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Principal Investigator
Peng Shi   Ph.D  
Title
Phone +86 871 65199318
Fax +86 871 65199318
E-mail ship@mail.kiz.ac.cn
Address Laboratory of Evolutionary & Functional Genomics Kunming Institute of Zoology, Chinese Academy of Sciences 21 Qingsong Road, Kunming , Yunnan 650223 P.R.China
Zip Code 650223
 
   Education and Appointments:

Education

1999.9-2004.7   Ph.D. in Zoology ,  Laboratory of Molecular Evolution and Genome Diversity ,  Kunming Institute of Zoology ,  CAS. 

  Thesis: Molecular Mechanism of Adaptive Evolution in

  MammalsBitter Taste Receptor Gene and Vomeronasal

  Receptor 1 Gene Analyses.

  Advisor: Dr. Ya-ping Zhang

1992.9-1996.7   B.S. in Biochemistry ,  Department of Biology ,  Xiamen University ,  Xiamen , Fujian , China.

EMPLOYMENT

2008.8-         Professor ,  Head of Laboratory of Evolutionary & Functional Genomics ,  Kunming Institute of Zoology ,  CAS

2007.1-2008.7   Research Scientist ,  Department of Molecular Genetics ,  German Institute of Human Nutrition

2004.10-2006.12 Postdoctoral Research Fellow ,  Department of Ecology and Evolutionary Biology ,  University of Michigan. 

  Professional Services
   Research Interests:

1. Molecular mechanism of adaptation to various environments in animals. We study the genotype-phenotype relationship at the genomic level under the guidance of natural selection theory ,  while combining multiple advanced techniques including NGS ,  bioinformatics and functional assays ,  etc.

2. Novel disease-related gene identification and the etiopathogenesis study. Through genomic analyses using non model organisms ,  we try to aid the comprehensive understanding of the etiopathogenesis in human longevity ,  cardiovascular diseases and tumors from a different angle.

PROFESSIONAL SERVICES

Reviewer:
Trends in Genetics , PNAS , Genome Research , PLoS Genetics , Molecular Biology and Evolution , Genome Biology and Evolution , PLoS One , Mammalian Genome , Journal of Molecular Evolution , Gene , Genome , Genetica , Acta Genetica Sinica , Hereditas(Beijing) , Zoological Research.

  Supported Projects:

1. National Natural Science Foundation of China (30930015) to P. S. (2010.1-2013.12) 1.79 Million.

2. National Natural Science Foundation of China (31325013) to P. S. (2014.1-2017.12) 3.2 Million.

3. Key Research Programof the Chinese Academy of Sciences KJZD-EW-L07to P. S. (2013.1-2015.12) 3.5 Million.

4. Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13000000)  to P. S. (2014.6-2019.5) 6.5 Million.

  Public Services:
  Honors:
  Selected Publications:
First author
  1. Shi ,  P# , Zhang ,  JZ*Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land , Genome Research,  17(2) ,  pp 166-174 ,  2007/2 , (5-Year IF=13.795) , 2007.02.23
  2. Shi ,  P# , Bakewell ,  M # , Zhang ,  JZ*Did brain-specific genes evolve faster in humans than in chimpanzees? , Trends in Genetics , 22(11):608-13 , 2006/11 ,  (5-Year IF=10.401) , 2006.11.10
  3. Shi ,  P # , Yu ,  L , Fu ,  YX , Huang ,  JF , Zhang ,  KQ , Zhang ,  YP*Evolutionary implications of avian infectious Bronchitis Virus (AIBV) analysis , Cell Research ,  16(3) ,  pp 323-327 ,  2006/3 ,  (5-Year IF=14.331) , 2006.03.24
  4. Shi ,  P#  , Zhang ,  JZ *Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes , Molecular Biology and Evolution ,  23(2) ,  pp 292-300 ,  2006/2 ,  (5-Year IF=14.558) , 2006.02.23
  5. Yang ,  H# , Zhang ,  YP , Zhang ,  JZ ,  Shi P#Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats , Genomics , 86(3):306-15 , 2005/9 , (5-Year IF=3.246) , 2005.05.10
  6. Shi ,  P# , Bielawski ,  JP , Yang ,  H , Zhang ,  YP  ,  *Adaptive diversification of vomeronasal receptor 1 genes in rodents , Journal of Molecular Evolution , 60(5):566-76. , 2005/5 , (5-Year IF=1.875). , 2005.05.06
  7. Grus ,  WE# , Shi ,  P# , Zhang ,  YP , Zhang ,  JZ , Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals , Proceedings of the National Academy of Sciences of the United States of America ,  (5-Year IF=10.414) , 2005.04.19
  8. Shi ,  P#  , Zhang ,  JZ , Yang ,  H , Zhang ,  YP * Adaptive diversification of bitter taste receptor genes in mammalian evolution , Molecular Biology and Evolution ,  20(5) ,  pp 805-814 ,  2003/5 ,  (5-Year IF=14.558)
  9. Shi ,  P#  , Lu ,  XM , Luo ,  HR , Xiang-Yu ,  JG , Zhang ,  YP*Melanocortin-1 receptor gene variants in four Chinese ethnic populations , Cell Research , 11(1) ,  pp 81-84 ,  2001/3 ,  (5-Year IF=14.331) , 2001.03.30
Corresponding author
  1. Tu Q, Hao J, Zhou X, Yan L, Dai H, Sun B, Yang D, An S, Lv L, Jiao B, Chen C, Lai R, Shi P*, Zhao X*, CDKN2B Deletion is Essential for Pancreatic Cancer Development Instead of Unmeaningful Co-deletion Due to Juxtaposition to CDKN2A,(2017), 1–11 Oncogene, (5-Year IF=7.272), 2017.9.11
  2. Li YY#  , Liu Z#*  , Qi FY , Zhou X , Shi P*Functional effects of a retained ancestral polymorphism in prestin , Molecular Biology and Evolution , 34(1):88-92 ,  2017/1 ,  (5-Year IF=14.558) , 2016.10.15
  3. Zhang ZG# , Xu DM#   , Wang L#  , Hao JJ , Wang JF , Zhou X , Wang WW , QiuQ , Huang XiD , Zhou JW , Long RJ * , Zhao FQ * ,  Shi P*Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals , Current Biology ,  26(14):1873-9 , 2016/7 , (5-Year IF=9.704) , 2016.7.25
  4. Liu Z#  , Qi FY , Zhou X , Ren HQ ,  Shi P*Parallel Sites Implicate Functional Convergence of the Hearing Gene Prestin among Echolocating Mammals , Molecular Biology and Evolution , 31(9):2415-24 ,  2014/9 ,  (5-Year IF=14.558) , 2014 .9.01
  5. Zhang ZG# , Geng JW # , Tang XD , Fan H , Xu JC , Wen XJ , Ma ZS *Shi P* , Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota , The ISME Journal , 8(4):881-93 ,  2014/4 , (5-Year IF=10.728) , 2014.4.01
  6. Mu D #   , Yang H , Zhu JW , Liu FL , Tian RR , Zheng HY , Han JB ,  Shi P* , Zheng YT  , *Independent Birth of a Novel TRIMCyp in Tupaia belangeri with a Divergent Function from Its Paralog TRIM5 , Molecular Biology and Evolution ,  31(11):2985-97 , 2014/11 , (5-Year IF=14.558) , 2014.11.01
  7.  Liu Z#  , Wang W , Zhang TZ , Li GH , He K , Huang JF , Jiang XL , Murphy RW , Shi P *Repeated functional convergent effects of Na(V)1.7 on acid insensitivity in hibernating mammals , Proceedings of the Royal Society B: Biological Sciences , (5-Year IF=5.417) 2014.2.7
  8.  Wu T # , Zhang ZG #  , Liu B , Hou DZ , Liang Y , Zhang J* ,  Shi P*Gut microbiota dysbiosis and bacterial community assembly associated withcholesterol gallstones in large-scale study , BMC Genomics , 2013/10 , 14:669 , (5-Year IF=4.284) , 2013.10.1
  9. Zhang ZG #* , Zhai HQ#  , Geng JW# *  , Yu R , Ren HQ , Fan H  ,   Shi P*Large scale survey of gut microbiota associated with MHE Via 16S rRNA-based pyrosequen , American Journal of Gastroenterology ,  108(10):1601-11 , 2013/10 , (5-Year IF=10.429) , 2013.10.30
  10. Gao TX  , Li N , Zhang YP , #Shi P*The complete mitochondrial genome of Japanese sandeel Ammodytes personatus (Perciformes ,  Ammodytidae): Rare structure in control region compared , Mitochondrial DNA , 24(4):320-2 , 2013/8 ,  (5-Year IF=3.672) , 2013.8.01
  11. Qiu , Q#   , Zhang , G#   , Ma , T#   , Qian , W#   , Wang , J#   , Ye , Z#   , (40-coauthor) , ShiP* , WangJ* , LiuJ*   ,  The yak genome and adaptation to life at high altitude , Nature Genetics ,  44(8) ,  pp946-949 ,  2012/7 ,  (5-Year IF=31.694) , 2012.07.27
  12. Liu ,  Z#  , Li ,  G , Huang ,  J , Murphy ,  RW ,  Shi P*Hearing Aid for Vertebrates via Multiple Episodic Adaptive Events on Prestin Genes , Molecular Biology and Evolution ,  29(9) ,  pp2187-2197 ,  2012/9 ,  (5-Year IF=14.558) , 2012.09.28
  13. Liu ,  Z#  , Li ,  S#   , Wang ,  W , Xu ,  D , Murphy ,  RW ,  Shi P*ParallelEvolution of KCNQ4 in Echolocating Bats , PLoS One ,  6(10) ,  p e26618 ,  2011/10(5-Year IF=3.394). , 2011.10.07
  14. Zhang ,  ZG#  , Ye ,  ZQ , Yu ,  L ,  Shi P* Phylogenomic reconstruction of lactic acid bacteria: an update , BMC Evolutionary Biology ,  11(1) ,  p1 ,  2011/1 , (5-Year IF=3.628) , 2011.01.01
  15. Yang ,  H # ,  Shi P*Molecular and evolutionary analyses of formyl peptide receptors suggest the absence of VNO-specific FPRs in primates , Journal of Genetics and Genomics 37(12) pp 771-778 ,  2010/12 , (5-Year IF=3.236) , 2010.12.24
  16. Wang ,  GD#  , Zhu ,  ZH , Zhang ,  YP ,  Shi P*More Functional V1R Genes Occur in Nest-Living and Nocturnal Terricolous Mammals , Genome Biology and Evolution ,  Vol 2 ,  pp 277-283 ,  2010 ,  (5-Year IF=4.008) , 2010.07.12
  17. Li ,  J#  , Yang ,  H , Li ,  JR , Li ,  HP , Ning ,  T , Pan ,  XR , Shi P * , Zhang ,  YP , Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication , Heredity ,  105(3):274-81 , 2010/9 ,  (5-Year IF=3.953) , 2010.02.24
  18. Shen YY#  ,  Sun YB , Zhang YP*  ,  Shi P *Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability , Genome Research ,  19(10) ,  pp 1760-1765 ,  2009/10 ,  (5-Year IF=13.795) ,  , 2009.10.15
  19. Wang ,  GD#  , Zhu , ZH ,  Zhang ,  YP ,  ShiP* Comparative genomic analysisreveals more functional nasal chemoreceptors in nocturnal mammals than in diurnal mammals , Chinese Science Bulletin ,  55(34) ,  pp 3901-3910 ,  2010 ,  (5-YearIF=1.738) , 2010.12.29
  20. 祁飞燕 # , 施鹏*脊椎动物附肢发育及进化机制的研究进展,科学通报2016.11.20 , (32):3413~3420
  21. 施鹏*  , 胡玲玲#Smallest bitter taste receptor (T2Rs) gene repertoire in carnivores , Zoological Research , 2013.4.10
  22. 施鹏*  , 胡玲玲#Latest advances on the studies of function and evolution of bitter taste receptor gene (T2R) family., Chinese Science Bulletin 2010, 54(17):2472-2482
Co-Author
  1. Lang F, Li X, Zheng W, Li Z, Lu D, Chen G, Gong D, Yang L, Fu J, Shi P, Zhou J*, CTCF prevents genomic instability by promoting homologous recombination-directed DNA double-strand break repair, Proceedings of the National Academy of Sciences. (5-Year IF=10.414), DOI: 10.1073/pnas.1704076114, 2017.9.25
  2. Li Y# , Liu Z #  , Zhang JZ*,  Shi P  The hearing gene Prestin unites echolocating bats and whales , Current Biology , 20(2):R55-6, 2010/1(5-Year IF=9.704) , 2010.01.26
  3. Smadja ,  C* ,  Butlin ,  RK , Robertson ,  HM  , # Shi ,  PLarge Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid ,  Acyrthosiphon pisum , Molecular Biology and Evolution ,  26(9) ,  pp 2073-2086 ,  2009/9 ,  (5-Year IF=14.558) , 2009.09.18
  4. Grus ,  WE* , Zhang ,  JZ  , #Shi ,  P Largest vertebrate vomeronasal type 1 receptor gene repertoire in the semiaquatic platypus , Molecular Biology and Evolution ,  24(10) ,  pp 2153-2157 ,  2007/10 ,  (5-Year IF=14.558) , 2007.10.26
  5. Bakewell ,  M# , Zhang JZ* ,  Shi ,  P More genes underwent positive selection in chimpanzee evolution than in human evolution , Proceedings of the National Academy of Sciences of the United States of America ,  (5-Year IF=10.414) , 2007.05.01
  6. Li ,  G* , Wang ,  YQ  , #Shi ,  P Evolutionary dynamics of the ABCA chromosome 17q24 cluster genes in vertebrates , Genomics , 89(3):385-91 , 2007/3 (5-Year IF=3.246) , 2007.03.22
  7. Li ,  Y#  , Ye ,  C ,  Zou ,  XJ , Xiao ,  R , Gong ,  YY , Zhang ,  YP * ,  Shi ,  P Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids , Journal of Molecular Endocrinology , 35(2):399-409 , 2005/10 ,  (5-Year IF=3.609) , 2005.11.08
  8. Ye ,  C#  , Li ,  Y ,   , Zhang ,  YP*   ,  Shi ,  P Molecular evolution of growth hormone gene family in old world monkeys and hominoids , Gene ,  350(2) , pp183-192 , 2005/5 , (5-Year IF=2.266). , 2005.05.30
  9.  Gu ,  Z# , Zhang ,  Y , Shi ,  P , Zhang ,  YP* , Zhu ,  D , Li ,  H , Comparison of avian myostatin genes , Animal Genetics ,  35(6):470-2.2014/12 , (5-Year IF=1.973) , 2004.12.17
  10. Chen ,  DY#  , Wen ,  DC , Zhang ,  YP*  , Sun ,  QY , Han ,  ZM , Liu ,  ZH ,   , L Shi ,  P ,  JS , Xiangyu ,  JG , Lian ,  L , Kou ,  ZH , Wu ,  YQ , Chen ,  YC , Wang ,  PY , Zhang ,  HM , In terspecies implantation and mitochondria fate of panda-rabbit cloned embryos , Biology of Reproduction ,  67(2) , pp637-642 , 2002 (5-Year IF=3.714). , 2002.08.29
  11. Ding ,  B# , Xiangyu ,  JG , Zhang ,  YP  , Chen ,  DY , Sun ,  QY , Li ,  Shi ,  P*GP , Wang ,  MK , Liu ,  YL , Kang ,  L , Han ,  ZM , Song ,  XF , Li ,  JS , Chen ,  YC , Microsatel lite DNA analysis proves nucleus of interspecies reconstructed blastocyst coming from that of donor giant panda , Chinese Science Bulletin ,  45(20) ,  pp 1883-1885 ,  2000/10 ,  (5-Year IF=1.738) , 2000.10.27
Invited book chapter:
  1. Behrens M ,  St?hler F ,  Shi P ,  Bufe B ,  and Meyerhof W. 2009. Taste: Topics in Chemical Biology. In: the Wiley Encyclopedia of Chemical Biology.
  2. Shi P#. and Zhang J Extraordinary diversity of chemosensory receptor gene repertoires among vertebrates. 2009. Chemosensory Systems in Mammals ,  Fishes ,  and Insects. W. Meyerhof & S. Korsching ,  eds. ,  Springer
  Research Team:

Research Assistants:

Dr. Hui Yang (from Emory University , USA)

Dr. Zhi-gang Zhang (from Yunnan University , China)

Dr. Junjun Hao (from Shanghai University , China)

Dr. Dongming Xu(from University of Chinese Academy of Sciences)

Technicians:

Rui Yu

Xin Zhou

Xingtong Li

Yangan Huang

Finance Assistant:

Yang Zhang

PhD students:

Jie Luo ,  Zhizhong Zheng ,  Tao Zhang ,  Yuanyuan Li ,  Lei Zhu ,  Qi Liu

Master students:

Yuanting Guo ,  Jie Chen ,  Qunfu Wu ,  Lili Yang ,  Menglong Lei ,  Wanzhi CaiJing Bai

 
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