Publication list: https://scholar.google.com/citations?hl=en&user=BjD0NDYAAAAJ 1. Grover CE, Pan M, Yuan D, Arick MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG: The Gossypium longicalyx genome as a resource for cotton breeding and evolution. G3: Genes, Genomes, Genetics 2020, 10(5):1457-1467. https://www.g3journal.org/content/10/5/1457 2. Grover CE, Yoo M-J, Lin M, Murphy MD, Harker DB, Byers RL, Lipka AE, Hu G, Yuan D, Conover JL: Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.). G3: Genes, Genomes, Genetics 2020, 10(2):731-754. https://www.g3journal.org/content/10/2/731 3. Li B, Liang S, Alariqi M, Wang F, Wang G, Wang Q, Xu Z, Yu L, Zafar MN, Sun L: The application of temperature sensitivity CRISPR/LbCpf1 (LbCas12a) mediated genome editing in allotetraploid cotton (G. hirsutum) and creation of nontransgenic, gossypol‐free cotton. Plant Biotechnology Journal 2020. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13470 4. Bao Y, Hu G, Grover CE, Conover J, Yuan D, Wendel JF: Unraveling cis and trans regulatory evolution during cotton domestication. Nature Communications 2019, 10(1):5399. https://www.nature.com/articles/s41467-019-13386-w 5. Hu L, Xu Z, Wang M, Fan R, Yuan D, Wu B, Wu H, Qin X, Yan L, Tan L, Sim S, Li W, Saski CA, Daniell H, Wendel JF, Lindsey K, Zhang X, Hao C, Jin S: The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis. Nature Communications 2019, 10(1):4702. https://www.nature.com/articles/s41467-019-12607-6 6. Li B, Rui HP, Li YJ, Wang QQ, Alariqi M, Qin L, Sun L, Ding X, Wang FQ, Zou JW, Wang YQ, Yuan DJ, Zhang XL, Jin SX: Robust CRISPR/Cpf1 (Cas12a)-mediated genome editing in allotetraploid cotton (Gossypium hirsutum). Plant Biotechnology Journal 2019, 17(10):1862-1864. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13147 7. Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF: De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri. G3-Genes Genomes Genetics 2019, 9(10):3079-3085. https://www.g3journal.org/content/9/10/3079/ 8. Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, 2nd, Masonbrink RE, Peterson DG, Wendel JF: The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Frontiers in plant science 2019, 10:1541-1541. https://www.frontiersin.org/articles/10.3389/fpls.2019.01541/ 9. Wang M, Tu L, Yuan D, Zhu D, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G: Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature genetics 2019, 51(2):224–229. https://www.nature.com/articles/s41588-018-0282-x 10. Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L: Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nature genetics 2017, 49(4):579–587. https://www.ncbi.nlm.nih.gov/pubmed/28263319 11. Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q: GbEXPATR, a species‐specific expansin, enhances cotton fibre elongation through cell wall restructuring. Plant biotechnology journal 2016, 14(3):951-963. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12450 12. Wang M, Wang P, Tu L, Zhu S, Zhang L, Li Z, Zhang Q, Yuan D, Zhang X: Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic acids research 2016, 44(9):4067-4079. https://www.ncbi.nlm.nih.gov/pubmed/27067544 13. Wang M, Yuan D, Tu L, Gao W, He Y, Hu H, Wang P, Liu N, Lindsey K, Zhang X: Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytologist 2015, 207(4):1181-1197. https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.13429 14. Wu Y, Min L, Wu Z, Yang L, Zhu L, Yang X, Yuan D, Guo X, Zhang X: Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton. Scientific reports 2015, 5:9608. https://www.ncbi.nlm.nih.gov/pubmed/26043720 15. Yuan D, Tang Z, Wang M, Gao W, Tu L, Jin X, Chen L, He Y, Zhang L, Zhu L: The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Scientific reports 2015, 5:17662. https://www.nature.com/articles/srep17662 16. Jin F, Hu L, Yuan D, Xu J, Gao W, He L, Yang X, Zhang X: Comparative transcriptome analysis between somatic embryos (SE s) and zygotic embryos in cotton: evidence for stress response functions in SE development. Plant biotechnology journal 2014, 12(2):161-173. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12123 17. Liu C, Yuan D, Lin Z: Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. Journal of genetics 2014, 93(3):689-697. https://www.ncbi.nlm.nih.gov/pubmed/25572227 18. Sun L, Zhu L, Xu L, Yuan D, Min L, Zhang X: Cotton cytochrome P450 CYP82D regulates systemic cell death by modulating the octadecanoid pathway. Nature communications 2014, 5:5372. https://www.nature.com/articles/ncomms6372 19. Xu L, Zhang W, He X, Liu M, Zhang K, Shaban M, Sun L, Zhu J, Luo Y, Yuan D: Functional characterization of cotton genes responsive to Verticillium dahliae through bioinformatics and reverse genetics strategies. Journal of experimental botany 2014, 65(22):6679-6692. 20. Li X, Yuan D, Zhang J, Lin Z, Zhang X: Genetic mapping and characteristics of genes specifically or preferentially expressed during fiber development in cotton. PLoS One 2013, 8(1):e54444. https://www.ncbi.nlm.nih.gov/pubmed/23372723 21. Liu C, Yuan D, Zhang X, Lin Z: Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP. Journal of genetics 2013, 92(2):175-181. https://pubmed.ncbi.nlm.nih.gov/23970073/ 22. Min L, Zhu L, Tu L, Deng F, Yuan D, Zhang X: Cotton GhCKI disrupts normal male reproduction by delaying tapetum programmed cell death via inactivating starch synthase. The Plant Journal 2013, 75(5):823-835. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12245/ 23. Wang M, Yuan D, Gao W, Li Y, Tan J, Zhang X: A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls. PLoS One 2013, 8(8):e72082. https://www.ncbi.nlm.nih.gov/pubmed/23951288 24. Xia J, Zhang X, Yuan D, Chen L, Webster J, Fang AC: Gene prioritization of resistant rice gene against Xanthomas oryzae pv. oryzae by using text mining technologies. BioMed research international 2013, 2013. https://www.hindawi.com/journals/bmri/2013/853043/ 25. Yang X, Wang L, Yuan D, Lindsey K, Zhang X: Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. Journal of experimental botany 2013, 64(6):1521-1536. https://www.ncbi.nlm.nih.gov/pubmed/23382553 26. Li X, Yuan D, Wang H, Chen X, Wang B, Lin Z, Zhang X: Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP. Genome 2012, 55(6):459-470. https://cdnsciencepub.com/doi/full/10.1139/g2012-032/ 27. Yang X, Zhang X, Yuan D, Jin F, Zhang Y, Xu J: Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC plant biology 2012, 12(1):110. https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-110 28. Yuan D, Liang S, Lin Z, Zhang X: In silico comparative analysis of EST-SSRs in three cotton genomes. African Journal of Biotechnology 2012, 11(69):13269-13371. 29. Hu L, Yang X, Yuan D, Zeng F, Zhang X: GhHmgB3 deficiency deregulates proliferation and differentiation of cells during somatic embryogenesis in cotton. Plant biotechnology journal 2011, 9(9):1038-1048. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1467-7652.2011.00617.x 30. Xu L, Zhu L, Tu L, Liu L, Yuan D, Jin L, Long L, Zhang X: Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. Journal of experimental botany 2011, 62(15):5607-5621. https://academic.oup.com/jxb/article/62/15/5607/561887 31. Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X: Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC 1 population between Gossypium hirsutum and G. barbadense. BMC genomics 2011, 12(1):15. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-15 32. Yuan D, Tu L, Zhang X: Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One 2011, 6(7):e22758. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022758 33. ZHU L-f, HE X, YUAN D-j, XU L, XU L, TU L-l, SHEN G-x, ZHANG H, ZHANG X-l: Genome-Wide Identification of Genes Responsive to ABA and Cold/Salt Stresses in Gossypium hirsutum by Data-Mining and Expression Pattern Analysis. Agricultural Sciences in China 2011, 10(4):499-508. https://www.sciencedirect.com/science/article/pii/S1671292711600308 34. Lin Z, Yuan D, Zhang X: Mapped SSR markers unevenly distributed on the cotton chromosomes. Frontiers of Agriculture in China 2010, 4(3):257-264. https://www.sciencedirect.com/science/article/pii/S1671292711600308 35. Daojun Y, AnGuo L, BaoZhong Y, LiYong H, ZhiXiong L, FangFang Z: Nutrition information extraction of rape canopy based on computer-vision technology. Transactions of the Chinese Society of Agricultural Engineering 2009, 25(12):174-179. 36. LIU Z-x, LIU A-g, YUAN D-j: Design and development of B/S Model-based Climate Information System. Agriculture Network Information 2008(12):13. 37. YUAN D-j, LIU A-g, LIU Z-x, ZHANG F-f: Application and expectation of computer-vision to plant. Agriculture Network Information 2007, 2:21-25. |
