1.理论群体遗传学研究和进化生物学研究 

如何准确检测近期发生的正选择，是半个世纪以来群体遗传学和进化生物学的核心难题之一，该理论研究方向和成果对认知科学、农业和癌症等医学研究均起到重要的促进作用。我们主要从以下几个方面进行原创性的研究：(1)创建从系统发育树角度检测正选择的新理论体系，并率先在数学上证明该检测理论体系不受群体历史的干扰，对于在基因组非编码区检测正选择尤为重要，并且已有多个国内和国际著名研究团队在这一新理论体系框架下进行了成功的研究；(2)创建高效算法估算遗传重组率，估值高度精确，并比牛津大学开发的、目前国际学术界使用最为普遍的LDhat算法体系快30万倍，在确定遗传重组热点时，估值甚至比LDhat还更为精确；(3)构建采用全基因组数据估计群体进化历史后再检测正选择的校准型经典方法体系。这些研究结果，对于准确定位受到正选择影响的基因、进行自然选择发生的分子机制、研究智力产生的遗传机制等等，均是极为重要的。

Zeng L, Ming C, Li Y, Su LY, Su YH, Otecko NO, Dalecky A, Donnellan S, Aplin K, Liu XH, Song Y, Zhang ZB, Esmailizadeh A, Sohrabi SS, Nanaei HA, Liu HQ, Wang MS, Atteynine SA, Rocamora G, Brescia F, Morand S, Irwin DM, Peng MS, Yao YG,Li HP, Wu DD, Zhang YP. 2018. Out of southern East Asia of the brown rat revealed by large scale genome sequencing.Molecular biology and evolution, 35(1), 149-158. 

Yang ZF, Li JR, Wiehe T,Li h. 2018. Detecting recent positive selection with a single locus test bi-partitioning the coalescent tree.Genetics, 208(2), 791-805. 

Li HP, Xiang-Yu JG, Dai GY, Gu ZL, Ming C, Yang ZF, Ryder OA, Li WH, Fu YX, Zhang YP. 2016. Large numbers of vertebrates began rapid population decline in the late 19th century.Proceedings of the National Academy of Sciences of the United States of America, 113(49), 14079-14084. 

Gao F, Ming C, Hu WJ,Li HP. 2016. New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era.G3-Genes Genomes Genet, 6(6), 1563-1571. 

Lin K, Futschik A,Li H. 2013. A Fast Estimate for the Population Recombination Rate Based on Regression.Genetics, 194(2), 473-484. 

Li HP, Wiehe T. 2013. Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation.Plos Computational Biology, 9(5), e1003060. 

Lin K,Li HP, Schlotterer C, Futschik A. 2011. Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics.Genetics, 187(1), 229-244. 

Li HP. 2011. A new test for detecting recent positive selection that is free from the confounding impacts of demography.Molecular biology and evolution, 28(1), 365-375. 

Chen L, Feng KY, Cai YD, Chou KC,Li HP. 2010. Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition.BMC bioinformatics, 11(1), 293. 

Stephan W,Li HP. 2007. The recent demographic and adaptive history of Drosophila melanogaster.Heredity, 98(2), 65-68. 

Li HP, Stephan W. 2006. Inferring the demographic history and rate of adaptive substitution in Drosophila.Plos Genetics, 2(10), 1580-1589. 

Li HP, Stephan W. 2005. Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome.Genetics, 171(1), 377-384. 

Li HP, Zhang YW, Zhang YP, Fu YX. 2003. Neutrality tests using DNA polymorphism from multiple samples.Genetics, 163(3), 1147-1151. 

Li HP, Meng SJ, Men ZM, Fu YX, Zhang YP. 2003. Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana).Genetics, 164(1), 269-275.