​Genome Evolution and Species Adaptation

Origin and Evolution of Important Animal Traits

Epigenetic Regulatory Mechanisms of Animal Development and Phenotypic Plasticity

2013-12--2016-09   University of Copenhagen, PhD
2010-09--2013-07   South China University of Technology, Master
2006-09--2010-07   South China University of Technology, Bachelor

   

2022-06~Now, BGI Research, Executive Director of the Digital Earth Institute
2016-09~2022-06, BGI Research, Director of Biodiversity Genomics Center

Animal Genomics

Basic Principles and Analytical Techniques of Epigenetics

   

[1] Qiye Li, Mingyue Wang, Pei Zhang, Yang Liu, Qunfei Guo, Yuanzhen Zhu, Tinggang Wen, Xueqin Dai, Xiafang Zhang, Manuel Nagel, Bjarke Hamberg Dethlefsen, Nianxia Xie, Jie Zhao, Wei Jiang, Lei Han, Liang Wu, Wenjiang Zhong, Zhifeng Wang, Xiaoyu Wei, Wei Dai, Longqi Liu, Xun Xu, Haorong Lu, Huanming Yang, Jian Wang, Jacobus J Boomsma, Chuanyu Liu, Guojie Zhang, Weiwei Liu. A single-cell transcriptomic atlas tracking the neural basis of division of labour in an ant superorganism. Nature Ecology & Evolution. 2022, 6(8): 1191-1204, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9349048/.
[2] Qiye Li, Mingyue Wang, Pei Zhang, Yang Liu, Qunfei Guo, Yuanzhen Zhu, Tinggang Wen, Xueqin Dai, Xiafang Zhang, Manuel Nagel, Bjarke Hamberg Dethlefsen, Nianxia Xie, Jie Zhao, Wei Jiang, Lei Han, Liang Wu, Wenjiang Zhong, Zhifeng Wang, Xiaoyu Wei, Wei Dai, Longqi Liu, Xun Xu, Haorong Lu, Huanming Yang, Jian Wang, Jacobus J Boomsma, Chuanyu Liu, Guojie Zhang, Weiwei Liu. A single-cell transcriptomic atlas tracking the neural basis of division of labour in an ant superorganism. Nature Ecology & Evolution. 2022, 6(8): 1191-1204, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9349048/.
[3] Altenburger, Andreas, Cai, Huimin, Li, Qiye, Drumm, Kirstine, Kim, Miran, Zhu, Yuanzhen, GarciaCuetos, Lydia, Zhan, Xiaoyu, Hansen, Per Juel, John, Uwe, Li, Shuaicheng, Lundholm, Nina. Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum. ISME JOURNAL[J]. 2021, 15(4): 1056-1072, http://dx.doi.org/10.1038/s41396-020-00830-9.
[4] Zhou, Yang, ShearwinWhyatt, Linda, Li, Jing, Song, Zhenzhen, Hayakawa, Takashi, Stevens, David, Fenelon, Jane C, Peel, Emma, Cheng, Yuanyuan, Pajpach, Filip, Bradley, Natasha, Suzuki, Hikoyu, Nikaido, Masato, Damas, Joana, Daish, Tasman, Perry, Tahlia, Zhu, Zexian, Geng, Yuncong, Rhie, Arang, Sims, Ying, Wood, Jonathan, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Li, Qiye, Yang, Huanming, Wang, Jian, Johnston, Stephen D, Phillippy, Adam M, Howe, Kerstin, Jarvis, Erich D, Ryder, Oliver A, Kaessmann, Henrik, Donnelly, Peter, Korlach, Jonas, Lewin, Harris A, Graves, Jennifer, Belov, Katherine, Renfree, Marilyn B, Grutzner, Frank, Zhou, Qi, Zhang, Guojie. Platypus and echidna genomes reveal mammalian biology and evolution. NATURE[J]. 2021, 592(7856): 756-+, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081666/.
[5] Altenburger, Andreas, Cai, Huimin, Li, Qiye, Drumm, Kirstine, Kim, Miran, Zhu, Yuanzhen, GarciaCuetos, Lydia, Zhan, Xiaoyu, Hansen, Per Juel, John, Uwe, Li, Shuaicheng, Lundholm, Nina. Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum. ISME JOURNAL[J]. 2021, 15(4): 1056-1072, http://dx.doi.org/10.1038/s41396-020-00830-9.
[6] Zhou, Yang, ShearwinWhyatt, Linda, Li, Jing, Song, Zhenzhen, Hayakawa, Takashi, Stevens, David, Fenelon, Jane C, Peel, Emma, Cheng, Yuanyuan, Pajpach, Filip, Bradley, Natasha, Suzuki, Hikoyu, Nikaido, Masato, Damas, Joana, Daish, Tasman, Perry, Tahlia, Zhu, Zexian, Geng, Yuncong, Rhie, Arang, Sims, Ying, Wood, Jonathan, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Li, Qiye, Yang, Huanming, Wang, Jian, Johnston, Stephen D, Phillippy, Adam M, Howe, Kerstin, Jarvis, Erich D, Ryder, Oliver A, Kaessmann, Henrik, Donnelly, Peter, Korlach, Jonas, Lewin, Harris A, Graves, Jennifer, Belov, Katherine, Renfree, Marilyn B, Grutzner, Frank, Zhou, Qi, Zhang, Guojie. Platypus and echidna genomes reveal mammalian biology and evolution. NATURE[J]. 2021, 592(7856): 756-+, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081666/.
[7] Li Qiye. On the origin and evolution of RNA editing in metazoans. bioRxiv. 2020, [8] Pei Zhang, JieSi Chen, QiYe Li, LongXiang Sheng, YiXing Gao, BingZheng Lu, WenBo Zhu, XiaoYu Zhan, Yuan Li, ZhiBing Yuan, Gang Xu, BiTao Qiu, Min Yan, ChunXue Guo, YouQiong Wang, YiJun Huang, JingXia Zhang, FuYu Liu, ZhongWei Tang, SuiZhen Lin, David N Cooper, HuanMing Yang, Jian Wang, YuQi Gao, Wei Yin, GuoJie Zhang, GuangMei Yan. Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys. Zoological Research[J]. 2020, 41(1): 3-19, http://lib.cqvip.com/Qikan/Article/Detail?id=7100883453.
[9] Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang. A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura:Limnodynastidae). GigaByte (2020)[J]. 2020, 1: https://doaj.org/article/249dc7e263f441fb875a912be321af46.
[10] Li Qiye. On the origin and evolution of RNA editing in metazoans. bioRxiv. 2020, [11] Pei Zhang, JieSi Chen, QiYe Li, LongXiang Sheng, YiXing Gao, BingZheng Lu, WenBo Zhu, XiaoYu Zhan, Yuan Li, ZhiBing Yuan, Gang Xu, BiTao Qiu, Min Yan, ChunXue Guo, YouQiong Wang, YiJun Huang, JingXia Zhang, FuYu Liu, ZhongWei Tang, SuiZhen Lin, David N Cooper, HuanMing Yang, Jian Wang, YuQi Gao, Wei Yin, GuoJie Zhang, GuangMei Yan. Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys. Zoological Research[J]. 2020, 41(1): 3-19, http://lib.cqvip.com/Qikan/Article/Detail?id=7100883453.
[12] Qiye Li, Qunfei Guo, Yang Zhou, Huishuang Tan, Terry Bertozzi, Yuanzhen Zhu, Ji Li, Stephen Donnellan, Guojie Zhang. A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura:Limnodynastidae). GigaByte (2020)[J]. 2020, 1: https://doaj.org/article/249dc7e263f441fb875a912be321af46.
[13] Farre, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A, Kulemzina, Anastasia I, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Graphodatsky, Alexander S, Zhang, Guoije, Larkin, Denis M, Lewin, Harris A. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). GIGASCIENCE. 2019, 8(8): https://www.webofscience.com/wos/woscc/full-record/WOS:000491875600005.
[14] Farre, Marta, Li, Qiye, Zhou, Yang, Damas, Joana, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Zhang, Guojie, Larkin, Denis M, Lewin, Harris A. A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. GIGASCIENCE. 2019, 8(2): https://www.webofscience.com/wos/woscc/full-record/WOS:000462551600007.
[15] Farre, Marta, Kim, Jaebum, Proskuryakova, Anastasia A, Zhang, Yang, Kulemzina, Anastasia, I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L, Perelman, Polina L, Johnson, Warren E, Warren, Wesley C, Kukekova, Anna, V, Zhang, Guojie, OBrien, Stephen J, Ryder, Oliver A, Graphodatsky, Alexander S, Ma, Jian, Lewin, Harris A, Larkin, Denis M. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. GENOME RESEARCH[J]. 2019, 29(4): 576-589, [16] Cai, Huimin, Li, Qiye, Fang, Xiaodong, Li, Ji, Curtis, Nicholas E, Altenburger, Andreas, Shibata, Tomoko, Feng, Mingji, Maeda, Taro, Schwartz, Julie A, Shigenobu, Shuji, Lundholm, Nina, Nishiyama, Tomoaki, Yang, Huanming, Hasebe, Mitsuyasu, Li, Shuaicheng, Pierce, Sidney K, Wang, Jian. A draft genome assembly of the solar-powered sea slug Elysia chlorotica. SCIENTIFIC DATA. 2019, 6: http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000460585500005.
[17] Li Qiye. Gonad Transcriptome Analysis of High Temperature Induced Sex Reversal in Chinese Tongue Sole, Cynoglossus semilaevis. Frontiers in Genetics. 2019, [18] Chen, Lei, Qin, Qiang, Jiang, Yu, Wang, Kun, Lin, Zeshan, Li, Zhipeng, Bibi, Faysal, Yang, Yongzhi, Wang, Jinhuan, Nie, Wenhui, Su, Weiting, Liu, Guichun, Li, Qiye, Fu, Weiwei, Pan, Xiangyu, Liu, Chang, Yang, Jie, Zhang, Chenzhou, Yin, Yuan, Wang, Yu, Zhao, Yue, Zhang, Chen, Wang, Zhongkai, Qin, Yanli, Liu, Wei, Wang, Bao, Ren, Yandong, Zhang, Ru, Zeng, Yan, da Fonseca, Rute R, Wei, Bin, Li, Ran, Wan, Wenting, Zhao, Ruoping, Zhu, Wenbo, Wang, Yutao, Duan, Shengchang, Gao, Yun, Zhang, Yong E, Chen, Chunyan, Hvilsom, Christina, Epps, Clinton W, Chemnick, Leona G, Doug, Yang, Mirarab, Siavash, Siegismund, Hans Redlef, Ryder, Oliver A, Gilbert, M Thomas P, Lewin, Harris A, Zhang, Guojie, Heller, Rasmus, Wang, Wen. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. SCIENCE[J]. 2019, 364(6446): 1152-+, http://dx.doi.org/10.1126/science.aav6202.
[19] Farre, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A, Kulemzina, Anastasia I, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Graphodatsky, Alexander S, Zhang, Guoije, Larkin, Denis M, Lewin, Harris A. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). GIGASCIENCE. 2019, 8(8): https://www.webofscience.com/wos/woscc/full-record/WOS:000491875600005.
[20] Farre, Marta, Li, Qiye, Zhou, Yang, Damas, Joana, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Zhang, Guojie, Larkin, Denis M, Lewin, Harris A. A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert. GIGASCIENCE. 2019, 8(2): https://www.webofscience.com/wos/woscc/full-record/WOS:000462551600007.
[21] Farre, Marta, Kim, Jaebum, Proskuryakova, Anastasia A, Zhang, Yang, Kulemzina, Anastasia, I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L, Perelman, Polina L, Johnson, Warren E, Warren, Wesley C, Kukekova, Anna, V, Zhang, Guojie, OBrien, Stephen J, Ryder, Oliver A, Graphodatsky, Alexander S, Ma, Jian, Lewin, Harris A, Larkin, Denis M. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. GENOME RESEARCH[J]. 2019, 29(4): 576-589, [22] Cai, Huimin, Li, Qiye, Fang, Xiaodong, Li, Ji, Curtis, Nicholas E, Altenburger, Andreas, Shibata, Tomoko, Feng, Mingji, Maeda, Taro, Schwartz, Julie A, Shigenobu, Shuji, Lundholm, Nina, Nishiyama, Tomoaki, Yang, Huanming, Hasebe, Mitsuyasu, Li, Shuaicheng, Pierce, Sidney K, Wang, Jian. A draft genome assembly of the solar-powered sea slug Elysia chlorotica. SCIENTIFIC DATA. 2019, 6: http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000460585500005.
[23] Li Qiye. Gonad Transcriptome Analysis of High Temperature Induced Sex Reversal in Chinese Tongue Sole, Cynoglossus semilaevis. Frontiers in Genetics. 2019, [24] Chen, Lei, Qin, Qiang, Jiang, Yu, Wang, Kun, Lin, Zeshan, Li, Zhipeng, Bibi, Faysal, Yang, Yongzhi, Wang, Jinhuan, Nie, Wenhui, Su, Weiting, Liu, Guichun, Li, Qiye, Fu, Weiwei, Pan, Xiangyu, Liu, Chang, Yang, Jie, Zhang, Chenzhou, Yin, Yuan, Wang, Yu, Zhao, Yue, Zhang, Chen, Wang, Zhongkai, Qin, Yanli, Liu, Wei, Wang, Bao, Ren, Yandong, Zhang, Ru, Zeng, Yan, da Fonseca, Rute R, Wei, Bin, Li, Ran, Wan, Wenting, Zhao, Ruoping, Zhu, Wenbo, Wang, Yutao, Duan, Shengchang, Gao, Yun, Zhang, Yong E, Chen, Chunyan, Hvilsom, Christina, Epps, Clinton W, Chemnick, Leona G, Doug, Yang, Mirarab, Siavash, Siegismund, Hans Redlef, Ryder, Oliver A, Gilbert, M Thomas P, Lewin, Harris A, Zhang, Guojie, Heller, Rasmus, Wang, Wen. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. SCIENCE[J]. 2019, 364(6446): 1152-+, http://dx.doi.org/10.1126/science.aav6202.
[25] Xiong, Heng, Liu, Dongbing, Li, Qiye, Lei, Mengyue, Xu, Liqin, Wu, Liang, Wang, Zongji, Ren, Shancheng, Li, Wangsheng, Xia, Min, Lu, Lihua, Lu, Haorong, Hou, Yong, Zhu, Shida, Liu, Xin, Sun, Yinghao, Wang, Jian, Yang, Huanming, Wu, Kui, Xu, Xun, Lee, Leo J. RED-ML: a novel, effective RNA editing detection method based on machine learning. GIGASCIENCE[J]. 2017, 6(5): 1-8, http://dx.doi.org/10.1093/gigascience/gix012.
[26] Gao, Jian, Li, Qiye, Wang, Zongji, Zhou, Yang, Martelli, Paolo, Li, Fang, Xiong, Zijun, Wang, Jian, Yang, Huanming, Zhang, Guojie. Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. GIGASCIENCE. 2017, 6(7): 1-6, https://www.webofscience.com/wos/woscc/full-record/WOS:000405825600001.
[27] Xiong, Heng, Liu, Dongbing, Li, Qiye, Lei, Mengyue, Xu, Liqin, Wu, Liang, Wang, Zongji, Ren, Shancheng, Li, Wangsheng, Xia, Min, Lu, Lihua, Lu, Haorong, Hou, Yong, Zhu, Shida, Liu, Xin, Sun, Yinghao, Wang, Jian, Yang, Huanming, Wu, Kui, Xu, Xun, Lee, Leo J. RED-ML: a novel, effective RNA editing detection method based on machine learning. GIGASCIENCE[J]. 2017, 6(5): 1-8, http://dx.doi.org/10.1093/gigascience/gix012.
[28] Gao, Jian, Li, Qiye, Wang, Zongji, Zhou, Yang, Martelli, Paolo, Li, Fang, Xiong, Zijun, Wang, Jian, Yang, Huanming, Zhang, Guojie. Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. GIGASCIENCE. 2017, 6(7): 1-6, https://www.webofscience.com/wos/woscc/full-record/WOS:000405825600001.

（1）On the origin and evolution of RNA editing in metazoans, the GECKO Conference, 2021-05-25
（2）Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior, International Union for the Study of Social Insects 2014 Conference, 2014-07-18

First Prize of Shenzhen Natural Science Award, 2017