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evolgen

What We Do?

Accelerated evolution

Over 5,400 different mammalian species exist globally and many have evolved highly distinctive phenotypic traits. The genomic mechanisms underlying these phenotypes are largely unknown but could be relevant for understanding human disease. Accelerated genomic regions may have roles in shaping these important traits. Thus we develop new theories to study accelerated evolution driven by positive selection. Recently, we successfully identified the social enhancer PAS1 that modulates social hierarchy in amniotes.

Demography estimation

It can never been underestimated the importance of demography, for example, the demographic histories of human, chimpanzee, cat, fish, insects and plants. However, you cannot infer demography when there are no proper theories. Therefore, by developing new theories, we aim to decipher demographic history of species. This is the beauty of theory as it can reveal evolutionary stories behind each species. These theories are essential for many research fields, for example, precision medicine and conservation.

Bioinformatics

Multiomic and evolutionary analyses have been booming recently, and interactive figures and software are believed to be important for these studies. We combine the advantages of cloud computing and desktop application, and design highly interactive user interfaces and pipelines to bridge the gap between multiomic and evolutionary analyses. Moreover, COVID-19 is spreading across the world. To fight with SARS-CoV-2, the shared enemy of human community, we launch Coronavirus GenBrowser for the public to rapidly access the latest information of SARS-CoV-2 genomes. It can closely monitor the frequency changes of mutations, identify the possible origin of newly emerged strains, and detect the non-neutral evolution of SARS-CoV-2.

Natural selection

Natural selection is one of the important evolutionary forces. By detecting genes and non-coding regions subject to natural selection, it could help us to study the function of genes and non-coding regions, and the interactions between genes and environment.
Our laboratory focuses on developing new theories for fast and efficient methods to detect positive selection. Moreover, since we introduced machine learning (or artificial intelligence) into the field of population genetics ten years ago, we keep exploring possibilities by applying different machine learning methods, for example, deep convolutional neural networks, to detect positive selection. These studies are important for identifying mutations associated with human metabolism and diseases.

Psychobiotics

Psychobiotics is a term used in preliminary research to refer to live bacteria that, when ingested in appropriate amounts, might confer a mental health benefit by affecting microbiota of the host organism.
Recent advances in nutritional psychiatry point to the importance of the intestinal microbiota to human health and wellbeing. Amazingly, cognitive and emotional processes can be altered by microbes acting through the brain-gut axis. The brain-gut axis provides bidirectional communication between the brain and the gut and includes the metabolically complex intestinal microbiota. However, we need new theories and methods to study why and how gut bacteria can positively or negatively influence the mental process.

Group Leader

LI Haipeng
Room: 329
Tel: 54920460
lihaipeng (at) sinh.ac.cn

Experiences

2007-present: Professor, Shanghai Institute of Nutrition and Health, 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, USA (Co-advisor: Prof. Yun-Xin Fu)
1996-2002: Ph.D. student, Genetics/Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences (Advisor: Prof. Ya-Ping Zhang)
1992-1996: B.S., Zoology, Shandong University, China

Research interests

Accelerated Evolution | Population Genetics | Bioinformatics | Natural Selection Detection | Psychobiotics

Staff Scientists

GU Zhili
Group Manager
Room: 335
Tel: 54920467
guzhili (at) sinh.ac.cn

DAI Guangyi
Staff Scientist
Room: 335
Tel: 54920467
daiguangyi (at) sinh.ac.cn

Students

LIN Xin
Ph.D Candidate
Room: 335
Tel: 54920467
linxin2018 (at) sinh.ac.cn

GU Shanshan
Ph.D Candidate
Room: 339
Tel: 54920467
gushanshan2019 (at) sinh.ac.cn

YANG Jianing
Ph.D Candidate
Room: 339
Tel: 54920467
yangjianing2019 (at) sinh.ac.cn

ZHOU Sumei
Ph.D Candidate
Room: 339
Tel: 54920467
zhousumei2020 (at) sinh.ac.cn

ZHANG Jianwei
Ph.D Candidate
Room: 339
Tel: 54920467
zhangjianwei2021 (at) sinh.ac.cn

ZHANG Wanyu
Graduate Student
Room: 339
Tel: 54920467
zhangwanyu2022 (at) sinh.ac.cn

LI Yangyang
Ph.D Candidate
Room: 335
Tel: 54920467
liyangyang2022 (at) sinh.ac.cn

PAN Yichen
Ph.D Candidate
Room: 339
Tel: 54920467
panyichen2023 (at) sinh.ac.cn

ZHOU Yiwen
Ph.D Candidate
Room: 339
Tel: 54920467
zhouyiwen2023 (at) sinh.ac.cn

Former members

YAN Fangqi
Staff Scientist
yanfangqi0818 (at) 163.com

XIANGYU Jinggong
Staff Scientist
xiangyujingong (at) picb.ac.cn

MU Hailong
Staff Scientist
mhl_dyx (at) 126.com

LASCOUX Martin
Visiting Scientist
Martin.Lascoux (at) ebc.uu.se

YANG Zongfeng
Ph.D
yangzongfeng (at) picb.ac.cn

LI Junrui
Ph.D
lijunrui (at) picb.ac.cn

LIN Kao
Ph.D
linkao (at) picb.ac.cn

GAO Feng
Ph.D
gaofeng (at) picb.ac.cn

MING Chen
Ph.D
mingchen (at) picb.ac.cn

WANG Yuting
Ph.D
wangyuting (at) picb.ac.cn

YANG Jinjin
Intern
yangjinjin2009 (at) gmail.com

HUANG Hongwei
Intern
huanghw1111 (at) 163.com

HU Wangjie
Ph.D
wangjie.hu (at) mssm.edu

HAO Ziqian
Ph.D
haoziqian (at) sdfmu.edu.cn

DU Pengyuan
Ph.D
dupengyuan (at) sdfmu.edu.cn

LIU Guopeng
Ph.D
guopeng.liu (at) abogenbio.com

YU Dalang
Ph.D
yudalang (at) ucas.edu.cn

SHI Yi
Ph.D
shiyi2017 (at) sinh.ac.cn

2024 (3)

  1. 潘逸萱*, 李海鹏* (2024) 多学科、多物种交叉融合研究早、中更新世人类祖先的物种形成和进化. 倡议书.
  2. Xin Lin, Guangyi Dai, Sumei Zhou, Yangyang Li, Yi-Hsuan Pan*, Haipeng Li* (2024) Sociability genetically separable from social hierarchy in amniotes. bioRxiv
  3. 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 (2)

  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 (5)

  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(5):442-446.
  2. Yang-Yang Li#, Qing-Yun Lv#, Gun-Tao Zheng, Di Liu, Ji Ma, Gui-Mei He, Li-Biao Zhang, Shan Zheng, Hai-Peng 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, 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. Briefings in Bioinformatics 23(2):bbab583.
  4. Ziqian Hao#, Pengyuan Du#, Yi-Hsuan Pan*, Haipeng Li* (2022) Fine human genetic map based on UK10K data set. Human Genetics 141(2):273–281.
  5. 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. Zoological Research 43(5):871-874.

2021 (2)

  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. Developmental Cell 56(4):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 (4)

  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, 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.
  2. Jing-Yang Hu#, Zi-Qian Hao#, Laurent Frantz, Shi-Fang Wu, Wu Chen, Yun-Fang Jiang, Hong Wu, Wei-Min Kuang, Hai-Peng Li*, Ya-Ping Zhang*, Li Yu* (2020) Genomic consequences of population decline in critically endangered pangolins and their demographic histories. National Science Review 7(4):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, Hai-Peng 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(6):952-963.
  4. Guopeng Liu, Haipeng Li* (2020) Social enhancer PAS1 and Lhx2 determines social hierarchies in amniotes. Chemistry of Life 40(6):984.

2019 (4)

  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, 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.
  2. Shi Yi, Haipeng Li* (2019) Population genetics: From classical statistics to supervised learning. Scientia Sinica Vitae 49(4):445-455.
  3. Feng-Juan Zhang, Ying Zhang, Xiao-Long Lv, Bei-Ying Xu, Hong-Dao Zhang, Jun Yan, Hai-Peng Li, Li-Gang Wu* (2019) Evolution of an X-linked miRNA family predominantly expressed in mammalian male germ cells. Mol Biol Evol 36(4):663-678.
  4. Wei-Min Kuang, Chen Ming, Hai-Peng 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(3):487-499.

2018 (3)

  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, Yao-Guang Zhang, Hai-Peng Li, Bing-Yu Mao, Robert W. Murphy, David B. Wake*, Ya-Ping 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.
  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, 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. (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(2):791-805.

2017 (4)

  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, Hai-Peng 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, Hai-Peng Li, Dong-Dong Wu*, 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(4):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, Xiang-Ting Wang, Ju-Min Zhou, Hai-Peng Li, Yong-Bin Chen*, 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(11):2888-2899.

2016 (5)

  1. Hai-Peng Li#, Jing-Gong Xiang-Yu#, Guang-Yi Dai, Zhi-Li Gu, Chen Ming, Zong-Feng 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 U S A 113(49):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(3):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(6):1563-1571.
  4. 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.
  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(10):e0165496.

Before 2015

  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):1286-1298.
  2. 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.
  3. 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.
  4. Kao Lin, Andreas Futschik, Haipeng Li* (2013) A fast estimate for the population recombination rate based on regression. Genetics 194(2):473-484.
  5. 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.
  6. Bi-Qing 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.
  7. 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.
  8. 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.
  9. 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.
  10. Yu-Fei Gao#, Lei Chen#, Guo-Hua Huang, Tao Zhang, Kai-Yan Feng, Hai-Peng Li, Yang Jiang* (2013) Prediction of drugs target groups based on ChEBI ontology. Biomed Res Int 2013:132724.
  11. 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.
  12. Haipeng Li* (2012) Beyond our naked eyes. Journal of Molecular Cell Biology 4(1):63.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. Le-Le Hu#，Si-Bao Wan#，Shen Niu，Xiao-He Shi, Hai-Peng Li*, Yu-Dong Cai*, Kuo-Chen Chou (2011) Prediction and analysis of protein palmitoylation sites. Biochimie 93(3):489-496.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. Kao Lin, Haipeng Li* (2009) Advances in detecting positive selection on genome. Hereditas 31(9):896-902.
  30. Xu H, Li J, Li H* (2009) Application of differential equation to the evolution of two groups. Zoological Research 30(1):11-16.
  31. Wen Zhang, Wangwei Cai, Weiping Zhou, Haipeng Li, Liang Li, Wei Yan, Qinkai Deng, Ya-Ping 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.
  32. Wolfgang Stephan*, Haipeng Li (2007) The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98(2):65-68.
  33. 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.
  34. Haipeng Li*, Wolfgang Stephan (2006) Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2(10):e166.
  35. 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.
  36. Zhongming Zhao, Haipeng Li, Xiaozhuang Wu, Yixi Zhong, Keqin Zhang, Ya-Ping Zhang, Eric Boerwinkle, Yun-Xin Fu* (2004) Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evolutionary Biology 4:21.
  37. Hai-Peng Li, Yun-Wu Zhang, Ya-Ping Zhang, Yun-Xin Fu* (2003) Neutrality tests using DNA polymorphism from multiple samples. Genetics 163(3):1147-1151.
  38. Hai-Peng Li, Shi-Jie Meng, Zheng-Ming Men, Yun-Xin Fu, Ya-Ping Zhang* (2003) Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana). Genetics 164(1):269-275.
  39. Ya-ping Zhang*, Xiao-xia Wang, Oliver A. Ryder, Haipeng Li, He-ming Zhang, Yange Yong, Peng-yan Wang (2002) Genetic diversity and conservation of endangered animal species. Pure Appl Chem 74(4):575-584.
  40. 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.
  41. Chun-Hua Wu, Hai-Peng Li, Ying-Xiang Wang, 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(5-6):149-155.
  42. Hai-Peng Li, Ya-Ping Zhang* (1999) A computer program for analyzing RFLP data from population study. Zoological Research 20(5):326.
  43. Hai-Peng Li, Ya-Ping Zhang*, Shi-Jie Meng, Zheng-Ming Men, Jian-Lin Han, Ning Feng, Guo-Qi 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.

Du

A single locus test for detecting recent positive selection by bi-partitioning the coalescent tree

Version

1.0

         

eGPS

A multi-functional software that enables users to perform comprehensive multi-omic and evolutionary analyses

Version

All

        

evolBoosting

A single locus test for detecting recent positive selection by bi-partitioning the coalescent tree

Version

1.0.0

        

1.0.1

       

FastEPRR

An extremely fast open-source software package to estimate population recombination rate based on intraspecific DNA polymorphism data

Version

1.0

               

2.0

               

KungFuPanda

A program for analysing the accelerated evolution of an internal branch in a user-defined tree, based on a user-defined configure file

Version

1.1

   

msmfs

A ms simulator generating simulation data under the condition of compact folded mutation frequency spectrum, missing data or multiple hits

Version

1.0

   

MFDM

A software for detecting recent positive selection reliably in natural populations

Version

1.0

   

1.1

   

NeutralityTest

A software for neutrality test

Version

1.2

       

FitCoal

A Fast Estimator for Population Demographic History Inference

Version

1.0

1.1

1.2

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