*corresponding author; †equal contribution.

39. Wang Yingnan, Wang Yu, Zhao Y, Kravchenko A, Merilä J, Guo Baocheng*. (2022) Phylogenomics of Northeast Asian Pungitius sticklebacks. Diversity and Distributions, doi: 10.1111/DDI.13423, in press. [link]

38. Wang Yingnan & Guo Baocheng*. (2022) Distribution status of Pungitius sticklebacks in China. Chinese Journal of Zoology, doi: 10.13859/j.cjz.202205000, in press. (in Chinese) [link]

37. Jin L, Li Z, Wang C, Wang Yingnan, Li X, Yang J, Zhao Y, Guo Baocheng*. Contrasting population differentiation in two sympatric Triplophysa loaches on the Qinghai-Tibet Plateau. Frontiers in Genetics, 13:958076. [link]

36. Guo, Baocheng*, Zou M, Sakamoto T, and Innan H*. (2022) Functional innovation through gene duplication followed by frameshift mutation. Genes, 13:190. [link]

35. Jin L & Guo Baocheng*. (2021). Detecting adaptive loci with population genomic data. Bio-101: e1010627. Doi: 10.21769/BioProtoc.1010627. (in Chinese) [link]

34. Jin L & Guo Baocheng*. (2021). Detecting loci underlying local adaptation using environmental association analysis. Bio-101: e1010615. Doi: 10.21769/BioProtoc.1010615. (in Chinese) [link]

33. Wang Yuwei & Guo Baocheng*. (2021) The divergence of alternative splicing between ohnologs in teleost fishes. BMC Ecology and Evolution, 21:98. [link]

32. Kemppainen P*, Li Z, Rastas P, Löytynoja A, Fang B, Yang J, Guo Baocheng, Shikano T, Merilä J. (2021) Genetic population structure constrains local adaptation in sticklebacks. Molecular Ecology, 30:1946–1961. [link]

Selected as cover story. [link]

Commentary by Yamasaki & Kitano. (2021) Multiple paths to the same destination: influence of gene flow on convergent evolution. Molecular Ecology, 30:1939–1942. [link]

Preprint: bioRxiv, 2020.01.17.908970. [link]

31. Wang Yingnan, Zhao Y, Wang Yu, Li Z, Guo Baocheng*, Merilä J. (2020) Population transcriptomics reveals weak parallel genetic basis in repeated marine and freshwater divergence in nine-spined sticklebacks. Molecular Ecology, 29:1642-1656. [link]

30. Yang T, Meng W*, Guo Baocheng*. (2020) Population genomic analysis of two endemic schizothoracins reveals their genetic differences and adaptation to altitude and temperature. Animals, 10: 447. [link]

29. Li X & Guo Baocheng*. (2020) Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies. Proceedings of the Royal Society B: Biological Sciences, 287: 20193008. [link]

28. Varadharajan S*, Rastas P, Löytynoja A, Matschiner M, Calboli FCF, Guo Baocheng, Nederbragt AJ, Jakobsen KS*, Merilä J. (2019) A high-quality assembly of the nine-spined stickleback (Pungitius pungitius) genome. Genome Biology and Evolution, 11:3291-3308. [link]

Preprint: bioRxiv, 741751. [link]

27. Wang Yingnan & Guo Baocheng*. (2019) Adaption to extreme environments: a perspective from fish genomics. Reviews in Fish Biology and Fisheries, 29:735–747. [link]

26. Guo Baocheng†, Fang B†, Shikano T, Momigliano P, Wang C, Kravchenko A, Merilä J*. (2019) A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius. Molecular Ecology, 28:4046-4064. [link]

25. Nielsen ES, Henriques R, Toonen RT, Knapp I, Guo Baocheng, von der Heyden S*. (2018) Complex signatures of genomic variation of two non-model marine species in a homogeneous environment. BMC Genomics, 19:347. [link]

24. Guo Baocheng*. (2017) Complex genes are preferentially retained after whole-genome duplication in teleost fish. Journal of Molecular Evolution, 84:253-258. [link]

23. Li Z*, Guo Baocheng, Yang J, Herczeg G, Gonda A, Balázs G, Shikano T, Calboli FCF, Merilä J. (2017) Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach. Molecular Ecology, 26:1557-1575. [link]

Commentary by Jon Slate. (2017) Robust inference of genetic architecture in mapping studies. Molecular Ecology, 26:1453-1455. [link]

22. Guo Baocheng*, Li Z, Merilä J. (2016) Population genomic evidence for adaptive differentiation in the Baltic Sea herring. Molecular Ecology, 25:3884–3900. [link]

21. Guo Baocheng, Lu D, Liao WB*, Merilä J. (2016) Genome-wide scan for adaptive differentiation along altitudinal gradient in the Andrew’s toad Bufo andrewsi. Molecular Ecology, 25:2833-2852. [link]

20. Yang J, Guo Baocheng*, Shikano T, Liu X*, Merilä J. (2016) Quantitative trait locus analysis of body shape divergence in nine-spined sticklebacks based on high-density SNP-panel. Scientific Reports, 6:26632. [link]

19. Rastas P†, Calbol FCF†, Guo Baocheng, Shikano T, Merilä J*. (2016) Construction of ultra-dense linkage maps using Lep-MAP2 as exemplified with stickleback F2 recombinant crosses. Genome Biology and Evolution, 8:78-93. [link]

Selected as cover story. [link]

18. Guo Baocheng, Shikano T, Vukic J, Sanda R, Merilä J*. (2016) Complete mitochondrial genome of the Ukrainian nine-spined stickleback Pungitius platygaster (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:68-69. [link]

17. Guo Baocheng, Shikano T, Wang C, Merilä J*. (2016) Complete mitochondrial genome of the smoot-tailed nine-spined stickleback Pungitius laevis (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:70-71. [link]

16. Guo Baocheng, Toli E, Merilä J*. (2016) Complete mitochondrial genome of the nine-spined stickleback Pungitius pungitius (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:72-73. [link]

15. Shikano T, Guo Baocheng, Vukic J, Sanda R, Merilä J*. (2016) Complete mitochondrial genome of the Greek nine-spined stickleback Pungitius hellenicus (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA Part B: Resources, 1:66-67. [link]

14. Shikano T, Guo Baocheng, Merilä J*. (2016) Complete mitochondrial genome of the Shakhalin nine-spined stickleback Pungitius tymensis (Gasterosteiformes, Gasterosteidae). Mitochondrial DNA: Resources Part B, 1:74-75. [link]

13. Guo Baocheng*, DeFaveri J, Sotelo G, Nair A, Merilä J. (2015) Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biology, 13:19. [link]

12. Zou M*, Guo Baocheng, Ma X. (2014) Characterizing the transcriptome of yellow-cheek carp (Elopichthys bambusa) enables evolutionary analyses within endemic East Asian Cyprinidae. Gene, 547:267-272. [link]

11. Guo Baocheng*, Chain FJ, Bornberg-Bauer E, Leder EH, Merilä J. (2013) Genomic divergence between nine- and three-spined sticklebacks. BMC Genomics, 14:756. [link]

10. Guo Baocheng, Zou M, Wagner A*. (2012) Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication. Molecular Biology and Evolution, 29:3005-3022. [link]

9. Zou M, Guo Baocheng, Tao W, Arratia G, He S*. (2012) Integrating multi-origin expression data improves resolution of the deep phylogeny of ray-finned fish (Actinopterygii). Scientific Reports, 2:665. [link]

8. Guo Baocheng, Wagner A, He S*. (2011) Duplicated gene evolution following whole-genome duplication in teleost Fish. Pp. 27-36. In: Felix Friedberg (Ed.), Gene Duplication. InTech, Rijeka, Croatia. [link]

7. Zou M, Guo Baocheng, He S*. (2011) The roles and evolutionary patterns of intronless genes in deuterostomes. Comparative and Functional Genomics, 2011:680673. [link]

6. Guo Baocheng, Zou M, Gan X, He S*. (2010) Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holacanthus genome sequencing. BMC Genomics, 11:396. [link]

5. Guo Baocheng, Gan X, He S*. (2010) Hox genes of the Japanese eel Anguilla japonica and Hox cluster evolution in teleosts. Journal of Experimental Zoology Part B: Molecular Development and Evolution, 314:135-147. [link]

4. Guo Baocheng, Tong C, He S*. (2009) Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative. Gene, 439:102-112. [link]

3. Tong C, Guo Baocheng, He S*. (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, 10:83. [link]

2. Li Z, Guo Baocheng, Li J, He S*, Chen Y. (2008) Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae: Sinocyclocheilus). Chinese Science Bulletin, 53:2342-2352. [link]

1. Guo Baocheng, Li J, Tong C, He S*. 2008. Cloning and sequence analysis of Sox genes in a tetraploid cyprinid fish, Tor douronensis. Chinese Science Bulletin, 53:1988-1995. [link]

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