• 1. Zheng Z , Wang X , Li M , ,..., Chen Y, Jiang Y. The origin of domestication genes in goats. Science Advances,(2020)(cover story)
• 2. Wang Y, Zhang C, Wang N, ,…,Jiang Y, Wang W, Q Qiang. Genetic basis of ruminant headgear and rapid antler regeneration. Science(2019)(cover story)
• 3. Chen N, Cai Y, Chen Q,..., Jiang Y, Lei C. Whole-genome resequencing reveals world-wide ancestry and multiple adaptive introgression events of domesticated cattle in East Asia. Accepted by Nature communications(2018)
• 4. Chen L#, Qiu Q#, Jiang Y#,,…,Heller R*, Wang W*. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science (2019) (cover story)
• 5. Jiang Y, Xie M, Chen W…, Wang W, Dalrymple B. 2014. The sheep genome illuminates biology of the rumen and lipid metabolism. Science(2014)

通讯作者及第一作者论文（按时间倒序）

2022

68. Li M, Sun C, Xu N, …, Hu X*, Jiang Y*, Yang N* (2022) De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions. Molecular Biology and Evolution, doi: 10.1093/molbev/msac066. (*通讯作者)

67. Billah M, Wang X, Jiantao Yu, Jiang Y* (2022) Real-time goat face recognition using convolutional neural network. Computers and Electronics in Agriculture, doi: 10.1016/j.compag.2022.106730. (*通讯作者)

66. Shang Z, Wang X, Jiang Y*, Li Z*, Ning J* (2022) Idenifying rumen protozoa in microscopic images of ruminant with improved YOLACT instance segmentation. Biosystems Engineering, doi: 10.1016/j.biosystemseng.2022.01.005. (*通讯作者)

65. Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. (2022) Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. Elife, doi: 10.7554/eLife.73346.

64. Li A, Yang Q, Li R, Dai X, Cai K*, Lei Y*, Jia K*, Jiang Y*, Zan L* (2022) Chromosome-level Genome Assembly for Takin (Budorcas taxicolor) Provides Insights into Its Taxonomic Status and Genetic Diversity. ResearchGate, doi: 10.22541/au.164275202.25941291/v1. (*通讯作者)

63. Shen J#, Chen Q#, Zhang F#, …, Jiang Y*, Lei C*(2022) Genome-wide association study identifies quantitative trait loci affecting cattle temperament. Zoological Research, doi: 10.24272/j.issn.2095-8137.2021.176. (*通讯作者)

62. Fu W, Wang R, Asadollahpour Nanaei H, Wang J, Hu D, Jiang Y*(2022) RGD v2.0: a major update of the ruminant functional and evolutionary genomics database. Nucleic Acids Research, doi: 10.1093/nar/gkab887. (*通讯作者)

61. Gong M, Yang P, Fang W, Li R, Jiang Y* (2022) Building a cattle pan-genome using more de novo assemblies. J Genet Genomics, doi: 10.1016/j.jgg.2022.01.003.(*通讯作者)

60. Wang F, Shao J, He S, …, Jiang Y* (2022) Allele-specific expression and splicing provide insight into the phenotypic differences between thin- and fat-tailed sheep breeds. J Genet Genomics, doi: 10.1016/j.jgg.2021.12.008.(*通讯作者)

59. Li Z, Wang X, Zhang Y, …, Jiang Y* (2022) Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates. BioRxiv, doi: 10.1101/2022.01.05.474053.

58. Fu W, Wang R, Xu N, Wang J, Li R, Asadollahpour Nanaei H, Nie Q, Zhao X, Han J, Yang N, Jiang Y. (2022) Galbase: a comprehensive repository for integrating chicken multi-omics data. BMC Genomics, doi: 10.1186/s12864-022-08598-2.

2021

57. Li R, Yang P, Dai X, …, Wang X & Jiang Y* (2021) A near complete genome for goat genetic and genomic research. Genetics Selection Evolution, doi: 10.1186/s12711-021-00668-5.(*通讯作者)

56. Pan X, Li Z, Li B, Zhao C, Wang Y, Chen Y & Jiang Y* (2021) Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats. BMC Genomics, doi: 10.1186/s12864-021-07595-1.

55. Fu W#, …, Jiang Y* (2021) GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions. Journal of Genetics and Genomics, doi: 10.1016/j.jgg.2021.03.003. (*通讯作者)

54. Huang Y#, Li Y#, Wang X#, ..., Jiang Y* (2021) An atlas of CNV maps in cattle, goat and sheep. Science China Life Sciences, doi: 10.1007/s11427-020-1850-x. (*通讯作者)

53. Li R#, Yang P#, Li M#, ..., Jiang Y* (2021) A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication. Science China Life Sciences, doi: 10.1007/s11427-020-1807-0. (*通讯作者)

52. Wang M, Zhang J, Guo X, Jiang Y, …, Bosse M*, Wu D*, Han J & Zhang Y* (2021) Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biology, doi: 10.1186/s12915-021-01052-x.

51. Xu N, Si W, Li M, Gong M, Larivière J, Nanaei H, Bian P, Jiang Y*, Zhao X* (2021) Genome-wide scan for selective footprints and genes related to cold tolerance in Chantecler chickens. Zool Res，doi: 10.24272/j.issn.2095-8137.2021.189.  (*通讯作者)

50. Bian P, Zhang Y, Jiang Y* (2021) Pan-genome: setting a new standard for high-quality reference genomes. Yi Chuan, doi: 10.16288/j.yczz.21-214. (*通讯作者)

49. Li J, Zhang J, Liu J, Zhou Y, Cai C, Xu L, Dai X, Feng S, Guo C, Rao J, Wei K, Jarvis E, Jiang Y, Zhou Z, Zhang G, Zhou Q (2021) A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. Gigascience, doi: 10.1093/gigascience/giaa142.

48. Pan X, Cai Y, Li Z, Chen X, Heller R, Wang N, Wang Y, Zhao C, Wang Y, Xu H, Li S, Li M, Li C, Hu S, Li H, Wang K, Chen L, Wei B, Zheng Z, Fu W, Yang Y, Zhang T, Hou Z, Yan Y, Lv X, Sun W, Li X, Huang S, Liu L, Mao S, Liu W, Hua J, Li Z, Zhang G, Chen Y, Wang X, Qiu Q, Dalrymple BP, Wang W, Jiang Y* (2021) Modes of genetic adaptations underlying functional innovations in the rumen. Sci China Life Sci, doi: 10.1007/s11427-020-1828-8. Epub 2020 Nov 5. (*通讯作者)

47. E G, Zhou D, Zheng Z, Yang B, Li X, Li L, Zhou R, Nai W, Jiang X, Zhang J, Hong Q, Ma Y, Chu M, Gao H, Zhao Y, Duan X, He Y, Na R, Han Y, Zeng Y, Jiang Y*, Huang Y (2021) Identification of a Goat Intersexuality-Associated Novel Variant Through Genome-Wide Resequencing and Hi-C. Front Genet, doi: 10.3389/fgene.2020.616743. (*通讯作者)

2020

46. Cai Y, Fu W, Cai D, …, Jiang Y*, Wang X*（2020）Ancient genomes reveal the evolutionary history and origin of cashmere producing goats in China. Molecular Biology and Evolution, doi: 10.1093/molbev/msaa103. (*通讯作者)

45. Zheng Z#, Wang X# , Li M#, …, Chen Y*, Jiang Y* (2020) The origin of domestication genes in goats. Science Advances, doi: 10.1126/sciadv.aaz5216. (*通讯作者)

44. Chen, N#, Fu W#, Zhao J#, ..., Jiang Y* (2020) The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures. Genomics, Proteomics & Bioinformatics, doi: 10.1101/802223. (*通讯作者)

43. Jiao F#, Lou R#, Dai X#, Liu H#, …, Qian Y*, Zhao A*, Jiang Y*（2020） Chromosome-level reference genome and population genomic analysis provide insight into the evolution and improvement of domesticated mulberry (Morus alba L), Molecular Plant, doi: 10.1016/j.molp.2020.05.005. (*通讯作者)

42. Sun T, Shen S, Achilli A, …, Jiang Y*, Lei C* (2020) Genomic Analyses Reveal Distinct Genetic Architectures and Selective Pressures in Buffaloes. GigaScience, doi: 10.1093/gigascience/giz166.(*通讯作者)

41. Pan X#, Cai Y#, Li Z#, ..., Wang W*, Jiang Y* (2020) Modes of genetic adaptations underlying functional innovations in the rumen. Science China Life Sciences, doi: 10.1007/s11427-020-1828-8. (*通讯作者)

40. Wang J#, Fu W#, ..., Jiang Y*, Kang Z* (2020) WGVD: an integrated web-database for wheat genome variation and selective signatures. Database, doi: 10.1093/database/baaa090. (*通讯作者)

39. Wang M#, Mukesh Thakur#, Peng M#, Jiang Y*#, ..., Wu D & Zhang Y* (2020) 863 genomes reveal the origin and domestication of chicken. Cell Research, doi: 10.1038/s41422-020-0349-y. (*通讯作者)

38. Shen J, Chen Q, Zhang F, Hanif Q, Huang B, Chen N, Qu K, Zhan J, Chen H, Jiang Y*, Lei C* (2021) Genome-wide association study identifies quantitative trait loci affecting cattle temperament. Zool Res, doi: 10.24272/j.issn.2095-8137.2021.176. (*通讯作者)

37. Wang F, Shao J, He S, Guo Y, Pan X, Wang Y, Nanaei HA Chen L, Li R, Xu H, Yang Z, Liu M, Jiang Y* (2021) Allele-specific expression and splicing provide insight into the phenotypic differences between thin- and fat-tailed sheep breeds. J Genet Genomics, doi: 10.1016/j.jgg.2021.12.008. (*通讯作者)

36. Gao S, Nanaei H, Wei B, Wang Y, Wang X, Li Z, Dai X, Wang Z, Jiang Y, Shao J* (2020) Comparative Transcriptome Profiling Analysis Uncovers Novel Heterosis-Related Candidate Genes Associated with Muscular Endurance in Mules. Animals (Basel), doi: 10.3390/ani10060980.

35. Tian X, Li R, Fu W, Li Y, Wang X, Li M, Du D, Tang Q, Cai Y, Long Y, Zhao Y, Li M, Jiang Y* (2020) Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. Science China Life Sciences, doi: 10.1007/s11427-019-9551-7.  (*通讯作者)

2019

34. Wang Y, Zhang C, Wang N, …, Jiang Y*,Wang W*, Qiang Q* (2019) Genetic basis of ruminant headgear and rapid antler regeneration. Science, doi: 10.1126/science.aav6335. (*通讯作者)

33. Tian X, Li R, Fu W, …, Li M*, Jiang Y* (2019) Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. Science China Life Sciences, doi: 10.1007/s11427-019-9551-7. (*通讯作者)

32. Chen H, Liu J, Wen J, …, Song W*, Sun Q*, Jiang Y* (2019) Frequent intra- and inter-species introgression shape the landscape of genetic variation in bread wheat. Genome Biology, doi: 10.1186/s13059-019-1744-x. (*通讯作者)

31. Wang Y, Gao S, Zhao Y, …, Jiang Y* (2019) Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids. ZOOLOGICAL RESEARCH, doi: 10.24272/j.issn.2095-8137.2019.042. (*通讯作者)

30. Li C, Li M, Li X, …, Jiang Y*，Hu S* (2019) Whole-genome resequencing reveals loci associated with thoracic vertebrae number in sheep. Frontiers in Genetics, doi: 10.3389/fgene.2019.00674. (*通讯作者)

29. Cao Y, Xu H, Li R, …, Luo J*, Jiang Y* (2019) Genetic Basis of Phenotypic Differences Between Chinese Yunling Black Goats and Nubian Goats Revealed by Allele-Specific Expression in Their F1 Hybrids. Frontiers in Genetics, doi: 10.3389/fgene.2019.00145. (*通讯作者)

28. Li R#, Fu W#, Su R#, ..., Li J*, Jiang Y*（2019）Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome. Frontiers in Genetics, doi: 10.3389/fgene.2019.01169. (*通讯作者)

27. Chen L#, Qiu Q#, Jiang Y#, …, Heller R*, Wang W* (2019) Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science, doi:eaav6202.

26. Li R, Tian X, Yang P, Fan Y, Li M, Zheng H, Wang X, Jiang Y* (2019) Recovery of non-reference sequences missing from the human reference genome. BMC Genomics, doi: 10.1186/s12864-019-6107-1. (*通讯作者)

25. Li G, Zhou S, Li C, Cai B, Yu H, Ma B, Huang Y, Ding Y, Liu Y, Ding Q, He C, Zhou J, Wang Y, Zhou G, Li Y, Yan Y, Hua J, Petersen B, Jiang Y, Sonstegard T, Huang X, Chen Y, Wang X (2019) Base pair editing in goat: nonsense codon introgression into FGF5 results in longer hair. FEBS J, doi: 10.1111/febs.14983.

2018

24. Chen N, Cai Y, Chen Q, ..., Jiang Y*, Lei C* (2018) Whole-genome resequencing reveals world-wide ancestry and multiple adaptive introgression events of domesticated cattle in East Asia. Nature communications, doi：10.1038/s41467-018-04737-0. (*通讯作者)

23. Zhou Z, Li M, Cheng H, ..., Hou S*, Jiang Y* (2018) An intercross population study reveals genes associated with body size and plumage color in ducks. Nature communications, doi: 10.1038/s41467-018-04868-4. (*通讯作者)

22. Wang X, Liu J, Niu Y, …, Huang X*, Jiang Y*, Chen Y* (2018) Low incidence of SNVs and indels in trio genomes of Cas9-mediated multiplex edited sheep. BMC Genomics, doi: 10.1186/s12864-018-4712-z. (*通讯作者)

2017

21. Wang X, Zheng Z, Cai Y, Chen T, Li C, Fu W, Jiang Y* (2017) CNVcaller: Highly Efficient and Widely Applicable Software for Detecting Copy Number Variations in Large Populations. GigaScience, doi: 10.1093/gigascience/gix115. (*通讯作者)

20. Li M#, Zhou H#, Pan X#, …, Zi X, Jiang Y*(2017) Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing. Scientific Reports, doi: 10.1038/srep45697. (*通讯作者)

19. Yang Y, Wang Y, Zhao Y, Zhang X, Li R, Chen L, Zhang G, Jiang Y, Qiu Q, Wang W, Wei H, Wang K (2017) Draft genome of the Marco Polo Sheep (Ovis ammon polii). Gigascience, doi: 10.1093/gigascience/gix106.

18. Li X, Su R, Wan W, Zhang W, Jiang H, Qiao X, Fan Y, Zhang Y, Wang R, Liu Z, Wang Z, Liu B, Ma Y, Zhang H, Zhao Q, Zhong T, Di R, Jiang Y, Chen W, Wang W, Dong Y, Li J (2017) Identification of selection signals by large-scale whole-genome resequencing of cashmere goats. Scientific Reports, doi: 10.1038/s41598-017-15516-0. 

17. Kang D, Zhou G, Zhou S, Zeng J, Wang X, Jiang Y*, Yang Y, Chen Y (2017) Comparative transcriptome analysis reveals potentially novel roles of Homeobox genes in adipose deposition in fat-tailed sheep. Scientific Reports, doi: 10.1038/s41598-017-14967-9. (*通讯作者)

16. Xu Y, Jiang Y, Shi T, Cai H, Lan X, Zhao X, Plath M, Chen H (2017) Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds. PLoS One, doi: 10.1371/journal.pone.0183921. 

15. Qiao X, Su R, Wang Y, Wang R, Yang T, Li X, Chen W, He S, Jiang Y, Xu Q, Wan W, Zhang Y, Zhang W, Chen J, Liu B, Liu X, Fan Y, Chen D, Jiang H, Fang D, Liu Z, Wang X, Zhang Y, Mao D, Wang Z, Di R, Zhao Q, Zhong T, Yang H, Wang J, Wang W, Dong Y, Chen X, Xu X, Li J (2017) Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat. Scientific Reports, doi: 10.1038/s41598-017-09285-z. 

14. Li C, Zhang X, Cao Y, Wei J, You S, Jiang Y, Cai K, Wumaier W, Guo D, Qi J, Chen C, Ni W, Hu S (2017) Multi-vertebrae variation potentially contribute to carcass length and weight of Kazakh sheep. Small Ruminant Research, https://doi.org/10.1016/j.smallrumres.2017.02.021.

2016

13. Wang X, Liu J, Zhou G, Guo J, Yan H, Niu Y, Li Y, Yuan C, Geng R, Lan X, An X, Tian X, Zhou H, Song J, Jiang Y, Chen Y (2016) Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits. Scientific Reports, doi: 10.1038/srep38932.

12. Wang X, Niu Y, Zhou J, Yu H, Kou Q, Lei A, Zhao X, Yan H, Cai B, Shen Q, Zhou S, Zhu H, Zhou G, Niu W, Hua J, Jiang Y, Huang X, Ma B, Chen Y (2016) Multiplex gene editing via CRISPR/Cas9 exhibits desirable muscle hypertrophy without detectable off-target effects in sheep. Scientific Reports, doi: 10.1038/srep32271.

11. Gao Y, Wang X, Yan H, Zeng J, Ma S, Niu Y, Zhou G, Jiang Y, Chen Y* (2016) Comparative Transcriptome Analysis of Fetal Skin Reveals Key Genes Related to Hair Follicle Morphogenesis in Cashmere Goats. PLoS One, doi: 10.1371/journal.pone.0151118.

2015

10. Dong Y, Zhang X, Xie M, …, Wang W*, Jiang Y* (2015) Reference genome of wild goat and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics, doi: 10.1186/s12864-015-1606-1. (*通讯作者)

9. Chen H, Jiang Y*(2015) Progress and Prospects in Domestic Animals and Breeding: a Review of Genomic Copy Number Variations. Biotechnology Bulletin, doi: 10.13560/j.cnki.biotech.bull.1985.2015.11.006. (*通讯作者)

8. Jiang Y#, Wang X#, Kijas J#, Dalrymple B# (2015) Beta globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B. Animal Genetics, doi: 10.1111/age.12318.

7. Zhou Z#, Jiang Y#, Wang Z#, …, Wang W*, Tian Z* (2015) Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nature biotechnology, doi: 10.1038/nbt.3096.

6. Wang Y, Wu J, Ma X, Liu B, Su R, Jiang Y, Wang W, Dong Y (2015) Single Base-Resolution Methylome of the Dizygotic Sheep. PLoS One, doi: 10.1371/journal.pone.0142034.

5. Wang X, Yu H, Lei A, Zhou J, Zeng W, Zhu H, Dong Z, Niu Y, Shi B, Cai B, Liu J, Huang S, Yan H, Zhao X, Zhou G, He X, Chen X, Yang Y, Jiang Y, Shi L, Tian X, Wang Y, Ma B, Huang X, Qu L, Chen Y (2015) Generation of gene-modified goats targeting MSTN and FGF5 via zygote injection of CRISPR/Cas9 system. Scientific Reports, doi: 10.1038/srep13878.

2014年及以前

4. Jiang Y#, Xie M#, Chen W#, …, Wang W*, Dalrymple B* (2014) The sheep genome illuminates biology of the rumen and lipid metabolism. Science, doi: 10.1126/science.1252806.

3. Dong Y#, Xie M#, Jiang Y#, …, Wang J*, Wang W* (2013) Sequencing and automated whole-genome optical mapping of the genome of a domestic goat. Nature Biotechnology, doi: 10.1038/nbt.2478.

2. Jiang Y#, Li Y#, Lee W#, …, Zhang Y*, Wang W*（2011）Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes. BMC Genomics, doi: 10.1186/1471-2164-12-1.

1. Li D#, Dong Y#, Jiang Y#, …, Wang W* (2010) A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand. Cell Research, doi: 10.1038/cr.2010.31.