Sustainable agriculture in the era of omics: knowledge-driven crop breeding, Li Q#, Yan J#, 2020
Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize, Xu J, Chen G, Hermanson PJ, Xu Q, Sun C, Chen W, Kan Q, Li M, Crisp PA, Yan J, Li L, Springer NM#, Li Q#, 2019
BRIF-Seq: Bisulfite-converted randomly integrated fragments sequencing at the single-cell level, Li X, Chen L, Zhang Q, Sun Y, Li Q#, Yan J#, 2019
Beyond pathways: genetic dissection of tocopherol content in maize kernels by combining linkage and association analyses, 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#, 2018
Subtle perturbations of the maize methylome reveal genes and transposons silenced by chromomethylase or RNA-Directed DNA methylation pathways, Anderson SN, Zynda GJ, Song J, Han Z, Vaughn MW, Li Q#, Springer NM#, 2018
The conserved and unique genetic architecture of kernel size and weight in maize and rice, 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#, 2017
RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome, Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D, Schmitz RJ, Vaughn MW, Springer NM, 2015
Examining the causes and consequences of context-specific differential DNA methylation in maize, Li Q*, Song J*, West PT, Zynda G, Eichten SR, Vaughn MW, Springer NM, 2015
Post-conversion targeted capture of modified cytosines in mammalian and plant genomes, Li Q*, Suzuki M*, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM, 2015
Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants, Li Q, Li Y, Moose SP, Hudson ME, 2015
Genetic perturbation of the maize methylome, Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM, 2014
Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines, Li Q, Eichten SR, Hermanson PJ, Springer NM, 2014
Genomic distribution of H3K9me2 and DNA methylation in a maize genome, West PT*, Li Q*, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM, 2014
Genome-wide association studies identified three independent polymorphisms associated with α-Tocopherol content in maize kernels, Li Q*, Yang X*, Xu S*, Cai Y, Zhang D, Han Y, Li L, Zhang Z, Gao S, Li J, Yan J, 2012
Relationship, evolutionary fate and function of two maize co-orthologs of rice GW2 associated with kernel size and weight, Li Q, Li L, Yang X, Warburton ML, Bai G, Dai J, Li J, Yan J, 2010
Cloning and characterization of a putative GS3 ortholog involved in maize kernel development, Li Q, Yang X, Bai G, Warburton ML, Mahuku G, Gore M, Dai J, Li J, Yan J, 2010
Identification and characterization of CACTA transposable elements capturing gene fragments in maize, Li Q, Li L, Dai J, Li J, Yan J, 2009
CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers, Zhang M, Ma X, Wang C, Li Q, Meyers BC, Springer NM, Walbot V, 2021
Evolutionary and functional genomics of DNA methylation in maize domestication and improvement, Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, Springer NM, Ross-Ibarra J, Yang J, 2020
The Kernel Size-Related Quantitative Trait Locus qKW9 Encodes a Pentatricopeptide Repeat Protein That Aaffects Photosynthesis and Grain Filling, Huang J, Lu G, Liu L, Raihan MS, Xu J, Jian L, Zhao L, Tran TM, Zhang Q, Liu J, Li W, Wei C, Braun DM, Li Q, Fernie AR, Jackson D, Yan J, 2020
Hybrid Decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize, Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF, 2019
QTG-Seq accelerates QTL fine mapping through QTL partitioning and whole-genome sequencing of bulked segregant samples, Zhang H, Wang X, Pan Q, Li P, Liu Y, Lu X, Zhong W, Li M, Han L, Li J, Wang P, Li D, Liu Y, Li Q, Yang F, Zhang YM, Wang G, Li L, 2019
Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize, Chen L, Zhang P, Fan Y, Lu Q, Li Q, Yan J, Muehlbauer GJ, Schnable PS, Dai M, Li L, 2018
The maize W22 genome provides a foundation for functional genomics and transposon biology, Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP, 2018
Heritable epigenomic changes to the maize methylome resulting from tissue culture, Han Z, Crisp PA, Stelpflug S, Kaeppler SM, Li Q, Springer NM, 2018
The repetitive landscape of the 5100 Mbp barley genome, Wicker T, Schulman AH, Tanskanen J, Spannagl M, Twardziok S, Mascher M, Springer NM, Li Q, Waugh R, Li C, Zhang G, Stein N, Mayer KFX, Gundlach H, 2017
Widespread natural variation of DNA methylation within angiosperms, Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ, 2016
Creating order from chaos: Epigenome dynamics in plants with complex genomes, Springer NM, Lisch D, Li Q, 2016
Epigenetic and genetic influences on DNA methylation variation in maize populations, Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM, 2013
Dissecting tocopherols content in maize (Zea mays L.), using two segregating populations and high-density single nucleotide polymorphism markers, Xu S, Zhang D, Cai Y, Zhou Y, Trushar S, Farhan A, Li Q, Li Z, Wang W, Li J, Yang X, Yan J, 2012
An 11-bp insertion in Zea mays fatb reduces the palmitic acid content of fatty acids in maize grain, Li L, Li H, Li Q, Yang X, Zheng D, Warburton M, Chai Y, Zhang P, Guo Y, Yan J, Li J, 2011
Rare genetic variation at CrtR-B1 increases β-carotene in maize grain, Yan J, Kandianis CB, Harjes CE, Bai L, Kim EH, Yang X, Skinner DJ, Fu Z, Mitchell S, Li Q, Fernandez MG, Zaharieva M, Babu R, Fu Y, Palacios N, Li J, Dellapenna D, Brutnell T, Buckler ES, Warburton ML, Rocheford T, 2010
Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection, Yang X, Yan J, Shah T, Warburton ML, Li Q, Li L, Gao Y, Chai Y, Fu Z, Zhou Y, Xu S, Bai G, Meng Y, Zheng Y, Li J, 2010
