Group leader
Dr. CHEN Hua is a professor and principal investigator of the Population Genetics and Computational Genomics Group at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS). Dr. Chen received the B.S. and M.S. degrees in Genetics from Fudan University, Shanghai, China in 2001. He received a Ph.D. in Integrative Biology (with emphasis in Computational Genomic Biology) from University of California, Berkeley, USA in December 2007 (advisor: Dr. Montgomery Slatkin). Dr. Chen did postdoctoral research in Harvard Medical School and School of Public Health, and the Broad Institute. He was a research assistant professor in Temple University, USA before joining BIG. Dr. Chen’s expertise is theoretical population genetics. His recent work includes coalescent theory for the joint allele frequency spectrum, the asymptotic coalescent distributions and statistical methods for detecting natural selection (hidden Markov model, XP-CLR etc).
Introduction
The Population Genetics and Computational Genomics Group (PGCG) has two research focuses: one goal is to develop computationally efficient statistical methods for analyzing genomic data. We also apply these methods in analyzing large scale genomic data from humans and various species, to address interesting biological questions, such as, the mechanism of evolutionary process; the evolutionary history of humans and other species; the genetic architecture of complex traits etc.
A sample of our current research interests:
Theory and methods in population genetics
· Coalescent theory for the joint allele frequency spectrum
· Asymptotic distributions of the coalescent process
· Methods for inferring demography from genomic data, including the very recent population growth rate
· Methods for inferring selection intensity and allele age
· Methods for identifying genes under positive selection
Human genetics and medical genetics
· Studying Mendelian disease using pedigrees, such as, osteogenesis imperfecta
· Computationally efficient methods for identifying population structure
· Statistical approaches for deciphering the genetic architecture of complex traits and diseases
High-altitude and environmental adaptation of multiple species
In collaboration with several research groups, we are working on high-altitude adaptation of humans and several other species.
Selected Publications
1. Chen H*, Hey J, Chen K. (2015). Inferring Very Recent Population Growth Rate from Population-Scale Sequencing Data: Using a Large-Sample Coalescent Estimator. Molecular Biology and Evolution. 32(11):2996-3011.
2. Chen H.*, Hey J., and Slatkin M. (2015). A hidden Markov model for investigating recent positive selection. Theoretical Population Biology. 99:18-30.
3. Chen H*. (2015). Population genetic studies in the genomic sequencing era. Zoological Research. 36(1): 1-11.
4.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.
5. 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.
6. Chen H.* and Slatkin M. (2013). Inferring selection intensity and allele age from multi-locus haplotype structure. Genes, Genomics, Genetics. 3 (8): 1429-1442.
7. 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.
8. 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.
9. 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.
10. 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.
11. Chen H.* (2012). The joint allele frequency spectrum of multiple populations: A coalescent theory approach. Theoretical Population Biology. 81(2):179-195.
12. 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.
13. Chen H.*, Patterson N. and Reich D*. (2010). Population differentiation as a test for selective sweeps. Genome Research. 20: 393-402.
Group Members
Staff
MA Liang: Research Assistant Professor (from Academy of Mathematics and System Science, CAS, 2015)
SHI Chengmin: Research Assistant Professor (from Institute of Zoology, CAS, 2015)
FANG Lu: Lab Manager (from Beijing Institute of Genomics, CAS, 2016)
WANG Feng: Research Associate (from Capital Normal University, 2016)
ZHAO Shilei: Research Associate (from Shandong University, 2016)
Graduate Students
2015
LIU Qi (Genomics, from Harbin Medical School)
LIU Yongming (Genomics, from Shangxi Agricultural University)
WU Fuquan (Genomics, from Nankai University)
YUAN Wuzhou (Genomics, from China Agricultural University)
2016
Aisha (Genomics, from Quaid-i-Azam University, Pakistan)
HUANG Ying (Genomics, from Beijing Jiaotong University)
WU Hao (Genomics, from Harbin Medical School)
