•                            

    2024

                               

    1. Jinggong Xiang-Yu#, Zhili Gu#, Haipeng Li*, Bao-Rong Lu* (2024). Demography as a confounding factor to explain highly diverged loci between cultivated and wild rice. Plant Genetic Resources 22(1):45-49.

  •                            

    2023

                               

    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. [Green open version, supplementary materials, and introduction slides]

                               

    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.

  •                            

    2022

                               

    1. 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卷第5期: 442-446.

                               

    2. Yang-Yang Li#, Qing-Yun Lv#, Gun-Tao Zheng, Di Liu, Ji Ma, Gui-Mei He, Li-Biao 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. Zoological Research, 43(1): 52-63.

                               

    3. Dalang Yu#, Xiao Yang#, Bixia Tang#, Yi-Hsuan Pan#, Jianing Yang#, Guangya Duan#, Junwei Zhu, Zi-Qian Hao, Hailong Mu, Long Dai, Wangjie Hu, Mochen Zhang, Ying Cui, Tong Jin, Cui-Ping 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. Briefings in Bioinformatics, bbab583

                               

    4. Ziqian Hao#, Pengyuan Du#, Yi-Hsuan Pan*, Haipeng Li* (2022) Fine human genetic map based on UK10K data set. Human Genetics, 141:273–281.

    5. Dalang Yu#, Junwei Zhu#, Jianing Yang#, Yi-Hsuan Pan#, Hailong Mu, Ruifang Cao, Bixia Tang, Guangya Duan, Zi-Qian Hao, Long Dai, Guo-Ping Zhao, Ya-Ping Zhang, Wenming Zhao*, Guoqing Zhang*, Haipeng Li* (2022) Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics. Zoological Research, 43(5): 871-874.

  •                            

    2021

    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, and Jia Yu (2021). Genome-wide analysis of pseudogenes reveals HBBP1’s human-specific essentiality in erythropoiesis and implication in β-thalassemia. Developmental Cell, 56:478-493.

    2. Guopeng Liu#, Chunxiao Zhang#, Yuting Wang#, Guangyi Dai, Shu-Qun 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.

    •                    

  • 2020

     

    1. 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 Research 30:408-420.

    2. Jing-Yang Hu#, Zi-Qian Hao#, Laurent Frantz, Shi-Fang Wu, Wu Chen, Yun-Fang Jiang, Hong Wu, Wei-Min Kuang, Haipeng Li*, Ya-Ping Zhang*, Li Yu* (2020) Genomic consequences of population decline in critically endangered pangolins and their demographic histories. National Science Review, 7:798-814.

    3. Dong-Dong Wu#*, Cui-Ping Yang#, Ming-Shan Wang#, Kun-Zhe Dong#, Da-Wei Yan#, Zi-Qian Hao#, Song-Qing Fan, Shu-Zhou Chu, Qiu-Shou Shen, Li-Ping Jiang, Yan Li, Lin Zeng, He-Qun Liu, Hai-Bing Xie, Yun-Fei Ma, Xiao-Yan Kong, Shu-Li Yang, Xin-Xing Dong, Ali Esmailizadeh Koshkoiyeh, David M. Irwin, Xiao Xiao, Ming Li, Yang Dong, Wen Wang, Peng Shi, Haipeng Li, Yue-Hui Ma*, Xiao Gou*, Yong-Bin Chen*, Ya-Ping Zhang* (2020) Convergent genomic signatures of high altitude adaptation among domestic mammals. National Science Review, 7:952-963.

    4. Guopeng Liu, Haipeng Li* (2020) Social enhancer PAS1 and Lhx2 determines social hierarchies in amniotes. Chemistry of Life, 40:984.

  • 2019

    1. 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, Yi-Xue Li, Yun-Xin Fu, Zhen Shao, Yiming Bao, Fangqing Zhao, Luo-Nan Chen, Guo-Qing Zhang*, Wenming Zhao*, Haipeng Li* (2019) eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses. National Science Review, 6:867-869.

    2. Shi Yi, Haipeng Li* (2019) Population genetics: From classical statistics to supervised learning. Scientia Sinica Vitae, 49:1-11.

    3. Feng-Juan Zhang, Ying Zhang, Xiao-Long Lv, Bei-Ying Xu, Hong-Dao Zhang, Jun Yan, Haipeng Li, Li-Gang Wu* (2019) Evolution of an X-linked miRNA family predominantly expressed in mammalian male germ cells. Mol. Biol. Evol., 36:663-678.

    4. Wei-Min Kuang, Chen Ming, Haipeng Li, Hong Wu, Laurent Frantz, Christian Roos, Ya-Ping Zhang, Cheng-Lin Zhang, Ting Jia, Jing-Yuan Yang, Li Yu* (2019) The origin and population history of the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Mol. Biol. Evol., 36:487-499.

  • 2018

    1. Guo-Dong Wang#, Bao-Lin Zhang#, 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.

    2. Lin Zeng#, Chen Ming#, 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, Haipeng 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., 35:149-158 (cover story).

    3. Zongfeng Yang, Junrui Li, Thomas Wiehe, Haipeng Li* (2018) Detecting recent positive selection with a single locus test bi-partitioning the coalescent tree. Genetics 208:791-805.

  • 2017

    1. Jiang-An Yin#, Ge Gao#, Xi-Juan Liu, Zi-Qian Hao, Kai Li, Xin-Lei Kang, Hong Li, Yuan-Hong Shan, Wen-Li Hu, Haipeng Li, Shi-Qing Cai* (2017) Genetic variation in glia-neuron signalling modulates ageing rate. Nature 551(7679): 198-203.

    2. Lin Zeng, Chen Ming, Yan Li, Ling-Yan Su, Yan-Hua Su, Newton O. Otecko, He-Qun Liu, Ming-Shan Wang, Yong-Gang Yao, Haipeng 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.

    3. 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:e0175185.

    4. Qi-Gang Li#, Yong-Han He#, Huan Wu#, Cui-Ping Yang#, Shao-Yan Pu, Song-Qing Fan, Li-Ping Jiang, Qiu-Shuo Shen, Xiao-Xiong Wang, Xiao-Qiong Chen, Qin Yu, Ying Li, Chang Sun, Xiangting Wang, Jumin Zhou, Haipeng Li, Yong-Bin Chen*, and Qing-Peng Kong* (2017). A normalization-free and nonparametric method sharpens large-scale transcriptome analysis and reveals common gene alteration patterns in cancers. Theranostics 7:2888-2899.

  • 2016

    1. Haipeng Li#, Jinggong Xiang-Yu#, Guangyi Dai, Zhili Gu, Chen Ming, Zongfeng Yang, Oliver A. Ryder, Wen-Hsiung Li*, Yun-Xin Fu*, Ya-Ping Zhang* (2016) A large number of vertebrates began rapid population decline in the late 19th century. Proc Natl Acad Sci USA 113:14079-14084.

    2. Jinggong Xiang-Yu, Zongfeng Yang, Kun Tang, Haipeng Li* (2016) Revisiting the false positive rate in detecting recent positive selection. Quantitative Biology 4:207–216.

    3. 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 6:1563-1571.

    4. Chen L.#, Xing Z.#, Huang T, Shu Y, Huang G, Haipeng Li* (2016) Application of the shortest path algorithm for the discovery of breast cancer-related genes. Current Bioinformatics11:51-58.

    5. 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: e0165496

  • 2015

  • 2014

    1. 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):1-13.

    2. Yu-Fei Gao#, Yang Shu#, Lei Yang, Yi-Chun He, Li-Peng Li, GuaHua Huang, Haipeng Li, and Yang Jiang* (2014). A graphic method for identification of novel glioma related genes. Biomed Res Int 2014, 891945.

    3. Jing Lu#, Guohua Huang#, Haipeng Li, Kai-Yan Feng, Lei Chen*, Ming-Yue Zheng*, and Yu-Dong Cai* (2014). Prediction of cancer drugs by chemical-chemical interactions. PLoS One 9, e87791.

  • 2013

    1. Kao Lin, Andreas Futschik, Haipeng Li* (2013) A fast estimate for the population recombination rate based on regression. Genetics 194:473-484.

    2. Haipeng Li, Thomas Wiehe* (2013) Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation. PLoS Computational Biology 9: e1003060.

    3. Bi-Qing Li, Jin You, Lei Chen, Jian Zhang, Ning Zhang, Haipeng Li, Tao Huang, Xiang-Yin Kong* and 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

    4. 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 & Peptide Letters 20:290-298.

    5. 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 & Peptide Letters 20:324-335.

    6. Tonghui Zhao, Min Jiang, Tao Huang, Biqing Li, Ning Zhang, Haipeng Li*, and Yudong Cai* (2013) A novel method of predicting protein disordered regions based on sequence features. BioMed Research International 2013:414327.

    7. Yu-Fei Gao#, Lei Chen#, Guo-Hua Huang, Tao Zhang, Kai-Yan Feng, Haipeng Li, and Yang Jiang* (2013). Prediction of drugs target groups based on ChEBI ontology. Biomed Res Int 2013, 132724.

    8. Junrui Li, Kristan A. Schneider, and Haipeng Li (2013). The hitchhiking effect of a strongly selected substitution in male germline on neutral polymorphism in a monogamy population. PLoS One 8, e71497.

  • 2012

    1. Haipeng Li* (2012) Beyond our naked eyes. Journal of Molecular Cell Biology 4:63.

    2. Zhonghu Li, Jiabin Zou, Kangshan Mao, Kao Lin, Haipeng Li, Jianquan Liu*, Källman Thomas, Martin Lascoux (2012) Population genetic evidence for complex evolutionary histories of four high altitude Juniper species in the QinHai-Tibetan Plateau. Evolution 66:831-845.

    3. 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 19:15-22.

    4. 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 21:28-44.

    5. Kate R. St. Onge#, John Paul Foxe#, Junrui Li#, Haipeng Li, Karl Holm, Pádraic Corcoran, Tanja Slotte, Martin Lascoux*, and 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, 1721-1733.

  • 2011

    1. Tao Huang#, Sibao Wan#, Zhongping Xu, Yufang Zheng, Kai-Yan 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:e16036.

    2. Le-Le Hu#, Zhen Li#, Kai Wang, Shen Niu, Xiaohe Shi, Yudong Cai* and Haipeng Li* (2011) Prediction and analysis of protein methylarginine and methyllysine based on multisequence features. Biopolymers 95:763-771.

    3. Le-Le Hu#，Si-Bao Wan#，Shen Niu，Xiao-He Shi, Haipeng Li*, Yu-Dong Cai*, Kuo-Chen Chou (2011) Prediction and analysis of protein palmitoylation sites. Biochimie 93:489-496.

    4. Kao Lin, Haipeng Li*, Christian Schlotterer, Andreas Futschik* (2011) Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics 187:229-244.

    5. Haipeng Li* (2011) A new test for detecting recent positive selection that is free from the confounding impacts of demography. Mol Biol Evol 28:365-375.

  • 2010

    1. 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.

    2. Kao Lin, Ziliang Qiang, Lin Lu, Lingyi Lu, Lihui Lai, Jieyi Gu, Zhenbing Zeng, Haipeng Li*, and Yudong Cai* (2010) Predicting miRNA's target from primary structure by the nearest neighbor algorithm. Mol Divers 14:719-729.

    3. Jin Li, Hui Yang, Jun-Rui Li, Haipeng Li, Tiao Ning, Pan, X.-R., Peng Shi*, and Ya-Ping Zhang* (2010) Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity 105:274-281.

    4. 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 3:672-676.

    5. 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 14:81-86.

    6. Lingyi Lu, Ziliang Qian, Xiaohe Shi, Haipeng Li*, Yudong Cai*, and Yixue Li* (2010) A knowledge-based method to predict the cooperative relationship between transcription factors. Molecular Diversity, 14:815-819.

                               

    7. 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 3:1061-1068.

  • 2009

    1. Kao Lin, Haipeng Li* (2009) Advances in detecting positive selection on genome. Hereditas, 31: 896-902.

    2. Xu, H., Li, J. and Haipeng Li* (2009) Application of differential equation to the evolution of two groups. Zoological Research, 30, 11-16.

  • 2008

    1. Wen Zhang, Wangwei Cai, Weiping Zhou, Haipeng Li, Liang Li, Wei Yan, Qinkai Deng, Ya-Ping Zhang, Yun-Xin Fu* and 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 66:436-445.

  • Before 2007

    1. Wolfgang Stephan* and Haipeng Li (2007) The recent demographic and adaptive history of Drosophila melanogaster. Heredity, 98:65-68.

    2. Stephan Hutter*, Haipeng Li, Steffen Beisswanger, David De Lorenzo, and Wolfgang Stephan (2007) A scan of autosomal sequence variation in D. melanogaster. Genetics 177:469-480.

    3. Haipeng Li* and Wolfgang Stephan (2006) Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2:e166.

    4. Haipeng Li* and Wolfgang Stephan (2005) Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171:377-384.

    5. Zhongming Zhao, Haipeng Li, Wu, X., Zhong, Y., Zhang, K., Zhang, Y.-P., Boerwinkle, E. and Yun-Xin Fu* (2004) Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evolutionary Biology 4:21.

    6. Haipeng Li, Yun-Wu Zhang, Ya-Ping Zhang and Yun-Xin Fu* (2003) Neutrality tests using DNA polymorphism from multiple samples.Genetics 163:1147-1151.

    7. Haipeng Li, Meng, S.-J., Men, Z.-M., Yun-Xin Fu, and Ya-Ping Zhang* (2003) Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana). Genetics 164:269-275.

    8. Ya-Ping Zhang*, Wang, X.-X., Ryder, O. A., Haipeng Li, Zhang, H.-M., Yong, Y. and Wang, P.-Y. (2002) Genetic diversity and conservation of endangered animal species. Pure Appl Chem 74:575-584.

    9. Ding, Y. C., Wooding, S., Harpending, H. C., Chi, H. C., Haipeng Li, Fu, Y.-X., Pang, J. F., Yao, Y. G., Yu, J. G., Moyzis, R. and Ya-Ping Zhang* (2000) Population structure and history in East Asia. Proc Natl Acad Sci USA 97:14003-14006.

    10. Chun-Hua Wu, Haipeng Li, Ying-Xiang Wang, and Ya-Ping Zhang* (2000) Low genetic variation of the Yunnan hare (Lepus comus G. Allen 1927) as revealed by mitochondrial cytochrome b gene sequences. Biochem Genet 38:149-155.

    11. Haipeng Li, and Ya-Ping Zhang* (1999) A computer program for analyzing RFLP data from population study. Zoological Research 20:326.

    12. Haipeng Li, Ya-Ping Zhang*, Meng, S.-J., Men, Z.-M., Han, J.-L., Feng, N. and Zhang, G.-Q. (1998) Low genetic diversity in Sichuan snub-nosed monkey revealed by protein electrophoresis and its significance to conservation biology. Zoological Research 19:417-421.

  Group of Evolutionary Genomics
SHANGHAI INSTITUTE OF  NUTRITION AND HEALTH, CAS