论文：

1.     Zhao SL#, Zhang T#, Liu Q, Wu H, Su B, Shi P ,Chen H*,Identifying Lineage-Specific Targets of Natural Selection by a Bayesian Analysis of Genomic Polymorphisms and Divergence from Multiple Species. Molecular Biology and Evolution,2019, 36(6): 1302-1315

2.     Liu Z#, Qi FY#, Xu DM#, Zhou X, Shi P*, Genomic and functional evidence reveals molecular insights into the origin of echolocation in whales, Science Advances ,2018, 4:eaat8821

3.     Tu Q#, Hao JJ#, zhou X#, Yan LZ, Dai HJ, Sun B, Yang D, An SQ, Lv LB, Jiao BW, Chen CS Lai R, Shi P*, Zhao XD*, CDKN2B deletion is essential for pancreatic cancer development instead of unmeaningful co-deletion due to juxtaposition to CDKN2A, Oncogene, 2018, 37(1): 128-138

4.     Li YY#  , Liu Z#*  , Qi FY , Zhou X , Shi P*,Functional effects of a retained ancestral polymorphism in prestin , Molecular Biology and Evolution , 2017 ,34(1):88-92

5.     Zhang ZG# , Xu DM#   , Wang L#  , Hao JJ , Wang JF , Zhou X , Wang WW , Qiu Q , Huang Xi D , Zhou JW , Long RJ * , Zhao FQ * ,  Shi P*，Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals , Current Biology ,  2016 , 26(14):1873-9

6.     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 , 2014 , 31(9):2415-2424

7.     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 , ISME Journal , 2014 , 8(4):881-893

8.      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 , 2014,  31(11):2985-2997

9.     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 , 14:669

10. 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 ,  2013, 108(10):1601-1611

11. 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 , 2013,24(4):320-322

12.  Liu Z#, Wang W#, Zhang TZ# , Li GH , He K , Huang JF , Jiang XL , Murphy RW , Shi P *,Repeated functional convergent effects of NaV1.7 on acid insensitivity in hibernating mammals , Proceedings of the Royal Society B:Biological Sciences ,  2013 , 281(1776), e20132950

13.  Hu LL# , Shi P*,Smallest bitter taste receptor (T2Rs) gene repertoire in carnivores , Zoological Research,2013, 34(3):75-81 

14. Qiu Q#, Zhang GJ#, Ma T#, Qian WB#, Wang JY#, Ye ZQ#, Cao CC, Hu QJ, Kim J, Larkin DM, Auvil L, Capitanu B, Ma J, Lewin HA, Qian XJ, Lang YS, Zhou R, Wang LZ, Wang K, Xia JQ, Liao SG, Pan SK, Lu X, Hou HL, Wang Y, Zang XT, Yin Y, Ma H, Zhang J, Wang ZF, Zhang YM, Zhang DW, Yonezawa T, Hasegawa M, Zhong Y, Liu WB, Zhang Y, Huang ZY, Zhang SX, Long RJ, Yang HM, Wang J, Lenstra JA, Cooper DN, Wu Y, Wang J*, Shi P*, Wang J*, Liu JQ*,  The yak genome and adaptation to life at high altitude , Nature Genetics ,   2012 , 44(8) ,  946-949 

15. Liu Z# , Li GH , Huang JF , Murphy RW ,Shi P*,Hearing Aid for Vertebrates via Multiple Episodic Adaptive Events on Prestin Genes , Molecular Biology and Evolution ,   2012, 29(9) : 2187-2197

16. Liu Z#, Li  S#, Wang W, Xu D , Murphy RW, Shi P*, Parallel Evolution of KCNQ4 in Echolocating Bats , PLoS One ,  2011, 6(10) , e26618 

17. Zhang ZG#, Ye  ZQ# , Yu  L*, Shi P*, Phylogenomic reconstruction of lactic acid bacteria: an update , BMC Evolutionary Biology ,   2011 ,11(1) ,  1 

18. 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 , 2010, 37(12):771-778

19. Wang GD#  ,  Shi P* ,Zhu ZH , Zhang YP* ,More Functional V1R Genes Occur in Nest-Living and Nocturnal Terricolous Mammals , Genome Biology and Evolution , 2010 ,2 : 277-283  

20.  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 ,2010,  105(3):274-81 

21. Wang GD# ,Zhu ZH#, Shi P*, Zhang YP*, Comparative genomic analysisreveals more functional nasal chemoreceptors in nocturnal mammals than in diurnal mammals, Chinese Science Bulletin , 2010,55(34):3901-3910

22. Li Y#, Liu Z#, Shi P, Zhang JZ*, The hearing gene Prestin unites echolocating bats and whales, Current Biology, 2010, 20(2):55-56

23. Shen YY# , Shi P *, Sun YB, Zhang YP* ,Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability , Genome Research ,  2009 , 19(10) : 1760-1765  

24. Smadja C#*, Shi P, Butlin RK, Robertson HM, Large Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid, Acyrthosiphon pisum, Molecular Biology and Evolution, 2009, 26(9): 2073-2086

25. 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, 2007, 17(2): 166-174

26. Grus WE#, Shi P, Zhang JZ*, Largest vertebrate vomeronasal type 1 receptor gene repertoire in the semiaquatic platypus, Molecular Biology and Evolution, 2007, 24(10): 2153-2157

27. Bakewell MA#, Shi P, Zhang JZ*, 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, 2007,104:7489-7494

28. Li G#, Shi P, Wang YQ*, Evolutionary dynamics of the ABCA chromosome 17q24 cluster genes in vertebrates, Genomics, 2007, 89(3): 385-391

29. Shi P#, Bakewell MA#, Zhang JZ*, Did brain-specific genes evolve faster in humans than in chimpanzees? Trends in Genetics, 2006, 22(11): 608-613Shi P#, Yu L#, Fu YX, Huang JF, Zhang KQ, Zhang YP*, Evolutionary implications of avian infectious Bronchitis Virus (AIBV) analysis, Cell Research, 2006, 16(3): 323-327

30. Shi P#, Zhang JZ*, Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes, Molecular Biology and Evolution, 2006, 23(2): 292-300

31. Yang H#, Shi P#, Zhang YP*, Zhang JZ*, Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats, Genomics, 2005, 86(3):306-315

32. Shi P#, Bielawski JP, Yang H, Zhang YP*, Adaptive diversification of vomeronasal receptor 1 genes in rodents, Journal of Molecular Evolution, 2005, 60(5):566-576.

33. 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, 2005, 102(16):5767-5772

34. Li Y#, Ye C#, Shi P, Zou XJ, Xiao R, Gong YY, Zhang YP*, Independent origin of the growth hormone gene family in New World monkeys and Old World monkeys/hominoids, Journal of Molecular Endocrinology, 2005, 35(2):399-409

35. Ye C#, Li Y#, Shi P, ZhangYP*, Molecular evolution of growth hormone gene family in old world monkeys and hominoids, Gene, 2005, 350(2): 183-192

36. Gu Z#, Zhang Y#, Shi P, Zhang YP, Zhu D*, Li H, Comparison of avian myostatin genes, Animal Genetics, 2004, 35(6):470-472

37.  Shi P#, Zhang JZ, Yang H, Zhang YP*, Adaptive diversification of bitter taste receptor genes in mammalian evolution , Molecular Biology and Evolution, 2003, 20(5): 805-814

38. Chen DY#*, Wen DC#, Zhang YP#, Sun QY, Han ZM, Liu ZH, Shi P, Li 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, 2002, 67(2): 637-642

39. Shi P#, Lu XM, Luo HR, Xiang-Yu JG, Zhang YP*, Melanocortin-1 receptor gene variants in four Chinese ethnic populations, Cell Research, 2001, 11(1): 81-84

40. Ding B#, Shi P, Xiangyu JG, Zhang YP*, Chen DY, Sun QY, Li GP,GP Wang MK, Liu YL, Kang L, Han ZM, Song XF, Li JS, Chen YC, Microsatellite DNA analysis proves nucleus of interspecies reconstructed blastocyst coming from that of donor giant panda, Chinese Science Bulletin, 2000, 45(20) : 1883-1885

Invited book chapter:

1.Behrens M , Stahler F , Shi P , Bufe B and Meyerhof W. 2009. Taste: Topics in Chemical Biology. Wiley Encyclopedia of Chemical Biology. Tadhg P. Begley (Eds.), Wiley online library. 

2. Shi P and Zhang J. 2009. Extraordinary diversity of chemosensory receptor gene repertoires among vertebrates. Chemosensory Systems in Mammals , Fishes , and Insects. Meyerhof, Wolfgang, Korsching, Sigrun (Eds.), Springer.