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Yongfeng Zhou - Publications

Affiliations: 
University of California, Irvine, Irvine, CA 
Area:
Population Genetics, Evolutionary Genomics, Plant domestication, Forest Genetics, Grape, Rice, Genomics and breeding
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 He H, Leng Y, Cao X, Zhu Y, Li X, Yuan Q, Zhang B, He W, Wei H, Liu X, Xu Q, Guo M, Zhang H, Yang L, Lv Y, ... ... Zhou Y, et al. The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice. Nature Communications. 15: 7291. PMID 39181885 DOI: 10.1038/s41467-024-51854-0  0.408
2024 Wang X, Liu Z, Zhang F, Xiao H, Cao S, Xue H, Liu W, Su Y, Liu Z, Zhong H, Zhang F, Ahmad B, Long Q, Zhang Y, Liu Y, ... ... Zhou Y, et al. Integrative genomics reveals the polygenic basis of seedlessness in grapevine. Current Biology : Cb. PMID 39094571 DOI: 10.1016/j.cub.2024.07.022  0.426
2024 Li X, Dai X, He H, Lv Y, Yang L, He W, Liu C, Wei H, Liu X, Yuan Q, Wang X, Wang T, Zhang B, Zhang H, Chen W, ... ... Zhou Y, et al. A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice. National Science Review. 11: nwae188. PMID 38962716 DOI: 10.1093/nsr/nwae188  0.349
2024 Wang P, Meng F, Yang Y, Ding T, Liu H, Wang F, Li A, Zhang Q, Li K, Fan S, Li B, Ma Z, Zhang T, Zhou Y, Zhao H, et al. assembling a high-quality genome sequence of Amur grape ( Rupr) gives insight into divergence and sex determination. Horticulture Research. 11: uhae117. PMID 38919553 DOI: 10.1093/hr/uhae117  0.342
2024 Yang X, Su Y, Huang S, Hou Q, Wei P, Hao Y, Huang J, Xiao H, Ma Z, Xu X, Wang X, Cao S, Cao X, Zhang M, Wen X, ... ... Zhou Y, et al. Comparative population genomics reveals convergent and divergent selection in the apricot-peach-plum-mei complex. Horticulture Research. 11: uhae109. PMID 38883333 DOI: 10.1093/hr/uhae109  0.437
2024 Su Y, Yang X, Wang Y, Li J, Long Q, Cao S, Wang X, Liu Z, Huang S, Chen Z, Peng Y, Zhang F, Xue H, Cao X, Zhang M, ... ... Zhou Y, et al. Phased Telomere-to-Telomere Reference Genome and Pangenome Reveal an Expansion of Resistance Genes during Apple Domestication. Plant Physiology. PMID 38743633 DOI: 10.1093/plphys/kiae258  0.402
2024 Zhang T, Peng W, Xiao H, Cao S, Chen Z, Su X, Luo Y, Liu Z, Peng Y, Yang X, Jiang GF, Xu X, Ma Z, Zhou Y. Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape. Journal of Integrative Plant Biology. PMID 38578160 DOI: 10.1111/jipb.13653  0.398
2024 Long Q, Cao S, Huang G, Wang X, Liu Z, Liu W, Wang Y, Xiao H, Peng Y, Zhou Y. Population comparative genomic analyses unveil gene gain and loss during grapevine domestication. Plant Physiology. PMID 38285049 DOI: 10.1093/plphys/kiae039  0.349
2023 Wang N, Chen P, Xu Y, Guo L, Li X, Yi H, Larkin RM, Zhou Y, Deng X, Xu Q. Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange. Horticulture Research. 11: uhad268. PMID 38371640 DOI: 10.1093/hr/uhad268  0.372
2023 Song Y, Peng Y, Liu L, Li G, Zhao X, Wang X, Cao S, Muyle A, Zhou Y, Zhou H. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. Horticulture Research. 11: uhad252. PMID 38269295 DOI: 10.1093/hr/uhad252  0.335
2023 Lv Y, Liu C, Li X, Wang Y, He H, He W, Chen W, Yang L, Dai X, Cao X, Yu X, Liu J, Zhang B, Wei H, Zhang H, ... ... Zhou Y, et al. A centromere map based on super pan-genome highlights the structure and function of rice centromeres. Journal of Integrative Plant Biology. PMID 38158885 DOI: 10.1111/jipb.13607  0.398
2023 Zhang X, Chen Y, Wang L, Yuan Y, Fang M, Shi L, Lu R, Comes HP, Ma Y, Chen Y, Huang G, Zhou Y, Zheng Z, Qiu Y. Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization. Horticulture Research. 10: uhad203. PMID 38046854 DOI: 10.1093/hr/uhad203  0.361
2023 Zhang K, Du M, Zhang H, Zhang X, Cao S, Wang X, Wang W, Guan X, Zhou P, Li J, Jiang W, Tang M, Zheng Q, Cao M, Zhou Y, et al. The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes. Horticulture Research. 10: uhad205. PMID 38046853 DOI: 10.1093/hr/uhad205  0.395
2023 Chen J, Liu Y, Liu M, Guo W, Wang Y, He Q, Chen W, Liao Y, Zhang W, Gao Y, Dong K, Ren R, Yang T, Zhang L, Qi M, ... ... Zhou Y, et al. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet. Nature Genetics. PMID 38036791 DOI: 10.1038/s41588-023-01571-z  0.418
2023 Xiao H, Liu Z, Wang N, Gaut BS, Zhou Y. Reply to Blanco-Pastor: Introgression and heterozygosity complicated grapevine domestication. Proceedings of the National Academy of Sciences of the United States of America. 120: e2314162120. PMID 38011557 DOI: 10.1073/pnas.2314162120  0.455
2023 Wang T, He W, Li X, Zhang C, He H, Yuan Q, Zhang B, Zhang H, Leng Y, Wei H, Xu Q, Shi C, Liu X, Guo M, Wang X, ... ... Zhou Y, et al. A rice variation map derived from 10 548 rice accessions reveals the importance of rare variants. Nucleic Acids Research. PMID 37843097 DOI: 10.1093/nar/gkad840  0.335
2023 Liu X, Arshad R, Wang X, Li WM, Zhou Y, Ge XJ, Huang HR. The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars. Scientific Data. 10: 631. PMID 37716992 DOI: 10.1038/s41597-023-02546-9  0.365
2023 Huang HR, Liu X, Arshad R, Wang X, Li WM, Zhou Y, Ge XJ. Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana. Horticulture Research. 10: uhad153. PMID 37701454 DOI: 10.1093/hr/uhad153  0.365
2023 Shang L, He W, Wang T, Yang Y, Xu Q, Zhao X, Yang L, Zhang H, Li X, Lv Y, Chen W, Cao S, Wang X, Zhang B, Liu X, ... ... Zhou Y, et al. A complete assembly of the rice Nipponbare reference genome. Molecular Plant. PMID 37553831 DOI: 10.1016/j.molp.2023.08.003  0.303
2023 Jin M, North HL, Peng Y, Liu H, Liu B, Pan R, Zhou Y, Zheng W, Liu K, Yang B, Zhang L, Xu Q, Elfekih S, Valencia-Montoya WA, Walsh T, ... ... Zhou Y, et al. Adaptive evolution to the natural and anthropogenic environment in a global invasive crop pest, the cotton bollworm. Innovation (Cambridge (Mass.)). 4: 100454. PMID 37388193 DOI: 10.1016/j.xinn.2023.100454  0.341
2023 Wang N, Cao S, Liu Z, Xiao H, Hu J, Xu X, Chen P, Ma Z, Ye J, Chai L, Guo W, Larkin RM, Xu Q, Morrell PL, Zhou Y, et al. Genomic conservation of crop wild relatives: A case study of citrus. Plos Genetics. 19: e1010811. PMID 37339133 DOI: 10.1371/journal.pgen.1010811  0.373
2023 Xiao H, Liu Z, Wang N, Long Q, Cao S, Huang G, Liu W, Peng Y, Riaz S, Walker AM, Gaut BS, Zhou Y. Adaptive and maladaptive introgression in grapevine domestication. Proceedings of the National Academy of Sciences of the United States of America. 120: e2222041120. PMID 37276420 DOI: 10.1073/pnas.2222041120  0.618
2023 Morales-Cruz A, Aguirre-Liguori J, Massonnet M, Minio A, Zaccheo M, Cochetel N, Walker A, Riaz S, Zhou Y, Cantu D, Gaut BS. Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate. Communications Biology. 6: 580. PMID 37253933 DOI: 10.1038/s42003-023-04938-4  0.512
2023 Shi X, Cao S, Wang X, Huang S, Wang Y, Liu Z, Liu W, Leng X, Peng Y, Wang N, Wang Y, Ma Z, Xu X, Zhang F, Xue H, ... ... Zhou Y, et al. The complete reference genome for grapevine ( L.) genetics and breeding. Horticulture Research. 10: uhad061. PMID 37213686 DOI: 10.1093/hr/uhad061  0.395
2023 Wu Y, Li D, Hu Y, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, et al. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell. PMID 37146612 DOI: 10.1016/j.cell.2023.04.008  0.354
2023 Li N, He Q, Wang J, Wang B, Zhao J, Huang S, Yang T, Tang Y, Yang S, Aisimutuola P, Xu R, Hu J, Jia C, Ma K, Li Z, ... ... Zhou Y, et al. Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nature Genetics. PMID 37024581 DOI: 10.1038/s41588-023-01340-y  0.444
2022 Wang N, Song X, Ye J, Zhang S, Cao Z, Zhu C, Hu J, Zhou Y, Huang Y, Cao S, Liu Z, Wu X, Chai L, Guo W, Xu Q, ... ... Zhou Y, et al. Structural variation and parallel evolution of apomixis in citrus during domestication and diversification. National Science Review. 9: nwac114. PMID 36415319 DOI: 10.1093/nsr/nwac114  0.628
2022 Wang N, Li C, Kuang L, Wu X, Xie K, Zhu A, Xu Q, Larkin RM, Zhou Y, Deng X, Guo W. Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification. Proceedings of the National Academy of Sciences of the United States of America. 119: e2206076119. PMID 36260744 DOI: 10.1073/pnas.2206076119  0.412
2022 Tang D, Jia Y, Zhang J, Li H, Cheng L, Wang P, Bao Z, Liu Z, Feng S, Zhu X, Li D, Zhu G, Wang H, Zhou Y, Zhou Y, et al. Addendum: Genome evolution and diversity of wild and cultivated potatoes. Nature. PMID 36100670 DOI: 10.1038/s41586-022-05298-5  0.373
2022 Shang L, Li X, He H, Yuan Q, Song Y, Wei Z, Lin H, Hu M, Zhao F, Zhang C, Li Y, Gao H, Wang T, Liu X, Zhang H, ... ... Zhou Y, et al. A super pan-genomic landscape of rice. Cell Research. PMID 35821092 DOI: 10.1038/s41422-022-00685-z  0.451
2022 Liao Y, Wang J, Zhu Z, Liu Y, Chen J, Zhou Y, Liu F, Lei J, Gaut BS, Cao B, Emerson JJ, Chen C. The 3D architecture of the pepper genome and its relationship to function and evolution. Nature Communications. 13: 3479. PMID 35710823 DOI: 10.1038/s41467-022-31112-x  0.584
2022 Tang D, Jia Y, Zhang J, Li H, Cheng L, Wang P, Bao Z, Liu Z, Feng S, Zhu X, Li D, Zhu G, Wang H, Zhou Y, Zhou Y, et al. Genome evolution and diversity of wild and cultivated potatoes. Nature. 606: 535-541. PMID 35676481 DOI: 10.1038/s41586-022-04822-x  0.401
2021 Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biology. 22: 254. PMID 34479604 DOI: 10.1186/s13059-021-02467-z  0.552
2020 Kou Y, Liao Y, Toivainen T, Lv Y, Tian X, Emerson JJ, Gaut BS, Zhou Y. Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication. Molecular Biology and Evolution. PMID 32681796 DOI: 10.1093/Molbev/Msaa185  0.645
2020 Zhou Y, Gaut BS. Large chromosomal variants drive adaptation in sunflowers. Nature Plants. 6: 734-735. PMID 32665649 DOI: 10.1038/S41477-020-0705-4  0.612
2020 Massonnet M, Cochetel N, Minio A, Vondras AM, Lin J, Muyle A, Garcia JF, Zhou Y, Delledonne M, Riaz S, Figueroa-Balderas R, Gaut BS, Cantu D. The genetic basis of sex determination in grapes. Nature Communications. 11: 2902. PMID 32518223 DOI: 10.1038/S41467-020-16700-Z  0.602
2019 Vondras AM, Minio A, Blanco-Ulate B, Figueroa-Balderas R, Penn MA, Zhou Y, Seymour D, Ye Z, Liang D, Espinoza LK, Anderson MM, Walker MA, Gaut B, Cantu D. The genomic diversification of grapevine clones. Bmc Genomics. 20: 972. PMID 31830913 DOI: 10.1186/S12864-019-6211-2  0.602
2019 Lv Y, Hu F, Zhou Y, Wu F, Gaut BS. Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response. Bmc Genomics. 20: 864. PMID 31729949 DOI: 10.1186/S12864-019-6245-5  0.491
2019 Zhou Y, Minio A, Massonnet M, Solares E, Lv Y, Beridze T, Cantu D, Gaut BS. The population genetics of structural variants in grapevine domestication. Nature Plants. 5: 965-979. PMID 31506640 DOI: 10.1038/S41477-019-0507-8  0.665
2018 Gaut BS, Seymour DK, Liu Q, Zhou Y. Demography and its effects on genomic variation in crop domestication. Nature Plants. PMID 30061748 DOI: 10.1038/S41477-018-0210-1  0.632
2018 Tian X, Wang Q, Zhou Y. Section (Euphorbiaceae), a New Section Endemic to the Hainan Island of China From Biogeographical, Karyological, and Phenotypical Evidence. Frontiers in Plant Science. 9: 660. PMID 29868103 DOI: 10.3389/Fpls.2018.00660  0.344
2017 Zhou Y, Massonnet M, Sanjak JS, Cantu D, Gaut BS. Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. Proceedings of the National Academy of Sciences of the United States of America. PMID 29042518 DOI: 10.1073/Pnas.1709257114  0.65
2017 Liu Q, Zhou Y, Morrell PL, Gaut BS. Deleterious variants in Asian rice and the potential cost of domestication. Molecular Biology and Evolution. PMID 28087781 DOI: 10.1093/Molbev/Msw296  0.599
2017 Zhou Y, Duvaux L, Ren G, Zhang L, Savolainen O, Liu J. Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions Heredity. 118: 211–220. PMID 27649619 DOI: 10.1038/hdy.2016.72  0.364
2016 Zhou Y, Duvaux L, Ren G, Zhang L, Savolainen O, Liu J. Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions. Heredity. PMID 27649619 DOI: 10.1038/Hdy.2016.72  0.631
2014 Zhou Y, Zhang L, Liu J, Wu G, Savolainen O. Climatic adaptation and ecological divergence between two closely related pine species in Southeast China Molecular Ecology. 23: 3504-3522. PMID 24935279 DOI: 10.1111/Mec.12830  0.613
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