Zhao S#, Liu Q#, Zhang X#, Sha T, Su Y, Zhao W, Bao Y, Xue Y*, Chen H*. Ongoing positive selection drives the evolution of SARS-CoV-2 genomes. Genomics Proteomics Bioinformatics. 2022. 20:1214-1223.

8.         Liu J#, Ji X#, Chen H*. Beta-PSMC: Uncovering more detailed population history using beta distribution. BMC Genomics. 2022. 23(1):785.doi.org/10.1186/s12864-022-09021-6.

9.         Zhao S#, Hou Y#, Zhang X#, Hughes A, Liu N, Peng M, Wang Q, Xue Y*, Chen H*. Pinpointing the animal origins of SARS-CoV-2: a genomic approach. Journal of Genetics and Genomics. 2022. 49(9):900-902.

10.     Zhang X#, Liu Q#, Zhang H#, Zhao S#, Huang J, Sovannary T, Bunnath L, Aun HS, Samnom H, Su B*, Chen H*. The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests. National Science Review. 2022. 9(3):nwab072.

11.     Ji X, Chi L, Xu Z, Peng Z, Ye J, Tu Z*, Chen H*. SMART: an analysis system for mixed STR profiles. Forensic Science and Technology. 2022. 47(1):1-9. DOI10.16467/j.1008-3650.2021.0136.

12.     Zhong HA, Kong XY, Zhang YW, Su YK, Zhang B, Zhu L, Chen H*, Gou X*, Zhang H*. Microevolutionary mechanism of high-altitude adaptation in Tibetan chicken populations from an elevation gradient. Evolutionary Applications. 2022.15(12):2100-2112.doi.org/10.1111/eva.13503.

13.     Zhang D#, Leng L#, Chen C, Huang J, Zhang Y, Yuan H, Ma C, Chen H and Zhang EY*. Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. Nature Ecology and Evolution. 2022.6(3):273-287.

14.     Zhao H#, Zhang Y#, Zhang H#, Song Y#, Zhao F#, Zhang Y#, Zhu S#, Zhang H, Zhou Z, Guo H, Li M, Li J,Gao Q, Han Q, Huang H, Copsey L, Li Q, Chen H, Coen E*, Zhang Y*, Xue Y*. Origin, loss and regain of self-incompatibility in angiosperms. Plant Cell. 2022. 34(1):579-596.

2021

15.     Zhao S, Sha T, Wu CI*, Xue Y*, Chen H*. Will the large-scale vaccination succeed in containing the COVID-19 pandemic and how soon? Quantitative Biology. 2021. 9(3): 304-316. DOI:10.15302/J-QB-021-0256

16.     Liu Q#, Du Z#, Zhao W, Chen H*, Xue Y*.  Metagenomic evidence for co-existence of SARS and H1N1 in patients from 2007-2012 flu seasons in France. Biosafety and Health. 2021.DOI10.1016/j.bsheal.2021.11.002.

17.     Yousaf A, Liu J*, Ye S, Chen H*. Current progress in evolutionary comparative genomics of great apes. Frontiers in Genetics. 2021. 12:657468. doi: 10.3389/fgene. 2021.657468.

18.     Wang Q*, Chen H, Shi Y, Hughes AC, Liu WJ, Jiang J, Gao GF, Xue Y, Tong Y. Tracing the origin of SARS-CoV-2: lessons learned from the past. Cell Research. 2021. 31(11):1139-1141.

19.     Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Research. 2021. 49:D8-D28.

20.     Wu CI, Wen H, Lu J, Su XD, Hughes AC, Zhai W, Chen C, Chen H, Li M, Song S, Qian Z, Wang Q, Chen B, Guo Z, Ruan Y, Lu X, Wei F, Jin L, Kang L, Xue Y, Zhao G, Zhang YP. On the origin of SARS-CoV-2-The blind watchmaker argument. Science China Life Science. 2021.64(9):1560-1563.

21.     Tan S, Ma H, Wang J, Wang M, Wang M, Yin H, Zhang Y, Zhang X, Shen J, Wang D, Banes GL, Zhang Z, Wu J, Huang X, Chen H, Ge S, Chen CL, Zhang YE. DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans. Nature Communications. 2021 Jul 13;12(1):4280. 

22.     Song S, Li C, Kang L, Tian D, Badar N, Ma W, Zhao S, Jiang X, Wang C, Sun Y, Li W, Lei M, Li S, Qi Q, Ikram A, Salman M, Umair M, Shireen H, Batool F, Zhang B, Chen H, Yang Y, Ali Abbasi A*, Li M*, Xue Y*, Bao Y*. Genomic Epidemiology of SARS-CoV-2 in Pakistan. Genomics Proteomics Bioinformatics. 2021 Oct 22: S1672-0229(21)00224-2. doi: 10.1016/j.gpb.2021.08.007.

23.     Li T, Liu J, Feng J, Liu Z, Liu S, Zhang M, Zhang Y, Hou Y, Wu D, Li C, Chen YB, Chen H, Lu X*. Variation in the life history strategy underlies functional diversity of tumors. National Science Review. 2021 8(2):nwaa124.

2020

24.     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. 2020.18(6):640-647.

25.     Song SH, Ma L, Zou D, Tian D, Li C, Zhu J, Chen M, Wang A, Ma Y, MLi 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. doi: 10.1016/j.gpb.2020.09.001.

26.     Park YH, Remmers EF, Lee W, Ombrello AK, Chung LK, Zhao S, Stone DL, Ivanov MI, Loeven NA, Barron KS, Hoffmann P, Nehrebecky M, Akkaya-Ulum YZ, Sag E, Balci-Peynircioglu B, Aksentijevich I, Gül A, Rotimi CN, Chen H, Bliska JB, Ozen S, Kastner DL, Shriner D, Chae JJ. Ancient familial Mediterranean fever mutations in human pyrin and resistance to Yersinia pestis. Nature Immunology.2020. 21 (8), 857-867.

27.     Zhao S, Chen H*. Modeling the epidemic dynamics and control of COVID-19 outbreak in China. Quantitative Biology. 2020; 8(1):11-19. (Listed as #1 in “the most accessed papers” and “the most highly-cited papers” of the Quantitative Biology journal)

28.     Lyu J#, Huang L#, Zhang S, Zhang Y, He W, Zeng P, Zeng Y, Huang G, Zhang J, Ning M, Bao Y, Zhao S, Fu Q, Wade LJ*, Chen H*, Wang W*, Hu F*. Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice. Nature Communications. 2020 Feb 5;11(1):725.

2019

29.     Chen H*. A Computational Approach for Modeling the Allele Frequency Spectrum of Populations with Arbitrarily Varying Size. Genomics Proteomics Bioinformatics. 2019; 17(6):635-644.

30.     Shao-Qing W, Ruo-Yu B, Bo-Yan Z, Pan-Xin D, Chang S, Liang C, Ya-Wei Z, Yu-Chun L, Mei-Sen S, Yin-Qiu C, Hua C, Hong Z, Li J, Hui L. China National DNA Martyry: a beacon of hope for the martyrs' coming home. Journal of Human Genetics. 2019 Oct;64(10):1045-1047.

31.     Shi CM, Liu Q, Zhao S, Chen H*. Ancestry informative SNP panels for discriminating the major East Asian populations: Han Chinese, Japanese and Korean. Annal of Human Genetics. 2019 Sep; 83(5):348-354. DOI: 10.1111/ahg.12320.

32.     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 GP*, Zhao W*, Li H*. eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses. National Science Review. 2019; 6:867-869. DOI:10.1093/nsr/nwz079.

33.     Du Z, Ma L, Qu H, Chen W, Zhang B, Lu X, Zhai W, Sheng X, Sun Y, Li W, Lei M, Qi Q, Yuan N, Shi S, Zeng J, Wang J, Yang Y, Liu Q, Hong Y, Dong L, Zhang Z, Zou D, Wang Y, Song S, Liu F, Fang X, Chen H, Liu X, Xiao J, Zeng C. Whole Genome Analyses of Chinese Population and De Novo Assembly of a Northern Han Genome. Genomics Proteomics Bioinformatics. 2019 Jun; 17(3):229-247.

34.     Zhao S, Zhang T, Liu Q, Wu H, Su B, Shi P, Chen H*. Identifying Lineage-Specific Targets of Natural Selection by a Bayesian Analysis of Genomic Polymorphisms and Divergence from Multiple Species. Molecular Biology and Evolution. 2019. 36(6):1302-1315.

35.     Shao Y, Chen C, Shen H, He BZ, Yu D, Jiang S, Zhao S, Gao Z, Zhu Z, Chen X, Fu Y, Chen H, Gao G, Long M, Zhang YE. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Research. 2019 29(4):682-696.

36.     Zhao S, Shi CM, Ma L, Liu Q, Liu Y, Wu F, Chi L, Chen H*. AIM-SNPtag: A computationally efficient approach for developing ancestry-informative SNP panels. Forensic Science International: Genetics. 2019 Jan 38:245-253.

2018

37.     Huang Y, Liu Q, Chi LJ, Shi CM, Wu Z, Hu M, Shi H, Chen H*. Application of BIG-Annotator in the genome sequencing data functional annotation and genetic diagnosis. Hereditas (Yi Chuan). 2018 Nov 20;40(11):1015-1023.

38.     Yang Z, Shi H, Ma P, Zhao S, Kong Q, Bian T, Gong C, Zhao Q, Liu Y, Qi X, Zhang X, Han Y, Liu J, Li Q, Chen H*, Su B*. Darwinian Positive Selection on the Pleiotropic Effects of KITLG Explain Skin Pigmentation and Winter Temperature Adaptation in Eurasians. Molecular Biology and Evolution. 2018 Sep 35(9):2272-2283.

39.     Zhou Z, Li M, Cheng H, Fan W, Yuan Z, Gao Q, Xu Y, Guo Z, Zhang Y, Hu J, Liu H, Liu D, Chen W, Zheng Z, Jiang Y, Wen Z, Liu Y, Chen H, Xie M, Zhang Q, Huang W, Wang W, Hou S, Jiang Y. An intercross population study reveals genes associated with body size and plumage color in ducks. Nature Communications. 2018 Jul; 9(1):2648.

40.     Shi CM, Li C, Ma L, Chi L, Zhao J, Yuan W, Zhou Z, Yan JW*, Chen H*. Inferring Chinese surnames with Y-STR profiles. Forensic Science International: Genetics. 2018. 33:66-71.

41.     Li GC, Zhang MJ, Chen H, An K#, Liu ZZ#, Du FX, Yang CY, Han X, Jin L, Li H, Zhang Y, Qiao J and Sun YL. Deep pedigree analysis reveals family specific “fingerprint” pattern of DNA methylation for men. Science Bulletin. 2018. 63(1): 7-10