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Shunping HE
Academic Title  

Personal Profile:

Personal Data:

1997. Ph.D. Laboratory of General and Applied Ichthyology, National Museum of Natural History (MNHN), Paris, France.

1988. MS. Laboratory of Ichthyology, Institute of Hydrobiology, Chinese Academy of Science.

1983. BS. Department of Biology, Southwestern Norms University, Chongqing.

2002. National Outstanding Young Scientists Award. Grant of NSFC

2007. 100 Talents Program of the Chinese Academy of Sciences. 
Research Experience:

1988-1991: Researcher Junior, Institute of Hydrobiology, Chinese Academy of Sciences.

1991-1995: Researcher Assistant, Institute of Hydrobiology, Chinese Academy of Science.

1995-1999: Researcher Associate, Institute of Hydrobiology, Chinese Academy of Science.

1999-present: Researcher Professorship, Institute of Hydrobiology, Chinese Academy of Science

Research Directions:
-Taxonomy and ontogeny of freshwater fishes;
·Molecular systematics, phylogeny, biogeography of the freshwater fishes in East Asia, especially Cypriniformes and Siluriformes;
·Molecular ecology and speciation of fishes;
·Evolution of important gene in osteichthysan fishes;
·Detection of SINE and its phylogenetic application in the family Cyprinidae;
·DNA barcoding of freshwater fishes;
·Phylogenomics and bioinformatics of fish genome.
Social Titles:

Awards & Honors:
Recent Publications:

  [1]  Yang, L. and S. He (2014). "A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)." Gene 533(1): 261-269. 

  [2]  Yang, L., M. Zou, et al. (2013). "Genome-wide identification, characterization, and expression analysis of lineage-specific genes within zebrafish." Bmc Genomics 14. 

  [3]  Tao, W., R. L. Mayden, et al. (2013). "Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses." Molecular Phylogenetics and Evolution 66(3): 603-616. 

  [4]  Tao, W., J. Yuan, et al. (2013). "Characterization of Gonadal Transcriptomes from Nile Tilapia (Oreochromis niloticus) Reveals Differentially Expressed Genes." Plos One 8(5). 

  [5]  Zou, M., B. Guo, et al. (2012). "Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)." Sci Rep 2. 

  [6]  Fu, B. and S. He (2012). "Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing." DNA Research 19(2): 131-142. 

  [7]  Chen, M., M. Zou, et al. (2011). "Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates." Plos One 6(7). 

  [8]  Fu, B., M. Chen, et al. (2010). "The rapid generation of chimerical genes expanding protein diversity in zebrafish." Bmc Genomics 11. 

  [9]  Zhao, K., Z. Y. Duan, et al. (2009). "The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake." Mol Ecol 18(17): 3616-3628. 

  [10]  Guo, B.C., Tong, C.B., He, S.P., 2009. Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative. Gene 439, 102-112. 

  [11]  Li, Z., He, S., 2009. Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus Sinocyclocheilus (Pisces: Cypriniformes). Hydrobiologia 624, 139-149. 

  [12]  Tong, C.B., Guo, B.C., He, S.P., 2009. Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation. BMC Genomics 10, -. 

  [13]  Duan, Z., Zhao, K., Peng, Z., Li, J., Diogo, R., He, S., Zhao, X., 2009. Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau. Mol Phylogenet Evol. 

  [14]  Guo, B., Li, J., Tong, C., He, S., 2008. Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis. Chin Sci Bull 53, 1988-1995. 

  [15]  He, S., Gu, X., Mayden, R.L., Chen, W.-J., Conway, K.W., Chen, Y., 2008b. Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome. Mol Phylogenet Evol 47, 419-425. 

  [16]  He, S., Mayden, R.L., Wang, X., Wang, W., Tang, K.L., Chen, W.-J., Chen, Y., 2008c. Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family. Mol Phylogenet Evol 46, 818-829. 

  [17]  Kong, X., Wang, X., Gan, X., Li, J., He, S., 2008. Molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei : Cypriniformes). Progr Nat Sci 18, 155-160. 

  [18]  Li, J., Wang, X., Kong, X., Zhao, K., He, S., Mayden, R.L., 2008. Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol 47, 472-487. 

  [19]  Li, Z., Guo, B., Li, J., He, S., Chen, Y., 2008. Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus). Chin Sci Bull 53, 2342-2352. 

  [20]  Mayden, R.L., Tang, K.L., Wood, R.M., Chen, W.-J., Agnew, M.K., Conway, K.W., Yang, L., Simons, A.M., Bart, H.L., Harris, P.M., Li, J., Wang, X., Saitoh, K., He, S., Liu, H., Chen, Y., Nishida, M., Miya, M., 2008. Inferring the Tree of Life of the order Cypriniformes, the earth's most diverse clade of freshwater fishes: Implications of varied taxon and character sampling. J Syst Evol 46, 424-438. 

  [21]  Sullivan, J.P., Peng, Z., Lundberg, J.G., Peng, J., He, S., 2008. Molecular evidence for diphyly of the Asian catfish family Amblycipitidae (Teleostei: Siluriformes) and exclusion of the South American Aspredinidae from Sisoroidea. Proc Acad Nat Sci Phila 157, 51-65. 

  [22]  Yang, L., He, S., 2008. Phylogeography of the freshwater catfish Hemibagrus guttatus (Siluriformes, Bagridae): Implications for South China biogeography and influence of sea-level changes. Mol Phylogenet Evol 49, 393-398. 

  [23]  Guo, X., He, S., Zhang, Y., 2007. Phylogenetic relationships of the Chinese sisorid catfishes: a nuclear intron versus mitochondrial gene approach. Hydrobiologia 579, 55-68. 

  [24]  Han, Y., He, S., Chen, Y., 2007. Identification of novel SINEs from Cyprinidae and their evolutionary significance. Progr Nat Sci 17, 270-279. 

  [25]  Huang, S., He, S., Peng, Z., Zhao, K., Zhao, E., 2007. Molecular phylogeography of endangered sharp-snouted pitviper (Deinagkistrodon acutus; Reptilia, Viperidae) in Mainland China. Mol Phylogenet Evol 44, 942-952. 

  [26]  Kong, X., Wang, X., Gan, X., He, S., 2007. The c-myc coding DNA sequences of cyprinids (Teleostei: Cypriniformes): Implications for phylogeny. Chin Sci Bull 52, 1491-1500. 

  [27]   Kong, X., Wang, X., Gan, X., Li, J., He, S., 2007. Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1. Sci China C Life Sci 50, 780-788. 

  [28]   Ku, X., Peng, Z., Diogo, R., He, S., 2007. MtDNA phylogeny provides evidence of generic polyphyleticism for East Asian bagrid catfishes. Hydrobiologia 579, 147-159. 

  [29]   Luo, J., Stadler, P.F., He, S., Meyer, A., 2007. PCR survey of hox genes in the goldfish Carassius auratus auratus. J Exp Zool Part B Mol Dev Evol 308, 250-258. 

  [30]   Mayden, R.L., Tang, K.L., Conway, K.W., Freyhof, J., Chamberlain, S., Haskins, M., Schneider, L., Sudkamp, M., Wood, R.M., Agnew, M., Bufalino, A., Sulaiman, Z., Miya, M., Saitoh, K., He, S., 2007. Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species. J Exp Zool Part B Mol Dev Evol 308B, 642-654. 

  [31]   Peng, Z., Ludwig, A., Wang, D., Diogo, R., Wei, Q., He, S., 2007. Age and biogeography of major clades in sturgeons and paddlefishes (Pisces: Acipenseriformes). Mol Phylogenet Evol 42, 854-862. 

  [32]   Wang, L., He, S., Chen, Y., 2007. Identification of the Angel-related elements in cyprinid fishes and their phylogenetic implications. Progr Nat Sci 17, 168-171. 

  [33]   Wang, X., Li, J., He, S., 2007. Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol 42, 157-170. 

  [34]   Wang, X., Wang, J., He, S., Mayden, R.L., 2007. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate. Gene 399, 11-19. 

  [35]   Zhao, K., Duan, Z.Y., Yang, G.S., Peng, Z., He, S., Chen, Y., 2007. Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei: Cyprinidae). Progr Nat Sci 17, 520-528. 

  [36]   Chen, J., Xie, Z., He, S., 2006. A taxonomic study of Oconnorella (Enchytraeidae, Oligochaeta) from Changbaishan Mountain, China. Zoological Science 23, 917-922. 

  [37]   Peng, Z., He, S., Wang, J., Wang, W., Diogo, R., 2006. Mitochondrial molecular clocks and the origin of the major Otocephalan clades (Pisces: Teleostei): A new insight. Gene 370, 113-124. 

  [38]   Peng, Z., Ho, S.Y.W., Zhang, Y., He, S., 2006. Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes. Mol Phylogenet Evol 39, 568-572. 

  [39]   Peng, Z., Wang, J., He, S., 2006. The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376, 290-297. 

  [40]   Xu, H.G., Ding, H., Li, M.Y., Qiang, S., Guo, J.Y., Han, Z.M., Huang, Z.G., Sun, H.Y., He, S.P., Wu, H.R., Wan, F.H., 2006. The distribution and economic losses of alien species invasion to China. Biol Invasions 8, 1495-1500. 

  [41]   Xu, H.G., Qiang, S., Han, Z.M., Guo, J.Y., Huang, Z.G., Sun, H.Y., He, S.P., Ding, H., Wu, H.R., Wan, F., 2006. The status and causes of alien species invasion in China. Biodivers Conserv 15, 2893-2904. 

  [42]   Yang, J., He, S., Freyhof, J., Witte, K., Liu, H., 2006. The Phylogenetic Relationships of the Gobioninae (Teleostei: Cyprinidae) Inferred from Mitochondrial Cytochrome b Gene Sequences. Hydrobiologia 553, 255-266. 

  [43]    Guo, X., He, S., Zhang, Y., 2005. Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences. Mol Phylogenet Evol 35, 344-362. 

  [44]    He, S., Wang, D., Wang, W., Chen, D., Zhao, Q., Gong, W., 2005. Genetic diversity in the Yangtze finless porpoise by RAPD analysis. High Technology Letters 11, 207-210. 

  [45]    Li, J.B., Wang, X.Z., He, S.P., Chen, Y.Y., 2005. Phylogenetic studies of Chinese labeonine fishes (Teleostei: Cyprinidae) based on the mitochondrial 16S rRNA gene. Progr Nat Sci 15, 213-219. 

  [46]    Peng, Z.G., Zhang, Y.G., He, S.P., Chen, Y.Y., 2005. Phylogeny of chinese catfishes inferred from mitochondrial cytochrome b sequences. Acta Genet Sin 32, 145-154. 

  [47]    Son, Y.-M., He, S.-P., 2005. Cobitis zhejiangensis, a new species from the Ling River, China (Teleostei: Cobitidae) Korean Journal of Ichthyology 17, 236-240. 

  [48]    Zhao, K., Li, J.B., Yang, G.S., Duan, Z.Y., He, S.P., Chen, Y.Y., 2005. Molecular phylogenetics of Gymnocypris (Teleostei: Cyprinidae) in Lake Qinghai and adjacent drainages. Chin Sci Bull 50, 1325-1333. 

  [49]    Chen, Y., Wang, Y., He, S., Zhu, Z., 2004. Cloning and sequencing of the growth hormone gene of large yellow croaker and its phylogenetic significance. Biochem Genet 42, 365-375. 

  [50]     He, S., Liu, H., Chen, Y., Kuwahara, M., Nakajima, T., Zhong, Y., 2004. Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences. Sci China Ser C Life Sci 47, 130-138. 

  [51]     Peng, Z., He, S., Zhang, Y., 2004. Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences. Mol Phylogenet Evol 31, 979-987. 

  [52]     Sun, Y., Liu, S.Y., Zhao, G., He, S.P., Wu, Q.J., Taniguchi, N., Yu, Q.X., 2004. Genetic structure of Chinese sucker population Myxocyprinus asiaticus in the Yangtze River based on mitochondrial DNA marker. Fisheries Science 70, 412-420. 

  [53]     Wang, X., Liu, H., He, S., Chen, Y., 2004. Sequence analysis of cytochrome b gene indicates that East Asian group of cyprinid subfamily Leuciscinae (Teleostei : Cyprinidae) evolved independently. Progr Nat Sci 14, 132-137. 

  [54]     Wang, W., He, S.P., Chen, Y.Y., 2002. Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes. Progr Nat Sci 12, 866-868. 

  [55]     Wang, X.Z., He, S.P., Chen, Y.Y., 2002. Sequence variations of the S7 ribosomal protein gene in primitive cyprinid fishes: Implication on phylogenetic analysis. Chin Sci Bull 47, 1638-1643. 

  [56]     Zhang, E., He, S.P., Chen, Y.Y., 2002. Revision of the cyprinid genus Placocheilus Wu, 1977 in China, with description of a new species from Yunnan. Hydrobiologia 487, 207-217. 

  [57]     He, S.P., Cao, W.X., Chen, Y.Y., 2001. The uplift of Qinghai-Xizang (Tibet) Plateau and the vicariance speciation of glyptosternoid fishes (Siluriformes : Sisoridae). Sci China Ser C Life Sci 44, 644-651. 

  [58]     He, S.P., Chen, Y.Y., Tsuneo, N., 2001. Sequences of cytochrome b gene for primitive cyprinid fishes in East Asia and their phylogenetic concerning. Chin Sci Bull 46, 661-665. 

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