Theoretical Population Genetics

Mathematical and Computational Biology 

Molecular Evolution

Coalescent Theory

Population Dynamics

Adaptive Evolution

Applied Stochastic Modeling in Biology 

Genomic Epidemiology

Forensic Genomics 

2003/09 - 2007/12   University of California, Berkeley, PhD in Integrative Biology (with Emphasis in Genomic and Computatinal Biology)

2015/2 - now, Principal Investigator, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation

2015/7 - now, Professor, School of Future Technology, School of Life Sciences and Sino-Danish College, Univesity of Chinese Academy of Sciences 

2018/1 - now, Affiliated member, CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences

2016-2023, Population Genetics and Molecular Evolution (graduate)

2020, Statistical and Quantitative Genetics (graduate)

2016-2018, Medical Genetics and Human Genomics (graduate)

2017, Health Data and Genomic Technology (graduate)

(2018-2023, *: corresponding author)

2023

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. DOI：10.16467/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.DOI：10.1016/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.

We are a computational lab working on theory, methodology and genomic data analysis. The research in my lab includes the following topics:

1. Population genetics

 We develop theoretical models and statistical methods for population genetics and computational genetics, and apply the methods to genomic data for the inference of population dynamics and natural selection. This line of research includes: 

using coalescent theory to analytically derive the joint allele frequency spectrum of multiple populations;

asymptotic distributions of coalescent times and ancestral lineage numbers

methods for inferring population history, such as, TNSFS

methods for  detecting positive selection, e.g., XP-CLR

methods for inferring selection intensity and allele age of mutants, e.g., HMM-Sweep, IS-Age

comparative population genomics, e.g. HDMKPRF.

2. Evolution of complex diseases and quantitative traits

We are working on the genetic architecture and evolutionary mechanism underlying human morphological traits and metabolic diseases.

We are enthusiastic over other topics involving mathematical modeling and inference of biological processes. 

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