Research Areas:

Professor Li Haipeng group works in the field of population genetics and bioinformatics. With regard to population genetics, our goals are to study the mechanism of recent adaptation due to positive selection in living organisms, such as humans, Drosophila and pathogens. We search for methods to detect selection which are not influenced by a high false positive rate because of the confounding impact of demography (i.e., varying population size and population structure) and genetic recombination. Our research activities can help us to understand the function of genes and the interaction between genes and environment. We are studying how natural selection has helped humans to adapt to environmental changes and especially how natural selection has accelerated the emergence of consciousness and language. In the field of bioinformatics, we develop comprehensive software to meet various needs in genetic data analysis.

Brief Biography:

2007 – present Professor, Principal Investigator,CAS-MPG Partner Institute for Computational Biology, China.

2006 – 2007 Postdoctoral Fellow, Institute of Genetics, University of Cologne, Germany.

2003 – 2006 Postdoctoral Fellow, Department of Biology II, University of Munich, Germany.

2002 – 2003 Research Fellow, Human Genetics Center, University of Texas at Houston, USA.

2000 – 2002 Exchange Ph.D. Student, Human Genetics Center, University of Texas at Houston, US (Co-advisor: Prof. Yun-Xin Fu).

1996 – 2002 Ph.D., Genetics/Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences (Advisor: Prof. Ya-Ping Zhang).

1992 – 1996 B.S., Zoology, Shandong University, China.

Selected Publications: (*Corresponding Author)

1. Wangjie Hu^#, Ziqian Hao^#, Pengyuan Du, Fabio Di Vincenzo, Giorgio Manzi, Jialong Cui, Yun-Xin Fu, Yi-Hsuan Pan*, Haipeng Li* (2023) Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition. Science 381:979-984.
2. Jianing Yang^#, Yingmin Cui^#, Dalang Yu^#, Guoqing Zhang^#, Ruifang Cao^#, Zhili Gu, Guangyi Dai, Xiaoxian Wu, Yunchao Ling, Chunyan Yi, Xiaoyu Sun, Bing Sun, Xin Lin, Yu Zhang, Guo-Ping Zhao*, Yixue Li*, Yi-Hsuan Pan*, Haipeng Li* (2023) A noncoding A-to-U Kozak site change related to the high transmissibility of Alpha, Delta, and Omicron VOCs. Molecular Biology and Evolution 40(6):msad142.
3. 苏枭^#, 何子文^#, 柳树群^#, 李海鹏* (^#共享第一作者, *通讯作者) (2022年4月) 从进化生物学角度谈为何中国目前需要动态清零而非与新冠病毒共存. 遗传 44(5):442-446.
4. Yangyang Li^#, Qingyun Lv^#, Guntao Zheng, Di Liu, Ji Ma, Guimei He, Libiao Zhang, Shan Zheng, Haipeng Li*, Yi-Hsuan Pan* (2022) Unexpected expression of heat-activated transient receptor potential (TRP) channels in winter torpid bats and cold-activated TRP channels in summer active bats. Zool Res Jan 18;43(1):52-63.
5. Dalang Yu^#, Xiao Yang^#, Bixia Tang^#, Yi-Hsuan Pan^#, Jianing Yang^#, Guangya Duan^#, Junwei Zhu, Ziqian Hao, Hailong Mu, Long Dai, Wangjie Hu, Mochen Zhang, Ying Cui, Tong Jin, Cuiping Li, Lina Ma, Language translation team, Xiao Su, Guoqing Zhang*, Wenming Zhao*, Haipeng Li* (2022) Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2. Brief Bioinform Mar 10;23(2):bbab583.
6. Ziqian Hao^#, Pengyuan Du^#, Yi-Hsuan Pan*, Haipeng Li* (2022) Fine human genetic map based on UK10K data set. Hum Genet Feb;141(2):273-281.
7. Dalang Yu^#, Junwei Zhu^#, Jianing Yang^#, Yi-Hsuan Pan^#, Hailong Mu, Ruifang Cao, Bixia Tang, Guangya Duan, Ziqian Hao, Long Dai, Guoping Zhao, Yaping Zhang, Wenming Zhao*, Guoqing Zhang*, Haipeng Li* (2022) Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics. Zool Res May;43(5):871-874.
8. Yanni Ma, Siqi Liu, Jie Gao, Chunyan Chen, Xin Zhang, Hao Yuan, Zhongyang Chen, Xiaolin Yin, Chenguang Sun, Yanan Mao, Fanqi Zhou, Yi Shao, Qian Liu, Jiayue Xu, Li Cheng, Daqi Yu, Pingping Li, Ping Yi, Jiahuan He, Guangfeng Geng, Qing Guo, Yanmin Si, Hualu Zhao, Haipeng Li, Graham L. Banes, He Liu, Yukio Nakamura, Ryo Kurita, Yue Huang, Xiaoshuang Wang, Fang Wang, Gang Fang, James Douglas Engel, Lihong Shi, Yong E. Zhang, Jia Yu (2021) Genome-wide analysis of pseudogenes reveals HBBP1’s human-specific essentiality in erythropoiesis and implication in β-thalassemia. Developmental Cell 56(4):478-493.
9. Guopeng Liu^#, Chunxiao Zhang^#, Yuting Wang^#, Guangyi Dai, Shuqun Liu, Wenshuai Wang, Yi-Hsuan Pan*, Jianping Ding*, Haipeng Li* (2021) New exon and accelerated evolution of placental gene Nrk occurred in the ancestral lineage of placental mammals. Placenta 114:14-21.
10. Yuting Wang^#, Guangyi Dai^#, Zhili Gu^#, Guopeng Liu^#, Ke Tang, Yi-Hsuan Pan, Yujie Chen, Xin Lin, Nan Wu, Haoshan Chen, Su Feng, Shou Qiu, Hongduo Sun, Qian Li, Chuan Xu, Yanan Mao, Yong E. Zhang, Philipp Khaitovich, Yanling Wang, Qunxiu Liu, Jing-Dong J. Han, Zhen Shao, Gang Wei, Chun Xu, Naihe Jing, Haipeng Li* (2020) Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies. Cell Research 30(5):408-420.
11. Jingyang Hu^#, Ziqian Hao^#, Laurent Frantz, Shifang Wu, Wu Chen, Yunfang Jiang, Hong Wu, Weimin Kuang, Haipeng Li*, Yaping Zhang*, Li Yu* (2020) Genomic consequences of population decline in critically endangered pangolins and their demographic histories. National Science Review 7(4):798-814.
12. Dongdong Wu^#*, Cuiping Yang^#, Mingshan Wang^#, Kunzhe Dong^#, Dawei Yan^#, Ziqian Hao^#, Songqing Fan, Shuzhou Chu, Qiushou Shen, Liping Jiang, Yan Li, Lin Zeng, Hequn Liu, Haibing Xie, Yunfei Ma, Xiaoyan Kong, Shuli Yang, Xinxing Dong, Ali Esmailizadeh Koshkoiyeh, David M. Irwin, Xiao Xiao, Ming Li, Yang Dong, Wen Wang, Peng Shi, Haipeng Li, Yuehui Ma*, Xiao Gou*, Yongbin Chen*, Yaping Zhang* (2020) Convergent genomic signatures of high-altitude adaptation among domestic mammals. National Science Review 7(6):952-963.
13. Guopeng Liu, Haipeng Li* (2020) Social enhancer PAS1 and Lhx2 determines social hierarchies in amniotes. Chemistry of Life 40(6):984.
14. Dalang Yu^#, Lili Dong^#, Fangqi Yan^#, Hailong Mu^#, Bixia Tang^#, Xiao Yang, Tao Zeng, Qing Zhou, Feng Gao, Zhonghuang Wang, Ziqian Hao, Hongen Kang, Yi Zheng, Hongwei Huang, Yuzhang Wei, Wei Pan, Yaochen Xu, Junwei Zhu, Shilei Zhao, Ciran Wang, Pengyu Wang, Long Dai, Mushan Li, Li Lan, Yiwei Wang, Hua Chen, Yixue Li, Yunxin Fu, Zhen Shao, Yiming Bao, Fangqing Zhao, Luonan Chen, Guoqing Zhang*, Wenming Zhao*, Haipeng Li* (2019) eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses. National Science Review 6(5):867-869.
15. Shi Yi, Haipeng Li* (2019) Population genetics: From classical statistics to supervised learning. Scientia Sinica Vitae 49(4):445-455.
16. Fengjuan Zhang, Ying Zhang, Xiaolong Lv, Beiying Xu, Hongdao Zhang, Jun Yan, Haipeng Li, Ligang Wu* (2019) Evolution of an X-linked miRNA family predominantly expressed in mammalian male germ cells. Mol Biol Evol 36(4):663-678.
17. Weimin Kuang, Chen Ming, Haipeng Li, Hong Wu, Laurent Frantz, Christian Roos, Yaping Zhang, Chenglin Zhang, Ting Jia, Jingyuan Yang, Li Yu* (2019) The origin and population history of the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Mol Biol Evol 36(3):487-499.
18. Guodong Wang^#, Baolin Zhang^#, Weiwei Zhou, Yongxin Li, Jieqiong Jin, Yong Shao, Hechuan Yang, Yanhu Liu, Fang Yan, Hongman Chen, Li Jin, Feng Gao, Yaoguang Zhang, Haipeng Li, Bingyu Mao, Robert W. Murphy, David B. Wake*, Yaping Zhang*, Jing Che* (2018) Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri. Proc Natl Acad Sci U S A 115(22):E5056-E5065.
19. Lin Zeng^#, Chen Ming^#, Yan Li, Lingyan Su, Yanhua Su, Newton O. Otecko, Ambroise Dalecky, Stephen Donnellan, Ken Aplin, Xiaohui Liu, Ying Song, Zhibin Zhang, Ali Esmailizadeh, Saeed S. Sohrabi, Hojjat Asadollahpour Nanaei, Hequn Liu, Mingshan Wang, Solimane Ag Atteynine, Gerard Rocamora, Fabrice Brescia, Serge Morand, David M. Irwin, Mingsheng Peng, Yonggang Yao, Haipeng Li*, Dongdong Wu*, Yaping Zhang* (2018) Out of southern East Asia of the brown rat revealed by large scale genome sequencing. Mol Biol Evol 35(1):149-158. (cover story)
20. Zongfeng Yang, Junrui Li, Thomas Wiehe, Haipeng Li* (2018) Detecting recent positive selection with a single locus test bi-partitioning the coalescent tree. Genetics 208(2):791-805.
21. Jiangan Yin^#, Ge Gao^#, Xijuan Liu, Ziqian Hao, Kai Li, Xinlei Kang, Hong Li, Yuanhong Shan, Wenli Hu, Haipeng Li, Shiqing Cai* (2017) Genetic variation in glia-neuron signalling modulates ageing rate. Nature 551(7679):198-203.
22. Lin Zeng, Chen Ming, Yan Li, Lingyan Su, Yanhua Su, Newton O. Otecko, Hequn Liu, Mingshan Wang, Yonggang Yao, Haipeng Li, Dongdong Wu*, Yaping Zhang* (2017) Rapid evolution of genes involved in learning and energy metabolism for domestication of the laboratory rat. Mol Biol Evol 34(12):3148-3153.
23. Lei Chen^#, Jing Yang^#, Zhihao Xing, Fei Yang, Yang Shu, Yunhua Zhang, Xiangyin Kong, Tao Huang*, Haipeng Li*, Yudong Cai* (2017) An integrated method for the identification of novel genes related to oral cancer. PLoS One 12(4):e0175185.
24. Qigang Li^#, Yonghan He^#, Huan Wu^#, Cuiping Yang^#, Shaoyan Pu, Songqing Fan, Liping Jiang, Qiushuo Shen, Xiaoxiong Wang, Xiaoqiong Chen, Qin Yu, Ying Li, Chang Sun, Xiangting Wang, Jumin Zhou, Haipeng Li, Yongbin Chen*, Qingpeng Kong* (2017) A normalization-free and nonparametric method sharpens large-scale transcriptome analysis and reveals common gene alteration patterns in cancers. Theranostics 7(11):2888-2899.
25. Haipeng Li^#, Jinggong Xiang-Yu^#, Guangyi Dai, Zhili Gu, Chen Ming, Zongfeng Yang, Oliver A. Ryder, Wen-Hsiung Li*, Yunxin Fu*, Yaping Zhang* (2016) A large number of vertebrates began rapid population decline in the late 19th century. Proc Natl Acad Sci U S A 113(49):14079-14084.
26. Jinggong Xiang-Yu, Zongfeng Yang, Kun Tang, Haipeng Li* (2016) Revisiting the false positive rate in detecting recent positive selection. Quantitative Biology 4(3):207-216.
27. Feng Gao, Chen Ming, Wangjie Hu, Haipeng Li* (2016) New software for the fast estimation of population recombination rates (FastEPRR) in the genomic era. G3-Genes Genomes Genetics 6(6):1563-1571.
28. Chen L^#, Xing Z^#, Huang T, Shu Y, Huang G, Li H* (2016) Application of the shortest path algorithm for the discovery of breast cancer-related genes. Current Bioinformatics 11(1):51-58.
29. Yuhang Zhang^#, Chen Chu^#, Shaopeng Wang^#, Lei Chen, Jing Lu, Xiangyin Kong, Tao Huang*, Haipeng Li*, Yudong Cai* (2016) The use of gene ontology term and KEGG pathway enrichment for analysis of drug half-life. PloS One 11(10):e0165496.
30. Tiao Ning, Jing Li, Kao Lin, Heng Xiao, John S. Wylie, Hua Shun, Haipeng Li*, Yaping Zhang* (2014) Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse. Current Molecular Medicine 14(10):1286-1298.
31. Yufei Gao^#, Yang Shu^#, Lei Yang, Yichun He, Lipeng Li, GuaHua Huang, Haipeng Li, Yang Jiang* (2014) A graphic method for identification of novel glioma related genes. Biomed Res Int 2014:891945.
32. Jing Lu^#, Guohua Huang^#, Haipeng Li, Kaiyan Feng, Lei Chen*, Mingyue Zheng*, Yudong Cai* (2014) Prediction of cancer drugs by chemical-chemical interactions. PLoS One 9(2):e87791.
33. Kao Lin, Andreas Futschik, Haipeng Li* (2013) A fast estimate for the population recombination rate based on regression. Genetics 194(2):473-484.
34. Haipeng Li, Thomas Wiehe* (2013) Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation. PLoS Computational Biology 9(5):e1003060.
35. Biqing Li, Jin You, Lei Chen, Jian Zhang, Ning Zhang, Haipeng Li, Tao Huang, Xiangyin Kong*, Yudong Cai* (2013) Identification of lung cancer related genes with the shortest path approach in a protein-protein interaction network. BioMed Research International 2013:267375.
36. Bing Niu*, Xiaocheng Yuan, Preston Roeper, Qiang Su, Chunrong Peng, Jingyuan Yin, Juan Ding*, Haipeng Li*, Wencong Lu (2013) HIV-1 protease cleavage site prediction based on two-stage feature selection method. Protein Pept Lett 20(3):290-298.
37. Shen Niu^#, Tao Huang^#, Kaiyan Feng, Zhisong He, Weiren Cui, Lei Gu, Haipeng Li*, Yudong Cai*, Yixue Li* (2013) Inter- and intra-chain disulfide bond prediction based on optimal feature selection. Protein Pept Lett 20(3):324-335.
38. Tonghui Zhao, Min Jiang, Tao Huang, Biqing Li, Ning Zhang, Haipeng Li*, Yudong Cai* (2013) A novel method of predicting protein disordered regions based on sequence features. Biomed Res Int 2013:414327.
39. Yufei Gao^#, Lei Chen^#, Guohua Huang, Tao Zhang, Kaiyan Feng, Haipeng Li, Yang Jiang* (2013) Prediction of drugs target groups based on ChEBI ontology. Biomed Res Int 2013:132724.
40. Junrui Li, Kristan A. Schneider, Haipeng Li* (2013) The hitchhiking effect of a strongly selected substitution in male germline on neutral polymorphism in a monogamy population. PLoS One 8(8):e71497.
41. Haipeng Li* (2012) Beyond our naked eyes. Journal of Molecular Cell Biology 4(1):63.
42. Zhonghu Li, Jiabin Zou, Kangshan Mao, Kao Lin, Haipeng Li, Jianquan Liu*, K？llman Thomas, Martin Lascoux (2012) Population genetic evidence for complex evolutionary histories of four high altitude Juniper species in the QinHai-Tibetan Plateau. Evolution 66(3):831-845.
43. Kai Wang, Lele Hu, Xiaohe Shi, Yingsong Dong, Haipeng Li*, Tieqiao Wen* (2012) PSCL: Predicting protein subcellular localization based on optimal functional domains. Protein & Peptide Letters 19(1):15-22.
44. Junrui Li, Haipeng Li, Mattias Jakobsson, Sen Li, Per Sjodin, Martin Lascoux* (2012) Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Molecular Ecology 21(1):28-44.
45. Kate R. St. Onge^#, John Paul Foxe^#, Junrui Li^#, Haipeng Li, Karl Holm, Pádraic Corcoran, Tanja Slotte, Martin Lascoux*, Stephen I. Wright* (2012) Coalescent-based analysis distinguishes between allo- and autopolyploid origin in Shepherd's Purse (Capsella bursa-pastoris). Molecular Biology and Evolution 29(7):1721-1733.
46. Tao Huang^#, Sibao Wan^#, Zhongping Xu, Yufang Zheng, Kaiyan Feng, Haipeng Li*, Xiangyin Kong*, Yudong Cai* (2011) Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS One 6(1):e16036.
47. Lele Hu^#, Zhen Li^#, Kai Wang, Shen Niu, Xiaohe Shi, Yudong Cai*, Haipeng Li* (2011) Prediction and analysis of protein methylarginine and methyllysine based on multisequence features. Biopolymers 95(11):763-771.
48. Lele Hu^#, Sibao Wan^#, Shen Niu, Xiaohe Shi, Haipeng Li*, Yudong Cai*, Kuochen Chou (2011) Prediction and analysis of protein palmitoylation sites. Biochimie 93(3):489-496.
49. Kao Lin, Haipeng Li*, Christian Schlotterer, Andreas Futschik* (2011) Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics 187(1):229-244.
50. Haipeng Li* (2011) A new test for detecting recent positive selection that is free from the confounding impacts of demography. Mol Biol Evol 28(1):365-375.
51. Lei Chen, Kaiyan Feng, Yudong Cai*, Kuochen Chou, Haipeng Li* (2010) Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinformatics 11:293.
52. Kao Lin, Ziliang Qiang, Lin Lu, Lingyi Lu, Lihui Lai, Jieyi Gu, Zhenbing Zeng, Haipeng Li*, Yudong Cai* (2010) Predicting miRNA's target from primary structure by the nearest neighbor algorithm. Mol Divers 14(4):719-729.
53. J Li^#, H Yang, J-R Li, H-P Li, T Ning, X-R Pan, P Shi*, Y-P Zhang* (2010) Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity 105(3):274-281.
54. Lingyi Lu, Kao Lin, Ziliang Qian, Haipeng Li*, Yudong Cai*, Yixue Li* (2010) Predicting DNA methylation status using word composition. J Biomedical Science and Engineering 3(7):672-676.
55. Lin Lu^#, Xiaohe Shi^#, Sujun Li, Zhiqun Xie, Yongli Feng, Wencong Lu, Yixue Li*, Haipeng Li*, Yudong Cai* (2010) Protein sumoylation sites prediction based on two-stage feature selection. Molecular Diversity 14(1):81-86.
56. Lingyi Lu, Ziliang Qian, Xiaohe Shi, Haipeng Li*, Yudong Cai*, Yixue Li* (2010) A knowledge-based method to predict the cooperative relationship between transcription factors. Molecular Diversity 14(4):815-819.
57. Yudong Cai*, Zhisong He, Lele Hu, Bing Li, Yi Zhou, Han Xiao, Zhiwen Wang, Kairui Feng, Lin Lu, Kaiyan Feng, Haipeng Li* (2010) Gene finding by integrating gene finders. J Biomedical Science and Engineering 3(11):1061-1068.
58. Kao Lin, Haipeng Li* (2009) Advances in detecting positive selection on genome. Hereditas 31(9):896-902.
59. Xu H, Li J, Li H* (2009) Application of differential equation to the evolution of two groups. Zoological Research 30(1):11-16.
60. Wen Zhang, Wangwei Cai, Weiping Zhou, Haipeng Li, Liang Li, Wei Yan, Qinkai Deng, Yaping Zhang, Yun-Xin Fu*, Xiangmin Xu* (2008) Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing β-Thalassemia in Southern China. J Mol Evol 66(5):436-445.
61. Wolfgang Stephan*, Haipeng Li (2007) The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98(2):65-68.
62. Stephan Hutter*, Haipeng Li, Steffen Beisswanger, David De Lorenzo, Wolfgang Stephan (2007) Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data. Genetics 177(1):469-480.
63. Haipeng Li*, Wolfgang Stephan (2006) Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2(10):e166.
64. Haipeng Li*, Wolfgang Stephan (2005) Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171(1):377-384.
65. Zhongming Zhao, Haipeng Li, Xiaozhuang Wu, Yixi Zhong, Keqin Zhang, Yaping Zhang, Eric Boerwinkle, Yunxin Fu* (2004) Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evolutionary Biology 4:21.
66. Haipeng Li, Yunwu Zhang, Yaping Zhang, Yunxin Fu* (2003) Neutrality tests using DNA polymorphism from multiple samples. Genetics 163(3):1147-1151.
67. Haipeng Li, Shijie Meng, Zhengming Men, Yunxin Fu, Yaping Zhang* (2003) Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana). Genetics 164(1):269-275.
68. Yaping Zhang*, Xiaoxia Wang, Oliver A. Ryder, Haipeng Li, Heming Zhang, Yange Yong, Pengyan Wang (2002) Genetic diversity and conservation of endangered animal species. Pure Appl Chem 74(4):575-584.
69. YC Ding^#, S Wooding, HC Harpending, HC Chi, HP Li, YX Fu, JF Pang, YG Yao, JG Yu, R Moyzis, YP Zhang* (2000) Population structure and history in East Asia. Proc Natl Acad Sci U S A 97(25):14003-14006.
70. Chunhua Wu, Haipeng Li, Yingxiang Wang, Yaping Zhang* (2000) Low genetic variation of the Yunnan hare (Lepus comus G. Allen 1927) as revealed by mitochondrial cytochrome b gene sequences. Biochem Genet 38(5-6):149-155.
71. Haipeng Li, Yaping Zhang* (1999) A computer program for analyzing RFLP data from population study. Zoological Research 20(5):326.
72. Haipeng Li, Yaping Zhang*, Shijie Meng, Zhengming Men, Jianlin Han, Ning Feng, Guoqi Zhang (1998) Low genetic diversity in Sichuan snub-nosed monkey revealed by protein electrophoresis and its significance to conservation biology. Zoological Research 19(6):417-421.