全体研究组长

李海鹏
博士 研究员 博士生导师

中科院计算生物学重点实验室,进化基因组学课题组组长

研究方向:适应性进化理论及分子机制开发检测算法

电子邮件(E-mail):lihaipeng@picb.ac.cn

电话(Tel):021-54920460

传真(Fax):021-54920451

课题组网站:http://www.picb.ac.cn/evolgen/

简历
2007-至     今:中国科学院-马普学会计算生物学伙伴研究所 研究员
2003-2007年:德国慕尼黑大学、科隆大学 博士后
2002-2003年:美国德克萨斯大学 博士后
1996-2002年:中国科学院昆明动物所 博士
1992-1996年:山东大学 学士

研究内容
长期致力于群体遗传学和生物信息学方面的研究工作。在群体遗传学方面,我们的目标是研究生物(比如人、果蝇和病原体等)中由于近期正选择(达尔文适应性进化)而产生的适应现象,避免因群体进化历史、遗传重组的干扰而导致检测结果的高假阳性。这些研究能够帮助我们了解基因的功能以及基因和环境的相互作用。我们希望了解自然选择是如何帮助人类适应环境的变化,特别是自然选择如何加速了意识和语言的产生。在生物信息学领域,我们研发普适性的软件分析平台以面对基因数据分析的各种需求。

代表性论文(*通讯作者)

  1. 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. Dev Cell Feb 22;56(4):478-493.
  2. 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, Yan-Ling 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 Res May;30(5):408-420.
  3. 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. Natl Sci Rev Apr;7(4):798-814.
  4. 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. Natl Sci Rev 7(6):952-963.
  5. Guopeng Liu, Haipeng Li*. (2020) Social enhancer PAS1 and Lhx2 determines social hierarchies in amniotes. Chemistry of life 40:984.
  6. 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. Natl Sci Rev 6(5):867-869.
  7. Shi Yi, Haipeng Li*. (2019) Population genetics: From classical statistics to supervised learning. Scientia Sinica Vitae 49(4):445-455.
  8. 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.
  9. 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.
  10. 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 USA 115(22):E5056-E5065.
  11. 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)
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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 USA 113(49):14079-14084.
  17. Jinggong Xiang-Yu, Zongfeng Yang, Kun Tang, Haipeng Li*. (2016) Revisiting the false positive rate in detecting recent positive selection. Quant Biol 4(3):207-216.
  18. 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 (Bethesda) 6(6):1563-1571.
  19. 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. Curr Mol Med 14(10):1286-1298.
  20. Kao Lin, Andreas Futschik, Haipeng Li*. (2013) A fast estimate for the population recombination rate based on regression. Genetics 194(2):473-484.
  21. Haipeng Li, Thomas Wiehe. (2013) Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation. PLoS Comput Biol 9(5):e1003060.
  22. 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 Res Int 2013:267375.
  23. 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.
  24. 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.
  25. Li HP*. (2012) Beyond our naked eyes. J Mol Cell Biol 4(1):63.
  26. Li ZH, Zou J, Mao K, Lin K, Li H, Liu J, Kallman T, Lascoux M. (2012) Population genetic evidence for complex evolutionary histories of four high altitude Juniper species in the QinHai-Tibetan Plateau. Evolution 66(3):831-845.
  27. Wang K, Hu L, Shi X, Dong Y, Li H*, Wen T. (2012) PSCL: Predicting protein subcellular localization based on optimal functional domains. Protein Pept Lett 19(1):15-22.
  28. Li J, Li HP, Jakobsson M, Li S, Sjodin P, Lascoux M. (2012) Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Mol Ecol 21(1):28-44.
  29. Huang T, Wan S, Xu Z, Zheng Y, Feng KY, Li HP*, Kong XY, Cai YD. (2011) Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS ONE 6(1):e16036.
  30. Hu L, Li Z, Wang K, Niu S, Shi XH, Cai YD, Li HP*. (2011) Prediction and analysis of protein methylarginine and methyllysine based on multisequence features. Biopolymers 95(11):763-771.
  31. Lin K, Li H*, Schlotterer C, Futschik A. (2011) Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics 187(1):229-244.
  32. Li H*. (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.
  33. Chen L, Feng K, Cai YD, Chou K, Li H*. (2010) Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinformatics 11:293.
  34. Lin K, Qiang Z, Lu L, Lu LY, Lai L, Gu J, Zeng Z, Li H*, Cai YD. (2010). Predicting miRNA's target from primary structure by the nearest neighbor algorithm. Mol Divers 14(4):719-729.
  35. Li J, Yang H, Li JR, Li H, Ning T, Pan XR, Shi P, Zhang YP. (2010) Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity 105(3):274-281.
  36. Lu L, Lin K, Qian Z, Li H*, Cai YD, Li Y. (2010) Predicting DNA methylation status using word composition. J Biomed Sci Eng 3(7):672-676.
  37. Lu L, Shi X, Li SJ, Xie ZQ, Feng YL, Lu WC, Li Y, Li HP*, Cai YD. (2010) Protein sumoylation sites prediction based on two-stage feature selection. Mol Divers 14(1):81-86.
  38. Lu LY, Qian Z, Shi X, Li H, Cai YD, Li Y. (2010) A knowledge-based method to predict the cooperative relationship between transcription factors. Mol Divers 14(4):815-819.