David O'Donnell, Jinliang Yang, P. Zamora, Anne Lorant, Chenyong Miao, A. Van Deynze, Alan B. Bennett, J. Ross-Ibarra (2025). HERITABILITY AND QTL MAPPING OF AERIAL ROOTS AND OTHER YIELD COMPONENT TRAITS WITH IMPLICATIONS FOR N2 FIXATION IN ZEA MAYS. bioRxiv.DOI
Gen Xu, Xue-Rong Yang, Ming-Yue Zhang, Congbin Kang, Ziang Tian, Yu Qi, Mei-Jie Luo, Peng Liu, J. Ross-Ibarra, Jinliang Yang, Hong-Jun Liu (2025). The dominance of gene expression controlled by trans-eQTL hotspots contributes to phenotypic heterosis in maize. bioRxiv.DOI
Xiao-Ming He, Danning Wang, Yong Jiang, Meng Li, M. Delgado-Baquerizo, Chloee M. McLaughlin, Caroline Marcon, Li Guo, Marcel Baer, Y. A. Moya, N. von Wirén, M. Deichmann, Gabriel Schaaf, H. Piepho, Zhikai Yang, Jinliang Yang, B. Yim, K. Smalla, S. Goormachtig, F. D. de Vries, Hubert Hüging, M. Baer, Ruairidh J. H. Sawers, J. Reif, F. Hochholdinger, Xin-Ping Chen, Peng Yu (2024). Heritable microbiome variation is correlated with source environment in locally adapted maize varieties. Nature Plants.DOI
Hongyu Jin, Alexa N Park, A. Sreedasyam, Guangyong Li, Yufeng Ge, K. Swaminathan, Jeremy Schmutz, Thomas E. Clemente, James C. Schnable, Jinliang Yang (2024). Nitrogen response and growth trajectory of sorghum CRISPR-Cas9 mutants using high-throughput phenotyping. bioRxiv.DOI
Hongyu Jin, Michael C. Tross, Ruijuan Tan, L. Newton, Ravi V. Mural, Jinliang Yang, Addie M. Thompson, James C. Schnable (2023). Imitating the ‘breeder’s eye’: predicting grain yield from measurements of non-yield traits. bioRxiv.DOI
Thomas Hartwig, M. Banf, G. Prietsch, Jia-Ying Zhu, Isabel Mora-Ramírez, Jos H. M. Schippers, Samantha J. Snodgrass, Arun S. Seetharam, B. Huettel, J. Kolkman, Jinliang Yang, J. Engelhorn, Zhi-Yong Wang (2023). Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize. Genome Biology.DOI
Xinyan Xie, Y. Ge, H. Walia, Jinliang Yang, Hongfeng Yu (2023). Leaf-Counting in Monocot Plants Using Deep Regression Models. Italian National Conference on Sensors.DOI
Delin Li, Qi Wang, Yu Tian, Xiang-Li Lyv, Hao Zhang, Ying-Lu Sun, Hui-Long Hong, Hua-Wei Gao, Yan-Fei Li, Chao-Yue Zhao, Jia-jun Wang, Ruizhen Wang, Jinliang Yang, Bin Liu, P. Schnable, James C. Schnable, Ying-Hui Li, L. Qiu (2023). Transcriptome brings variations of gene expression, alternative splicing, and structural variations into gene-scale trait dissection in soybean. bioRxiv.DOI
N. Wijewardane, Hui-Chun Zhang, Jinliang Yang, James C. Schnable, D. Schachtman, Y. Ge (2023). A leaf-level spectral library to support high-throughput plant phenotyping: predictive accuracy and model transfer. Journal of Experimental Botany.DOI
Shichao Sun, Bao-Bao Wang, Chang-Yu Li, Gen Xu, Jinliang Yang, M. Hufford, J. Ross-Ibarra, Hai-Yang Wang, Li Wang (2023). Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding. Molecular biology and evolution.DOI
Xiaoming, He, Danning, Wang, Yong, Jiang, Meng, Li, Manuel, Delgado, Baquerizo, Chloee M. McLaughlin, Caroline Marcon, Li Guo, Marcel Baer, Y. A. Moya, Nicolaus von Wirén, M. Deichmann, Gabriel Schaaf, H. Piepho, Zhikai Yang, Jinliang Yang, B. Yim, K. Smalla, S. Goormachtig, F. D. de Vries, Hubert Hüging, Ruairidh J. H. Sawers, J. Reif, F. Hochholdinger, Xin-Ping Chen, Peng Yu (2023). Heritable maize microbiomes contribute to local adaptation and 1 host stress resilience 2.
Zhikai Yang, Tian-Jing Zhao, Hao Cheng, Jinliang Yang (2023). Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize. bioRxiv.DOI
Xia Zhao, Shuai-Lin Wang, Tao Wen, Jiamin Xu, Bao-Long Huang, Shu-Feng Yan, Gangqiang Gao, Ya-Li Zhao, Hongping Li, Jiang-Fang Qiao, Jinliang Yang, Lian-Hai Wu, Hongwei Wang, Tianxue Liu, X. Mu (2023). On correlation between canopy vegetation and growth indexes of maize varieties with different nitrogen efficiencies. Open Life Sciences.DOI
Jingjie Hao, Ying Yang, Stephanie L Futrell, Elisabeth A. Kelly, Claire M. Lorts, B. Nebié, S. Runo, Jinliang Yang, S. Alvarez, Jesse R. Lasky, D. Schachtman (2023). CRISPR/Cas9-Mediated Mutagenesis of Carotenoid Cleavage Dioxygenase (CCD) Genes in Sorghum Alters Strigolactone Biosynthesis and Plant Biotic Interactions. Phytobiomes Journal.DOI
Zhikai Yang, Gen Xu, Qi Zhang, T. Obata, Jinliang Yang (2022). Genome-wide mediation analysis: an empirical study to connect phenotype with genotype via intermediate transcriptomic data in maize. Genetics.DOI
Delin Li, Dong Bai, Yu Tian, Ying-Hui Li, Chao-Yue Zhao, Qi Wang, Shi-Yu Guo, Yongzhe Gu, Xiaoyan Luan, Ruizhen Wang, Jinliang Yang, M. Hawkesford, James C. Schnable, Xiu-Liang Jin, L. Qiu (2022). Time Series Canopy Phenotyping Enables the Identification of Genetic Variants Controlling Dynamic Phenotypes in Soybean. Journal of Integrative Plant Biology.DOI
Siwen Deng, M. Meier, Daniel F. Caddell, Jinliang Yang, Devin Coleman-Derr (2022). Plant Microbiome-Based Genome-Wide Association Studies. Methods in molecular biology.DOI
M. Meier, Gen Xu, M. López-Guerrero, Guangyong Li, Christine Smith, B. Sigmon, Joshua R. Herr, J. Alfano, Y. Ge, James C. Schnable, Jinliang Yang (2022). Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize. eLife.DOI
Liang-Hong Yin, Gen Xu, Jinliang Yang, Meixia Zhao (2022). The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments. Molecular biology and evolution.DOI
Semra Palali Delen, Gen Xu, Jenifer Velazquez-Perfecto, Jinliang Yang (2022). Estimating the genetic parameters of yield-related traits under different nitrogen conditions in maize. bioRxiv.DOI
Gen Xu, Jing Lyu, T. Obata, Sanzhen Liu, Y. Ge, James C. Schnable, Jinliang Yang (2022). A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding. bioRxiv.DOI
Qi Zhang, Zhikai Yang, Jinliang Yang (2022). MedDiC: high dimensional mediation analysis via difference in coefficients. bioRxiv.DOI
Eric Rodene, Gen Xu, Semra Palali Delen, Xia Zhao, Christine Smith, Yu-Feng Ge, James C. Schnable, Jinliang Yang (2022). A UAV‐based high‐throughput phenotyping approach to assess time‐series nitrogen responses and identify trait‐associated genetic components in maize. The Plant Phenome Journal.DOI
Marcin W. Grzybowski, Ravi V. Mural, Gen Xu, J. Turkus, Jinliang Yang, James C. Schnable (2022). A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity. bioRxiv.DOI
Yavuz Delen, Ravi V. Mural, Gen Xu, Semra Palali Delen, James C. Schnable, Jinliang Yang, I. Dweikat (2022). Dissecting the genetic architecture of sunflower head diameter using genome-wide association study. bioRxiv.DOI
M. Meier, Gen Xu, M. López-Guerrero, Guangyong Li, Christine Smith, B. Sigmon, Joshua R. Herr, J. Alfano, Y. Ge, James C. Schnable, Jinliang Yang (2021). Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance. bioRxiv.DOI
Jinliang Yang, Sofiane Mezmouk, A. Baumgarten, E. Buckler, K. Guill, M. McMullen, Rita H. Mumm, J. Ross-Ibarra (2021). Correction: Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genetics.DOI
L. F. Samayoa, B. Olukolu, C. Yang, Qiuyue Chen, Markus G. Stetter, Alessandra M. York, Jose de Jesus Sanchez-Gonzalez, J. Glaubitz, Peter J. Bradbury, M. Romay, Qi Sun, Jinliang Yang, J. Ross-Ibarra, E. Buckler, J. Doebley, J. Holland (2021). Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte. bioRxiv.DOI
Cheng He, Jacob D. Washburn, Yangfan Hao, Zhiwu Zhang, Jinliang Yang, Sanzhen Liu (2021). Trait Association and Prediction Through Integrative K-mer Analysis. bioRxiv.DOI
M. Meier, M. López-Guerrero, M. Guo, M. Schmer, Joshua R. Herr, James C. Schnable, J. Alfano, Jinliang Yang (2021). Rhizosphere Microbiomes in a Historical Maize-Soybean Rotation System Respond to Host Species and Nitrogen Fertilization at the Genus and Subgenus Levels. Applied and Environmental Microbiology.DOI
Gen Xu, Jing Lyu, Qing Li, Han Liu, Da-Fang Wang, Mei Zhang, Nathan M. Springer, J. Ross-Ibarra, Jinliang Yang (2020). Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nature Communications.DOI
Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable (2020). Semantic Segmentation of Sorghum Using Hyperspectral Data Identifies Genetic Associations. Plant Phenomics.DOI
Chenyong Miao, Alice Guo, Addie M. Thompson, Jinliang Yang, Y. Ge, James C. Schnable (2020). Automation of Leaf Counting in Maize and Sorghum Using Deep Learning. bioRxiv.DOI
Gen Xu, Jing Lyu, Qing Li, Han Liu, Da-Fang Wang, Mei Zhang, Nathan M. Springer, J. Ross-Ibarra, Jinliang Yang (2020). Adaptive evolution of DNA methylation reshaped gene regulation in maize.DOI
Lin Zhang, Xiu-Wei Yang, Ming-Fei Sun, Congbin Kang, Yujian Wu, Xiao-Han Li, Yahui Ding, Xing Zeng, Hongjun Liu, Jinliang Yang, Xue-Rong Yang (2019). Enriched and depleted microbes at phyla level in humic acid (HA) fertilizer associated with delayed drought responses in maize.DOI
Chenyong Miao, Thomas P Hoban, Alejandro Pages, Zheng Xu, Eric Rodene, Jordan R. Ubbens, I. Stavness, Jinliang Yang, James C. Schnable (2019). Simulated Plant Images Improve Maize Leaf Counting Accuracy. bioRxiv.DOI
Y. Ge, A. Atefi, Hui-Chun Zhang, Chenyong Miao, Raghuprakash Kastoori Ramamurthy, B. Sigmon, Jinliang Yang, James C. Schnable (2019). High-throughput analysis of leaf physiological and chemical traits with VIS–NIR–SWIR spectroscopy: a case study with a maize diversity panel. Plant Methods.DOI
Chenyong Miao, Jingping Fang, Delin Li, Ping-Ping Liang, Xing-Tan Zhang, Jinliang Yang, James C. Schnable, Hai-Bao Tang (2018). Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations. Scientific Reports.DOI
Rui-Xin Shao, Hui-Fang Zheng, Jinliang Yang, Shuang-Jie Jia, Tianxue Liu, Yong-Chao Wang, Jiameng Guo, Qing-Hua Yang, Guo-Zhang Kang (2018). Proteomics analysis reveals that nitric oxide regulates photosynthesis of maize seedlings under water deficiency. Nitric oxide.DOI
Chenyong Miao, Jinliang Yang, James C. Schnable (2018). Optimising the identification of causal variants across varying genetic architectures in crops. bioRxiv.DOI
Jinliang Yang, C. Yeh, Raghuprakash Kastoori Ramamurthy, Xinshuai Qi, R. Fernando, J. Dekkers, D. Garrick, D. Nettleton, P. Schnable (2018). Empirical Comparisons of Different Statistical Models To Identify and Validate Kernel Row Number-Associated Variants from Structured Multi-parent Mapping Populations of Maize. G3: Genes, Genomes, Genetics.DOI
Margaret Bezrutczyk, Thomas Hartwig, Marc Horschman, S. N. Char, Jinliang Yang, Bing Yang, W. Frommer, Davide Sosso (2018). Impaired phloem loading in zmsweet13a,b,c sucrose transporter triple knock-out mutants in Zea mays. New Phytologist.DOI
Zhikai Liang, S. Gupta, C. Yeh, Yang Zhang, Daniel W. Ngu, Ramesh Kumar, H. T. Patil, K. D. Mungra, D. Yadav, A. Rathore, R. Srivastava, Rajeev Gupta, Jinliang Yang, R. Varshney, P. Schnable, James C. Schnable (2018). Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids. G3: Genes, Genomes, Genetics.DOI
Jingjie Hao, Jinliang Yang, Jiangli Dong, S. Fei (2017). Characterization of BdCBF genes and genome-wide transcriptome profiling of BdCBF3-dependent and -independent cold stress responses in Brachypodium distachyon. Plant Science.DOI
Margaret Bezrutczyk, Thomas Hartwig, Marc Horshman, S. N. Char, Jinliang Yang, Bing Yang, W. Frommer, Davide Sosso (2017). Impaired phloem loading in genome-edited triple knock-out mutants of SWEET13 sucrose transporters. bioRxiv.DOI
Zhaobin Dong, Wei Li, Erica Unger-Wallace, Jinliang Yang, E. Vollbrecht, G. Chuck (2017). Ideal crop plant architecture is mediated by tassels replace upper ears1, a BTB/POZ ankyrin repeat gene directly targeted by TEOSINTE BRANCHED1. Proceedings of the National Academy of Sciences of the United States of America.DOI
Jinliang Yang (2017). Yang et al., 2017 Data for PVP deleterious alleles.DOI
Paul Bilinski, Patrice S. Albert, Jeremy J. Berg, J. Birchler, M. N. Grote, Anna Lóránt, J. Quezada, Kelly L. Swarts, Jinliang Yang, J. Ross-Ibarra (2017). Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays. bioRxiv.DOI
Jinliang Yang, Sofiane Mezmouk, A. Baumgarten, E. Buckler, K. Guill, M. McMullen, Rita H. Mumm, J. Ross-Ibarra (2016). Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. bioRxiv.DOI
Davide Sosso, Dangping Luo, Qin-Bao Li, Joelle Sasse, Jinliang Yang, G. Gendrot, Masaharu Suzuki, K. Koch, D. R. McCarty, P. Chourey, P. Rogowsky, J. Ross-Ibarra, Bing Yang, W. Frommer (2015). Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport. Nature Genetics.DOI
Jinliang Yang, Haiying Jiang, C. Yeh, Jian-Ming Yu, J. Jeddeloh, D. Nettleton, P. Schnable (2015). Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel. The Plant Journal.DOI
Samuel Leiboff, Xian-Ran Li, H. Hu, Natalie R. Todt, Jinliang Yang, Xiao Li, Xiao-Qing Yu, G. Muehlbauer, M. Timmermans, Jian-Ming Yu, P. Schnable, M. Scanlon (2015). Genetic control of morphometric diversity in the maize shoot apical meristem. Nature Communications.DOI
Jinliang Yang (2014). Genome-wide association studies to dissect the genetic architecture of yieldrelated traits in maize and the genetic basis of heterosis.DOI
Sanzhen Liu, Kai Ying, C. Yeh, Jinliang Yang, Ruth A. Swanson-Wagner, Wei Wu, T. Richmond, D. J. Gerhardt, Jinsheng Lai, Nathan M. Springer, D. Nettleton, J. Jeddeloh, P. Schnable (2012). Changes in genome content generated via segregation of non-allelic homologs. The Plant Journal.DOI
L. Koesterke, D. Stanzione, M. Vaughn, S. Welch, Waclaw Kusnierczyk, Jinliang Yang, C. Yeh, D. Nettleton, P. Schnable (2011). An Efficient and Scalable Implementation of SNP-Pair Interaction Testing for Genetic Association Studies. IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum.DOI