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.#, Hou Y.#, Zhang X.#, Hughes A., Liu N., Peng M., Wang Q., Xue Y*. and Chen H*. Pinpointing the animal origins of SARS-CoV-2: a genomic approach. Journal of Genetics and Genomics. 2022. pp.S1673-8527.

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

3.      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.

4.      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. DOI:10.16467/j.1008-3650.2021.0136.

5.      Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research. 2022.

6.      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.

7.      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.

8.      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

9.      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.

10.   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.

11.   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.

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

13.   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.

14.   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. 

15.   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.

16.   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 tumorsNational Science Review. 2021 8(2):nwaa124.

17.   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.

18.   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.

19.   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.

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

21.   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.

22.   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.

23.   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.

24.   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.

25.   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.

26.   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.

27.   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.

28.   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.

29.   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: Genetics2019 Jan 38:245-253.

30.   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.

31.   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.

32.   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.

33.   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.

34.   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.

35.   Zheng WS, He YX, Cui CY, Ouzhu L, Deji Q, Peng Y, Bai CJ, Duoji Z, Gongga L, Bian B, Baima K, Pan YY, Qu, Kang M, Ciren Y, Baima Y, Guo W, Yang, Zhang H, Zhang XM, Guo YB, Xu SH, Chen H, Zhao SG, Cai Y, Liu SM, Wu TY, Qi XB, Su B. P300 contributes to high-altitude adaptation in Tibetans by regulating nitric oxide production. Zoological Research. 2017. 18;38(3):163-170.

36.   Guo YB, He YX, Cui CY, Ouzhu L, Baima K, Duoji Z, Deji Q, Bian B, Peng Y, Bai CJ, Gongga L, Pan YY, Qu, Kang M, Ciren Y, Baima Y, Guo W, Yang, Zhang H, Zhang XM, Zheng WS, Xu SH, Chen H, Zhao SG, Cai Y, Liu SM, Wu TY, Qi XB, Su B. GCH1 plays a role in the high-altitude adaptation of Tibetans. Zoological Research. 2017. 18;38(3):155-162.

37.   Xia EH, Yang DR, Jiang JJ, Zhang QJ, Liu Y, Liu YL, Zhang Y, Zhang HB, Shi C, Tong Y, Kim C, Chen H, Peng YQ, Yu Y, Zhang W, Eichler EE, Gao LZ. The caterpillar fungus, Ophiocordyceps sinensis, genome provides insights into highland adaptation of fungal pathogenicity. Scientific Report. 2017. 11;7(1):1806.

38.   Peng Y, Cui C, He Y, Ouzhuluobu, Zhang H, Yang D, Zhang Q, Bianbazhuoma, Yang L, He Y, Xiang K, Zhang X, Bhandari S, Shi P, Yangla, Dejiquzong, Baimakangzhuo, Duojizhuoma, Pan Y, Cirenyangji, Baimayangji, Gonggalanzi, Bai C, Bianba, Basang, Ciwangsangbu, Xu S, Chen H, Liu S, Wu T, Qi X, Su B. Down-Regulation of EPAS1 Transcription and Genetic Adaptation of Tibetans to High-Altitude Hypoxia. Molecular Biology and Evolution. 2017. 34(4):818-830.

39.   Shi L, Hu E, Wang Z, Liu J, Li J, Li M, Chen H, Yu C, Jiang T, Su B. Regional selection of the brain size regulating gene CASC5 provides new insight into human brain evolution. Human Genetics. 2017. 136(2):193-204.

40.   Xue C, Chen H, Yu F. Base-Biased Evolution of Disease-Associated Mutations in the Human Genome. Human Mutation. 2016. 37(11):1209-1214.

41.   Yang Z, Zhong H, Chen J, Zhang X, Zhang H, Luo X, Xu S, Chen H, Lu D, Han Y, Li J, Fu L, Qi X, Peng Y, Xiang K, Lin Q, Guo Y, Li M, Cao X, Zhang Y, Liao S, Peng Y, Zhang L, Guo X, Dong S, Liang F, Wang J, Willden A, Seang Aun H, Serey B, Sovannary T, Bunnath L, Samnom H, Mardon G, Li Q, Meng A, Shi H, Su B. A Genetic Mechanism for Convergent Skin Lightening during Recent Human Evolution. Molecular Biology and Evolution. 2016. 33(5):1177-87.

42.   Yang D, Peng Y, Ouzhuluobu, Bianbazhuoma, Cui C, Bianba, Wang L, Xiang K, He Y, Zhang H, Zhang X, Liu J, Shi H, Pan Y, Duojizhuoma, Dejiquzong, Cirenyangji, Baimakangzhuo, Gonggalanzi, Liu S, Gengdeng, Wu T, Chen H, Qi X, Su B. HMOX2 Functions as a Modifier Gene for High-Altitude Adaptation in Tibetans. Human Mutation. 2016. 37(2):216-23.

43.   Chen H*, Hey J, Chen K. Inferring Very Recent Population Growth Rate from Population-Scale Sequencing Data: Using a Large-Sample Coalescent Estimator. Molecular Biology and Evolution. 2015. 32(11):2996-3011.

44.   Chen H*. Population genetic studies in the genomic sequencing era. Zoological Research 2015. 36(4):223-32.

45.   Chen H.*, Hey J., and Slatkin M. A hidden Markov model for investigating recent positive selection. Theoretical Population Biology. 2015. 99:18-30.

46.Macholdt E., Lede V., Barbieria C., Mpolokab SW., Chen H., Slatkin M., Pakendorfd B., and Stoneking M. Tracing prehistoric pastoralist migrations: lactase persistence alleles in southern Africa. Current Biology. 2014. 24(8): 875-879.

47.López S., García Ó., Yurrebaso I., Flores C., Acosta-Herrera M., Chen H., Gardeazabal J., Careaga JM., Boyano MD., Sánchez A., Ratón-Nieto JA., Sevilla A., Smith-Zubiaga I., Galdeano AG., Martinez-Cadenas C., Izagirre N., Rúa C., and Alonso S. The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population. 2014. PLoS One. 9(8): e104367.

48.   Chen H.* and Chen K. Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. Genetics. 2013. 194 (3): 721–736.

49.   Chen H.* and Slatkin M. (2013). Inferring selection intensity and allele age from multi-locus haplotype structure. Genes, Genomics, Genetics. 3 (8): 1429–1442. .

50.   Chen H.* (2013). Intercoalescence time distribution of incomplete genealogies in temporally varying populations, and applications in population genetic inference. Annals of Human Genetics. 77 (2): 158-173.

51.   Yana K., Wang S., Tan J., Gerbault P., Wark A., Tan L., Yang Y., Li S., Tang K., Chen H., Powell A., Itan Y., Fuller D., Lohmueller J., Mao J., Schachar A., Paymer M., Hostetter E., Byrne E., Burnett E., McMahon AP., Thomas MG., Lieberman DE., Jin L., Tabin CJ., Morgan BA. and Sabeti PC. (2013). Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR VariantCell. 152 (4): 691-702.

52.   Qi X., Cui C., Peng Y., Zhang X., Yang Z., Zhong H., Xiang K, Cao X, Wang Y, Ouzhuluobu, Basang, Ciwangsangbu, Bianba, Gonggalanzi, Wu T, Chen H, Shi H, and Su B. (2013). Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau. Molecular Biology and Evolution. 30(8):1761-1778.

53.   Xiang K., Ouzhuluobu, Peng Y., Yang Z., Zhang X., Cui C., Zhang H., Li M., Zhang Y., Bianba, Gonggalanzi, Basang, Ciwangsangbu, Wu T., Chen H., Shi H., Qi X., and Su B. (2013). Identification of a Tibetan-specific mutation in the hypoxic gene EGLN1 and its contribution to high-altitude adaptation. Molecular Biology and Evolution. 30(8):1889-1898.

54.   Chen H.* (2012). The joint allele frequency spectrum of multiple populations: A coalescent theory approach. Theoretical Population Biology81(2):179-195.

55.   Peng Y., Yang Z., Zhang H., Cui C., Qi X., Luo X., Tao X., Wu T., Ouzhuluobu, Basang, Ciwangsangbu, Danzengduohie, Chen H., Shi H., and Su B. (2011). Genetic variations in Tibetan populations and high altitude adaptation at the Himalayas. Molecular Biology Evolution 28(2): 1075-1081.

56.   Kosoy R., Ransom RM., Chen H., Marconi M., Macciardi F., Glorioso N., Gregersenm PK., Cusiand D., and Seldin MF. (2011). Evidence for malaria selection of a CR1 haplotype in Sardinia. Genes and Immunity. 12: 582-588. 

57.   Chen H.*, Patterson N. and Reich D*. (2010). Population differentiation as a test for selective sweeps. Genome Research20: 393-402.