About me

I am currently a Research Assistant Professor at the Center for Computational Genetics and Genomics led by Jody Hey in Temple University. My academic training was in theoretical population genetics. I earned my Ph.D. degree in Integrative Biology (with emphasis in Computational and Genomic Biology) in December 2007 at University of California, Berkeley, and was supervised by Monty Slatkin.

Research interests

My research is in population genetics and computational genetics. I work on theoretical study and statistical methodology development in population genetics and their applications in inference of natural selection and demography from genetic polymorphism data of single or multiple populations.

I am also enthusiastic on other computational genomic topics, such as, comparative genomic analysis of sequences from multiple species methodology development and data analysis on association studies and mapping of complex diseases using data of expression array, RNAseq and SNP arrays.

Please see more details of my research projects here.

Publications

(2009-2014. *: corresponding author)

1. 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.

2. Chen H* and Slatkin M. 2013 Inferring selection intensity and allele age from multi-locus haplotype structure. G3: Genes, Genomics, Genetics 3 (8), 1429–1442. .

3. 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.

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

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

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

7. López, S., García, Ó., Yurrebaso, I., Flores, C., Acosta-Herrera, M., Chen, H., … & 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.

8. 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, 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.

9. 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, 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.

10. 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 human evolution in mice: An adaptive variant of EDAR drives pleiotropic changes in mice and humans Cell 152 (4): 691-702.

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

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

13. Yu F., Keinan A., Chen H, Ferland RJ, Hill RS, Mignault AA, Walsh CA, Reich D, 2009 Detecting natural selection by empirical comparison to random regions of the genome. Human Molecular Genetics 18:4853-4867.

In revision:

1. Chen H*. 2014 Computationally efficient estimation of the number of founders for colonized populations (in revision).

2. Chen H*, Hey J and Slatkin M. 2014 A hidden Markov model for investigating recent positive selection (in revision).

3. Chen H*, Chen K and Hey J. 2014 A large-sample coalescent estimator of recent population growth rate from population resequencing data (in revision).

4. Chen H*, Patterson N and Reich D. Population differentiation as a test for soft sweeps on standing variation (in revision).