Recent Publications(* Corresponding author)

  1. Guo-Dong Wang1, Bao-Lin Zhang1, Wei-Wei Zhou, Yong-Xin Li, Jie-Qiong Jin, Yong Shao, He-chuan Yang, Yan-Hu Liu, Fang Yan, Hong-Man Chen, Li Jin, Feng Gao, Yaoguang Zhang, Haipeng Li, Bingyu Mao, Robert W. Murphy, David B. Wake*, Ya-Ping Zhang*, and Jing Che*. 2018. Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri. PNAS, 115(22):E5056-E5065 [pdf]
  2. Lin Zeng1, Chen Ming1, Yan Li, Ling-Yan Su, Yan-Hua Su, Newton O. Otecko, Ambroise Dalecky, Stephen Donnellan, Ken Aplin, Xiao-Hui Liu, Ying Song, Zhi-bin Zhang, Ali Esmailizadeh, Saeed S. Sohrabi, Hojjat Asadollahpour Nanaei, He-Qun Liu, Ming-Shan Wang, Solimane Ag Atteynine, Gerard Rocamora, Fabrice Brescia, Serge Morand, David M. Irwin, Ming-sheng Peng, Yong-Gang Yao, Hai-peng Li*, Dong-Dong Wu*, Ya-Ping Zhang*. 2018. Out of southern East Asia of the brown rat revealed by large scale genome sequencing. Mol. Biol. Evol. 35(1): 149-158 [pdf]
  3. Zongfeng Yang, Junrui Li, Thomas Wiehe, Haipeng Li*. 2017. Detecting Recent Positive Selection With a Single Locus Test Bi-Partitioning the Coalescent Tree. Genetics, DOI:10.1534/genetics.117.300401 [pdf]
  4. Jiang-An Yin1, Ge Gao1, Xi-Juan Liu, Zi-Qian Hao, Kai Li, Xin-Lei Kang, Hong Li, Yuan-Hong Shan, Wen-Li Hu, Hai-Peng Li, Shi-Qing Cai*. 2017. Genetic variation in glia-neuron signalling modulates ageing rate. Nature, 551(7679): 198-203 [pdf]
  5. Lin Zeng, Chen Ming, Yan Li, Ling-Yan Su, Yan-Hua Su, Newton O. Otecko, He-Qun Liu, Ming-Shan Wang, Yong-Gang Yao, Hai-Peng Li, Dong-Dong Wu, and Ya-Ping 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. [pdf]
  6. CHEN Lei1, YANG Jing1, XING Zhihao, YANG Fei, SHU Yang, ZHANG Yunhua, KONG Xiangyin, HUANG Tao, LI Haipeng*, CAI Yudong* (2017). An integrated method for the identification of novel genes related to oral cancer. PLoS ONE, 12(4): e0175185. [pdf]
  7. LI Haipeng1, XIANG-YU Jinggong1, DAI Guangyi, GU Zhili, MING Chen, YANG Zongfeng, RYDER Oliver A., LI Wen-Hsiung*, FU Yun-Xin*, ZHANG Ya-Ping* (2016). Large numbers of vertebrates began rapid population decline in the late 19th century. PNAS, 113(49): 14079-14084. [pdf]
  8. CHEN Lei1, XING Zhihao1, HUANG Tao, SHU Yang, HUANG Guohua, LI Haipeng* (2016). Application of the Shortest Path Algorithm for the Discovery of Breast Cancer-Related Genes. Current Bioinformatics 11(1): 51-58. [pdf]
  9. ZHANG Yuhang1, CHU Chen1, WANG Shaopeng1, CHEN Lei, LU Jing, KONG Xiangyin, HUANG Tao*, LI Haipeng*, CAI Yudong* (2016). The Use of Gene Ontology Term and KEGG Pathway Enrichment for Analysis of Drug Half-Life. PloS ONE 11(10): e0165496. [pdf]
  10. GAO Feng, MING Chen, HU Wangjie, LI Haipeng* (2016). New software for the fast estimation of population recombination rates (FastEPRR) in the genomic era. G3-Genes Genomes Genetics, 6(6): 1563-1571. [pdf]
  11. XIANG-YU Jinggong, YANG Zongfeng, TANG Kun, LI Haipeng* (2016). Revisiting the false positive rate in detecting recent positive selection. Quantitative Biology 4(3): 207-216. [pdf]
  12. NING Tiao, LI Jing, LIN Kao, XIAO Heng, WYLIE John S., SHUN Hua, LI Haipeng*, ZHANG Yaping (2014). Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse. Current Molecular Medicine 14(10):1-13. [pdf]
  13. WANG Qian, ABBOTT Richard J., YU Qiushi, LIN Kao, LIU Jianquan (2013). Pleistocene climate change and the origin of two desert plant species, Pugionium cornutum and Pugionium dolabratum (Brassicaceae), in northwest China. New Phytologist 199:277-287. [pdf]
  14. LI Junrui, SCHNEIDER Kristan A., LI Haipeng* (2013). The Hitchhiking Effect of a Strongly Selected Substitution in Male Germline on Neutral Polymorphism in a Monogamy Population. PLoS ONE 8(8):e71497. [pdf]
  15. LIN Kao, FUTSCHIK Andreas, LI Haipeng* (2013). A fast estimate for the population recombination rate based on regression. Genetics 194:473-484. [pdf]
  16. LI Haipeng, WIEHE Thomas (2013). Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation. PLoS Comput Biol 9: e1003060. [pdf]
  17. LI Biqing, YOU Jin, CHEN Lei, ZHANG Jian, ZHANG Ning, LI Haipeng, HUANG Tao, KONG Xiangyin, CAI Yudong(2013). Identification of lung cancer related genes with the shortest path approach in a protein-protein interaction network. BioMed Research International [pdf]
  18. NIU Shen, HUANG Tao, FENG Kaiyan, HE Zhisong, CUI Weiren, GU Lei, LI Haipeng, CAI Yudong, LI Yixue (2013). Inter- and intra-chain disulfide bond prediction based on optimal feature selection. Protein & Peptide Letters 20:324-335. [pdf]
  19. NIU Bing, YUAN Xiaocheng, ROEPER Preston, SU Qiang, PENG Chunrong, YIN Jingyuan, DING Juan, LI Haipeng*, LU Wencong (2013). HIV-1 protease cleavage site prediction based on two-stage feature selection method. Protein & Peptide Letters 20:290-298. [pdf]
  20. ONGE Kate R.St., FOXE John Paul, LI Junrui, LI Haipeng, HOLM Karl, CORCORAN Pdraic, SLOTTE Tanja, LASCOUX Martin, WRIGHT Stephen I.(2012). Coalescent-based analysis distinguishes between allo- and autopolyploid origin in Shepherd's Purse (Capsella bursa-pastoris). Mol Biol Evol 29:1721-1733. [pdf]
  21. LI Junrui, LI Haipeng, JAKOBSSON Mattias, LI Sen, SJÖDIN Per, LASCOUX Martin (2012). Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Mol Ecol 21:28-44. [pdf]
  22. WANG Kai, HU Lele, SHI Xiaohe, DONG Yingsong, LI Haipeng*, WEN Tieqiao (2012). PSCL: Predicting protein subcellular localization based on optimal functional domains. Protein & Peptide Letters 19:15-22. [pdf]
  23. LI Zhonghu, ZOU Jiabin, MAO Kangshan, LIN Kao, LI Haipeng, LIU Jianquan, Källman Thomas, LASCOUX Martin (2012). Population genetic evidence for complex evolutionary histories of four high altitude Juniper species in the QinHai-Tibetan Plateau. Evolution 66:831-845. [pdf]
  24. LI Haipeng* (2012). Beyond our naked eyes. J Mol Cell Biol 4:63. [pdf]
  25. HU Lele, LI Zhen, WANG Kai, NIU Shen, SHI Xiaohe, CAI Yudong, LI Haipeng* (2011). Prediction and analysis of protein methylarginine and methyllysine based on multisequence features. Biopolymers 95:763-771. [pdf]
  26. HUANG Tao, WAN Sibao, XU Zhongping, ZHENG Yufang, FENG Kai-Yan, LI Haipeng*, KONG Xiangyin, CAI Yudong (2011). Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS ONE 6:e16036. [pdf]
  27. LIN Kao, LI Haipeng*, SCHLÖTTERER Christian, FUTSCHIK Andreas (2011). Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics 187:229-244. [pdf]
  28. LI Haipeng* (2011). A new test for detecting recent positive selection that is free from the confounding impacts of demography. Mol Biol Evol 28:365-375. [pdf]
  29. LU Lingyi, LIN Kao, QIAN Ziliang, LI Haipeng*, CAI Yudong, LI Yixue (2011). Predicting DNA methylation status using word composition. J. Biomedical Science and Engineering 3:672-676. [pdf]
  30. CHEN Lei, FENG Kaiyan, CAI Yudong, CHOU Kuochen, LI Haipeng* (2010). Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinformatics 11:293. [pdf]
  31. LIN Kao, QIAN Ziliang, LU Lin, LU Lingyi, LAI Lihui, GU Jieyi, ZENG Zhenbing, LI Haipeng*, CAI Yudong (2010). Predicting miRNA's target from primary structure by the nearest neighbor algorithm. Mol Divers 14:719-729. [pdf]
  32. LI J, YANG H, LI Junrui, LI Haipeng, NING T, PAN XR, SHI P, ZHANG YP (2010). Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity 105:274-281. [pdf]
  33. LIN Kao, LI Haipeng* (2009). Advances in detecting positive selection on genome. Hereditas(Beijing) 31:896-902. [pdf]
  34. XU Huijun, LI Junrui, LI Haipeng* (2009). Application of differential equation to the evolution of two groups. Zoological Research 30:11-16. [pdf]
  35. LU Lingyi, QIAN Ziliang, SHI Xiaohe, LI Haipeng*, CAI Yudong, LI Yixue (2009). A knowledge-based method to predict the cooperative relationship between transcription factors. Mol Divers 14:815-819. [pdf]
  36. LU Lin, SHI Xiaohe, LI Sujun, XIE Zhiqun, FENG Yongli, LU Wencong, LI Yixue, LI Haipeng*, CAI Yudong (2009). Protein sumoylation sites prediction based on two-stage feature selection. Mol Divers 14:81-86. [pdf]
  37. ZHANG Wen, CAI Wangwei, ZHOU Weiping, LI Haipeng, LI Liang, YAN Wei, DENG Qinkai, ZHANG Yaping, FU Yunxin, XU Xiangmin (2008). Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing -Thalassemia in Southern China. J Mol Evol 66:436-445. [pdf]

Selected Publications before 2007

  1. STEPHAN Wolfgang, LI Haipeng (2007). The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98:65-68. [pdf]
  2. HUTTER Stephan, LI Haipeng, BEISSWANGER Steffen, DE LORENZO David, STEPHAN Wolfgang (2007). Distinctly Different Sex Ratios in African and European Populations of Drosophila melanogaster Inferred From Chromosomewide Single Nucleotide Polymorphism Data. Genetics 177:469-480. [pdf]
  3. LI Haipeng*, STEPHAN Wolfgang (2006). Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2:e166. [pdf]
  4. LI Haipeng*, STEPHAN Wolfgang (2005). Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171:377-384. [pdf]
  5. ZHAO Zhongming, LI Haipeng, WU Xiaozhuang, ZHONG Yixi, ZHANG Keqin, ZHANG Yaping, BOERWINKLE Eric, FU Yunxin (2004). Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evol Biol 4:21. [pdf]
  6. LI Haipeng, ZHANG Yunwu, ZHANG Yaping, FU Yunxin (2003). Neutrality tests using DNA polymorphism from multiple samples. Genetics 163:1147-1151. [pdf]
  7. LI Haipeng, MENG Shijie, MEN Zhengming, FU Yunxin, ZHANG Yaping (2003). Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana). Genetics 164:269-275. [pdf]
  8. DING Yuanchun, WOODING Stephen, HARPENDING Henry C., CHI Hanchang, LI Haipeng, FU Yunxin, PANG Junfeng, YAO Yonggang, YU Jinggong Xiang, MOYZIS Robert, ZHANG Yaping(2000). Population structure and history in East Asia. Proc Natl Acad Sci USA 97:14003-14006. [pdf]
Group of Evolutionary Genomics, PICB