Publications

☆ 2025 ☆

● Liu H-J^*, Fu J, Xu S, Nordborg M. Potential Synthetic Associations Created by Epistasis. Genome Biol, 2025. [In revision]

● Li K^#, Yu Y^#, Yan S^#, Li W^#, Xu J, Li G, Li W, Liu J, Qi X, Huang W, Zhang Q, Kong Q, Xiao Y, Zhang N, Luo J, Chen L, Zhu W, Wen T, Xie L, Li Y, Lu W, Li C, Gui S, Xiao Y, Yang N, Zhuo L, Fernie AR, Liu H-J^*, Hu J^*, Yan J^*. Beyond sweetness: genetic basis of flavor complexity in sweet corn. Nat Genet, 2025. [Accepted]

● Igolkina A^#, Vorbrugg S^#, Rabanal F^#, Liu H-J^#, Ashkenazy H^#, Kornienko A^#, Fitz J, Collenberg M, Kubica C, Morales M. A, Jaegle B, Wrightsman T, Voloshin V, Llaca V, Nizhynska V, Reichardt I, Lanz C, Bemm F, Flood J. P, Nemomissa S, Hancock A, Guo Y-L, Kersey P, Weigel D^*, Nordborg M^*. Towards an unbiased characterization of genetic polymorphism. Nat Genet, 2025. 19 August 2025.

○ Lian T^#, Guo W^#, Wang Y^#, Wen W^#, Wang W^#, Jiang L, Liang Q, Liu J, Liu H, Liu H-J, Xue Y, Pan L, Liu Q, Yin P, Zhang D^*, Yan J^*, Zhang C^*. An Allele of Glutamate Formiminotransferase Triggers 5-Methyl-Tetrahydrofolate-to-MeFox Conversion and Facilitates Folate Biofortification in Maize. Advanced Science, 2025, 21 August 2025.

● Wang Y^#, Zhang P^#, Xiao Y^#, Liu H-J^*, Ding J, Qu Y, Gao J, Li W, Guo X, Wang A, Li W, Chen G, Shi C-Q, Liu J, Liu JX, Zhang Jian, Xu J, Zhang H, Zhang Jianan, Zhao J, Tang J, Wang H^*, Zhang Z^*, Chen Z^*, Yan J^*. GAIN: a long-term maize germplasm innovation plan. Mol Plant, 2025; 18(6):915-919.

● Wei W^#, Gui S^#, Yang J, Garrison E, Yan J, Liu H-J^*. wgatools: an ultrafast toolkit for manipulating whole genome alignments. Bioinformatics, 2025;41(4):btaf132.

● Liu H-J^*, Liu J^*, Zhai Z, Dai M, Tian F, Wu Y, Tang J, Lu Y, Wang H, Jackson D, Yang X, Qin F, Xu M, Fernie AR, Zhang Z, Yan J^*. Maize2035: A decadal vision for intelligent maize breeding. Mol Plant, 2025; 18(2):313-332.

○ Yu Y^#, Li W^#, Liu Y^#, Liu Y, Zhang Q, Ouyang Y, Ding W, Xue Y, Zou Y, Yan J, Jia A, Yan J, Hao X, Gou Y, Zhai Z, Liu L, Zheng Y, Zhang B, Xu J, Yang N, Xiao Y, Zhuo L, Lai Z, Yin P, Liu H, Fernie AR, Jackson D, Yan J^*. A Zea genus-specific micropeptide controls kernel dehydration in maize. Cell, 2025, 188(1):44-59.e21.

☆ 2024 ☆

○ Clauw P, Ellis TJ, Liu H-J, Sasaki E^*. Beyond the Standard GWAS — A Guide for Plant Biologists. Plant Cell Physiol, 2024, pcae079.

☆ 2023 ☆

○ Jin M, Liu H, Liu X, Guo T, Guo J, Yin Y, Ji Y, Li Z, Zhang J, Wang X, Qiao F, Xiao Y, Zan Y^*, Yan J^*. Complex genetic architecture underlying the plasticity of maize agronomic traits. Plant Commun, 2023, 4(3):100473.

☆ 2022 ☆

○ Zhu F, Alseekh S, Koper K, Tong H, Nikoloski Z, Naake T, Liu H, Yan J, Brotman Y, Wen W, Maeda H, Cheng Y^*, Fernie AR^*. Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis. Plant Cell, 2022, 34(1):557-578.

☆ 2021 ☆

● Liang Y^#, Liu H-J^#, Yan J^*, Tian F^*. Natural Variation in Crops: Realized Understanding, Continuing Promise. Annu Rev Plant Biol, 2021, 72:357-385.

☆ 2020 ☆

● Wang S^#, Tian L^#, Liu H^#, Li X, Zhang J, Chen X, Jia X, Zheng X, Wu S, Chen Y, Yan J^*, Wu L^*. Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline. Mol Plant, 2020, 13(7):1078-1093.

● Liu H-J^#, Wang X^#, Xiao Y^#, Luo J^#, Qiao F^#, Yang W^#, Zhang R^#, Meng Y, Sun J, Yan S, Peng Y, Niu L, Jian L, Song W, Yan J, Li C, Zhao Y, Liu Y, Warburton ML, Zhao J^*, Yan J^*. CUBIC: an atlas of genetic architecture promises directed maize improvement. Genome Biol. 2020, 21(1):20.

● Liu H-J^#, Jian L^#, Xu J^#, Zhang Q, Zhang M, Jin M, Peng Y, Yan J, Han B, Liu J, Gao F, Liu X, Huang L, Wei W, Ding Y, Yang X, Li Z, Zhang M, Sun J, Bai M, Song W, Chen H, Sun X, Li W, Lu Y, Liu Y, Zhao J, Qian Y, Jackson D, Fernie AR, Yan J^*. High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize. Plant Cell, 2020, 32(5):1397-1413.

○ Luo J, Wei C, Liu H, Cheng S, Xiao Y, Wang X, Yan J, Liu J^*. MaizeCUBIC: a comprehensive variation database for a maize synthetic population. Database (Oxford), 2020, 2020:baaa044.

○ Liu J^*, Tian Z, Xiao Y, Liu H, Hao S, Zhang X, Wang C, Sun J, Yu H, Yan J^*. Gene Regulatory Relationship Mining Using Improved Three-Phase Dependency Analysis Approach. IEEE/ACM Trans Comput Biol Bioinform, 2020, 17(1):339-346.

○ Deng M, Zhang X, Luo J, Liu H, Wen W, Luo H, Yan J, Xiao Y^*. Metabolomics analysis reveals differences in evolution between maize and rice. Plant J, 2020, 103(5):1710-1722.

☆ 2019 ☆

● Sun J^#, Liu H^#, Liu J, Cheng S, Peng Y, Zhang Q, Yan J, Liu H-J^*, Chen L-L^*. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics, 2019, 35(14):2501-2503.

● Liu H-J^*, Yan J^*. Crop genome-wide association study: A harvest of biological relevance. Plant J, 2019, 97: 8-18.

☆ 2018 ☆

● Chen Q^#, Han Y^#, Liu H^#, Wang X, Sun J, Zhao B, Li W, Tian J, Liang Y, Yan J, Yang X^, Tian F^. Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize. Plant Cell, 2018, 30(7):1404-1423.

○ Jin M, Liu X^*, Jia W, Liu H, Li W, Peng Y, Du Y, Wang Y, Yin Y, Zhang X, Liu Q, Deng M, Li N, Cui X, Hao D, Yan J^*. ZmCOL3, a CCT gene represses flowering in maize by interfering with the circadian clock and activating expression of ZmCCT. J Integr Plant Biol, 2018, 60(6):465-480.

○ Wang H, Xu S, Fan Y, Liu N, Zhan W, Liu H, Xiao Y, Li K, Pan Q, Li W, Deng M, Liu J, Jin M, Yang X, Li J, Li Q, Yan J^*. Beyond pathways: genetic dissection of tocopherol content in maize kernels by combining linkage and association analyses. Plant Biotechnol J, 2018, 16(8):1464-1475.

○ Wen W^#, Jin M^#, Li K, Liu H, Xiao Y, Zhao M, Alseekh S, Li W, de Abreu E Lima F, Brotman Y, Willmitzer L, Fernie AR^*, Yan J^*. An integrated multi-layered analysis of the metabolic networks of different tissues uncovers key genetic components of primary metabolism in maize. Plant J, 2018, 93(6):1116-1128.

☆ 2017 ☆

● Liu H^#, Luo X^#, Niu L, Xiao Y, Chen L, Liu J, Wang X, Jin M, Li W, Zhang Q, Yan J^*. Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize. Mol Plant, 2017, 10(3):414-426.

● Xiao Y^#, Liu H^#, Wu L^#, Warburton M, Yan J^*. Genome-wide Association Studies in Maize: Praise and Stargaze. Mol Plant, 2017, 10(3):359-374.

● Liu H^*, Yan J^*. Rice domestication: An imperfect African solution. Nat Plants, 2017, 3:17083. [Comment]

○ Liu J, Huang J, Guo H, Lan L, Wang H, Xu Y, Yang X, Li W, Tong H, Xiao Y, Pan Q, Qiao F, Raihan MS, Liu H, Zhang X, Yang N, Wang X, Deng M, Jin M, Zhao L, Luo X, Zhou Y, Li X, Zhan W, Liu N, Wang H, Chen G, Li Q^, Yan J^. The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice. Plant Physiol, 2017, 175(2):774-785.

○ Deng M, Li D, Luo J, Xiao Y, Liu H, Pan Q, Zhang X, Jin M, Zhao M, Yan J^*. The genetic architecture of amino acids dissection by association and linkage analysis in maize. Plant Biotechnol J, 2017, 15(10):1250-1263.

☆ 2016 & Before ☆

○ Xiao Y^#, Tong H^#, Yang X, Xu S, Pan Q, Qiao F, Raihan MS, Luo Y, Liu H, Zhang X, Yang N, Wang X, Deng M, Jin M, Zhao L, Luo X, Zhou Y, Li X, Liu J, Zhan W, Liu N, Wang H, Chen G, Cai Y, Xu G, Wang W, Zheng D, Yan J^*. Genome-wide dissection of the maize ear genetic architecture using multiple populations. New Phytol, 2016, 210(3):1095-106.

○ Zhang X, Warburton ML, Setter T, Liu H, Xue Y, Yang N, Yan J, Xiao Y^*. Genome-wide association studies of drought-related metabolic changes in maize using an enlarged SNP panel. Theor Appl Genet, 2016, 129(8):1449-63.

○ Wen W^*, Liu H, Zhou Y, Jin M, Yang N, Li D, Luo J, Xiao Y, Pan Q, Tohge T, Fernie AR, Yan J. Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel. Plant Physiol, 2016, 170(1):136-46.

● Jin M^#, Liu H^#, He C^#, Fu J^*, Xiao Y, Wang Y, Xie W, Wang G, Yan J^*. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep, 2016, 6:18936.

● Liu H, Wang F, Xiao Y, Tian Z, Wen W, Zhang X, Chen X, Liu N, Li W, Liu L, Liu J, Yan J, Liu J^*. MODEM: multi-omics data envelopment and mining in maize. Database (Oxford), 2016, 2016:baw117.

○ Li X^*, Liu N, You L, Ke X, Liu H, Huang M, Waddington SR. Patterns of Cereal Yield Growth across China from 1980 to 2010 and Their Implications for Food Production and Food Security. PLoS One, 2016, 11(7):e0159061.

● Liu H^#, Wang X^#, Warburton ML, Wen W, Jin M, Deng M, Liu J, Tong H, Pan Q, Yang X, Yan J^*. Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding. Mol Plant, 2015, 8(6):871-84.

○ Zuo W^#, Chao Q^#, Zhang N^#, Ye J, Tan G, Li B, Xing Y, Zhang B, Liu H, Fengler KA, Zhao J, Zhao X, Chen Y, Lai J, Yan J, Xu M^*. A maize wall-associated kinase confers quantitative resistance to head smut. Nat Genet, 2015, 47(2):151-7.

○ Wen W, Li K, Alseekh S, Omranian N, Zhao L, Zhou Y, Xiao Y, Jin M, Yang N, Liu H, Florian A, Li W, Pan Q, Nikoloski Z, Yan J^*, Fernie AR^*. Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population. Plant Cell, 2015, 27(7):1839-56.

○ Wen W^#, Li D^#, Li X, Gao Y, Li W, Li H, Liu J, Liu H, Chen W, Luo J^*, Yan J^*. Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights. Nat Commun, 2014, 5:3438.

○ Yan W^#, Liu H^#, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y^*. Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res, 2013, 23(7):969-71.

★ Patents ★

刘海军, 许洁婷, 严建兵. 一种基因组特定区域的DNA测序方法: 中国, 201811606050.9. 2021-4-2.

金敏亮, 刘海军, 刘相国, 许洁婷, 严建兵. 降低玉米株高或延迟开花的方法: 中国, 202010109172.8. 2022-5-3.

金敏亮, 刘海军, 刘相国, 许洁婷, 严建兵. 控制玉米株高和花期的基因及其应用: 中国, 202010080086.9. 2020-2-4.