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Publication

1. 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.

2. 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.

3. 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.

4. 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. 2020

5. 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 downloaded paper list and #1 in the most cited paper list of Quantitative Bio)

6. 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.

7. 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.

8. 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. J Hum Genet. 2019 Oct;64(10):1045-1047.

9. Shi CM#, Liu Q#, Zhao S#, Chen H*. Ancestry informative SNP panels for discriminating the major East Asian populations: Han Chinese, Japanese and Korean. Ann Hum Genet. 2019 Sep; 83(5):348-354.

10. 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.

11. 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.

12. 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. Mol Biol Evol. 2019 1;36(6):1302-1315.

13. 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 Res. 2019 29(4):682-696.

14. 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 Sci Int Genet. 2019 Jan;38:245-253.

15. 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. Yi Chuan. 2018 Nov 20;40(11):1015-1023.

16. 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. Mol Biol Evol. 2018 Sep 1;35(9):2272-2283.

17. 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 ssociated with body size and plumage color in ducks. Nat Commun. 2018 Jul 17;9(1):2648.

18. 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 Sci Int Genet. 2018 Mar;33:66-71.

19. 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

20. 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. Zool Res. 2017 May 18;38(3):163-170.

21. 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. Zool Res. 2017 May 18;38(3):155-162.

22. 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. Sci Rep. 2017 May 11;7(1):1806.

23. 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. Mol Biol Evol. 2017 Apr 1;34(4):818-830.

24. 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. Hum Genet. 2017 Feb;136(2):193-204.

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

26. 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. Mol Biol Evol. 2016 May;33(5):1177-87.

27. 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. Hum Mutat. 2016 Feb;37(2):216-23.

28. Chen H*, Hey J, Chen K. Inferring Very Recent Population Growth Rate from Population-Scale Sequencing Data: Using a Large-Sample Coalescent Estimator. Mol Biol Evol. 2015 Nov;32(11):2996-3011.

29. Chen H*. Population genetic studies in the genomic sequencing era. Zoological Research 2015 Jul 18;36(4):223-32.

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

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

32. 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. (2014). The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population. PLoS One. 9(8): e104367.

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

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

35. 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.

36. 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 Variant. Cell. 152 (4): 691-702.

37. 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.

38. 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.

39. Chen H.* (2012). The joint allele frequency spectrum of multiple populations: A coalescent theory approach. Theoretical Population Biology. 81(2):179-195.

40. 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.

41. 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.

42. Chen H.*, Patterson N. and Reich D*. (2010). Population differentiation as a test for selective sweeps. Genome Research. 20: 393-402.

 

 

 


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