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Plant Quantitative Genetics and Statistical Genomics |
Google Scholar: H-Index [ 22 ], i10-Index [ 33 ], and total citations [ 2298 ] as of Nov, 2024.
G. Xu, J. Lyu, T. Obata, S. Liu, Y. Ge, J. C. Schnable, J. Yang, A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding, bioRxiv, 2022.
10.1101/2022.02.09.479784
J. Li, D. Cheng, S. Guo, Z. Yang, M. Chen, C. Chen, Y. Jiao, W. Li, C. Liu, Y. Zhong, X. Qi,
J. Yang, S. Chen, Genomic selection to optimize doubled haploid-based hybrid breeding in maize, bioRxiv, 2020.
10.1101/2020.09.08.287672
J. Lu, Y. Xie, C. Li, J. Yang, J. Fu, Tensor decomposition reveals trans-regulated gene modules in maize drought response, Journal of Genetics and Genomics, 2024.
Y. Delen, R. V. Mural, S. Palali Delen, G. Xu, J. C. Schnable, I. Dweikat, J. Yang, Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study, Plant Direct, 2024.
Preprint | GitHub
H. Mukhtar, J. Hao, G. Xu, E. Bergmeyer, M. Ulutas, J. Yang, D. P. Schachtman, Nitrogen input differentially shapes the rhizosphere microbiome diversity and composition across diverse maize lines, Biology and Fertility of Soils, 2024.
Data on NCBI
C. He, J. Washburn, N. Schleif, Y. Hao, H. Kaeppler, S. Kaeppler, Z. Zhang, J. Yang, S. Liu, Trait Association and Prediction Through Integrative K-mer Analysis, The Plant Journal, 2024.
Preprint | Data:CyVerse
Y. Delen, S. Palali-Delen, G. Xu, M. Neji, J. Yang, I. Dweikat, Dissecting the genetic architecture of morphological traits in sunflower, Genes, 2024.
Data | GitHub
X. Wei, M. Chen, Q. Zhang, J. Gong, J. Liu, K. Yong, Q. Wang, J. Fan, S. Chen, H. Hua, Z. Luo, X. Zhao, X. Wang, W. Li, J. Cong, X. Yu, Z. Wang, R. Huang, J. Chen, X. Zhou, J. Qiu, P. Xu, J. Murray, H. Wang, Y. Xu, C. Xu, G. Xu, J. Yang, B. Han, X. Huang, Genomic investigation of 18,421 lines reveals the genetic architecture of rice, Science, 2024.
Data | Figshare | GitHub
D. Li, Q. Wang, Y. Tian, X. Lyv, H. Zhang, H. Hong, H. Gao, Y.-F. Li, C. Zhao, J. Wang, R. Wang, J. Yang, B. Liu, P. S. Schnable, J. C. Schnable, Y.-H. Li, L.-J. Qi, TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean, Plant Communications, 2024.
Data | Figshare | GitHub
Z. Yang, Q. Zhang, J. Yang, High dimensional mediation analysis for causal inference, Bio-Protocol, 2024.
GitHub
J. Li, D. Zhang, F. Yang, Q. Zhang, S.i Pan, X. Zhao, Q. Zhang, Y. Han, J. Yang, K. Wang, C. Zhao, TrG2P: A transfer learning-based tool integrating multi-trait data for accurate prediction of crop yield, Plant Communications, 2024.
Web-based tool | GitHub
Q. Zhang, Z. Yang, J. Yang, Dissecting the colocalized GWAS and eQTLs with mediation analysis for high dimensional exposures and confounders, Biometrics, 2024.
Preprint | GitHub
E. Rodene, G. D. Fernando, V. Piyush, Y. Ge, J. C. Schnable, S. Ghosh, J. Yang, Image filtering to improve maize tassel detection accuracy using machine learning algorithms, Sensors, 2024.
Preprint
H. Jin, M. C. Tross, R. Tan, L. Newton, R. V. Mural, J. Yang, A. M. Thompson, J. C. Schnable, Imitating the ‘breeder’s eye’: predicting grain yield from measurements of non-yield traits, The Plant Phenome Journal, 2024.
Preprint | GitHub | Data
X. He, D. Wang, Y. Jiang, M. Li, M. Delgado-Baquerizo, C. McLaughlin, C. Marcon, M. Baer, L. Guo, Y. A.T. Moya, N. von Wiren, M. Deichmann, G. Schaaf, H.-P. Piepho, Z. Yang, J. Yang, B. Yim, K. Smalla, S. Goormachtig, F. T. de Vries, H. Huging, R. J. H. Sawers, J. C. Reif, F. Hochholdinger, X. Chen, P. Yu, Heritable microbiome variation is correlated with source environment in locally adapted maize varieties, Nature Plants, 2024.
Preprint | GitHub | Data: BioProject ID PRJNA889703
Z. Yang, T. Zhao, H. Cheng, and J. Yang, Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize, G3, 2023.
Preprint | GitHub
Y. Zou, J. Wang, D. Peng, X. Zhang, L. R. Tembrock, J. Yang, J. Zhao, H. Liao, Z. Wu, Multi-integrated genomic data for Passiflora foetida provides insights into genome size evolution and floral development in Passiflora, Molecular Horticulture, 2023.
Data
S. Palali Delen, J. Lee, J. Yang, Improving the metal composition of plants for reduced Cd and increased Zn content: molecular mechanisms and genetic regulations, Cereal Research Communications, 2023.
S. Sun, B. Wang, C. Li, G. Xu, J. Yang, M. B. Hufford, J. Ross-Ibarra, H. Wang, L. Wang, Unraveling prevalence and effects of deleterious mutations in maize elite lines across decades of modern breeding, Molecular Biology and Evolution, 2023.
2 citations
T. Hartwig, M. Banf, G. Passaia Prietsch, J. Yang, J. Engelhorn, Z. Wang, Hybrid allele-specific ChIP-Seq analysis links variation in transcription factor binding to traits in maize, Genome Biology, 2023.
Preprint | GitHub | 6 citations
N. K. Wijewardane, H. Zhang, J. Yang, J. C. Schnable, D. P. Schachtman, Y. Ge, A leaf-level spectral library to support high throughput plant phenotyping: Predictive accuracy and model transfer, Journal of Experimental Botany, 2023.
15 citations
J. Hao, Y. Yang, S. Futrell, E. A. Kelly, C. M. Lorts, B. Nebie, S. Runo, J. Yang, S. Alvarez, J. R. Lasky, D. P. Schachtman, CRISPR/Cas9-mediated mutagenesis of carotenoid cleavage dioxygenase (CCD) genes in sorghum alters strigolactone biosynthesis and plant biotic interactions, Phytobiomes Journal, 2023.
13 citations
X. Xie, Y. Ge, H. Walia, J. Yang, H. Yu, Leaf Counting in Monocot Plants using Deep Regression Models, Sensors, 2023.
9 citations
M. W. Grzybowski, R. V. Mural, G. Xu, J. Turkus, J. Yang, J. C. Schnable, A Common Resequencing-Based Genetic Marker Dataset for Global Maize Diversity, The Plant Journal, 2023.
Preprint | CyVerse | Dryad | 23 citations
S. Palali Delen, G. Xu, J. Velazquez-Perfecto, J. Yang, Estimating the genetic parameters of yield-related traits under different nitrogen conditions in maize, Genetics, 2023.
Preprint | GitHub | 5 citations
D. Li, D. Bai, Y. Tian, Y. Li, C. Zhao, Q. Wang, S. Gou, Y. Gu, X. Luan, R. Wang, J. Yang, M. J. Hawkesford, J. C. Schnable, X. Jin, L. Qiu, Time series canopy phenotyping enables the identification of genetic variants controlling dynamic phenotypes in soybean, Journal of Integrative Plant Biology, 2023.
Data | 18 citations
X. Liao, Y. Ye, X. Zhang, D. Peng, Me. Hou, G. Fu, J. Tan, J. Zhao, R. Jiang, Y. Xu, J. Liu, J. Yang, W. Liu, L. R. Tembrock, G. Zhu, Z. Wu, The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation, aBIOTECH, 2022.
Data | 16 citations
L. Yin, G. Xu, J. Yang, M. Zhao, The heterogeneity in the landscape of gene dominance in maize is accompanied by unique chromatin environments, Molecular Biology and Evolution, 2022.
Data | 12 citations
M. A. Meier, G. Xu, M. G. Lopez-Guerrero, G. Li, C. Smith, B. Sigmon, J. R. Herr, J. R. Alfano, Y. Ge, J. C. Schnable, J. Yang, Association analyses of host genetics, rootcolonizing microbes, and plant phenotypes under different nitrogen conditions in maize, eLife, 2022.
Preprint | GitHub | NCBI PRJNA772177 (n=3,313 samples) | 33 citations
S. Deng, M. A. Meier, D. Caddell, J. Yang, and D. Coleman-Derr, Plant Microbiome-Based Genome-Wide Association Studies, Part of the Methods in Molecular Biology book series, 2022.
Z. Yang, G. Xu, Q. Zhang, T. Obata, J. Yang, Genome-wide mediation analysis: an empirical study to connect phenotype with genotype via intermediate transcriptomic data in maize, Genetics, 2022.
Preprint | GitHub | GC-MS Data | 13 citations
E. Rodene, G. Xu, S. P. Delen, X. Zhao, C. Smith, Y. Ge, J. C. Schnable, J. Yang, 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, 2022.
Preprint | GitHub | 32 citations
L. F. Samayoa, B. A. Olukolu, C. J. Yang, Q. Chen, M. G. Stetter, A. M. York,, J. de J. Sanchez-Gonzalez, J. C. Glaubitz, P. J. Bradbury, M. C. Romay, Q. Sun, J. Yang, J. Ross-Ibarra, E. S. Buckler, J. F. Doebley, and J. B. Holland, Domestication Reshaped the Genetic Basis of Inbreeding Depression in a Maize Landrace Compared to its Wild Relative, Teosinte, PLOS Genetics, 2021.
Preprint | 12 citations
C. Miao, A. Guo, A. Thompson, J. Yang, Y. Ge, J. C. Schnable, Automation of Leaf Counting in Maize and Sorghum Using Deep Learning, The Plant Phenome Journal, 2021.
Preprint | GitHub | 30 citations
S. Deng, G. Xu, D. Caddell, L. Dahlen, L. Washington, J. Yang, D. Coleman-Derr, Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome,
The ISME Journal, 2021.
Preprint | Github | 148 citations
M. A. Meier, M. G. Lopez-Guerrero, M. Guo, M. R. Schmer, J. R. Herr, J. C. Schnable, J. R. Alfano, J. Yang, Rhizosphere Microbiomes in a Historical Maize/Soybean Rotation System respond to Host Species and Nitrogen Fertilization at Genus and Sub-genus Levels, Applied and Environmental Microbiology, 2021.
Preprint | GitHub | 29 citations
G. Xu, J. Lyu, Q. Li, H. Liu, D. Wang, M. Zhang, N. M. Springer, J. Ross-Ibarra, J. Yang, Evolutionary and functional genomics of DNA methylation in maize domestication and improvement, Nature Communications, 2020.
Preprint | Github | 88 citations
C. Miao, A. Pages, Z. Xu, E. Rodene, J. Yang, and J. C. Schnable, Semantic segmentation of sorghum using hyperspectral data identifies genetic associations, Plant Phenomics, 2020.
GitHub | 45 citations
C. Miao, T. P. Hoban, A. Pages, Z. Xu, E. Rodene, J. Ubbens, I. Stavness, J. Yang, and J. C. Schnable, Simulated plant images improve maize leaf counting accuracy, bioRxiv, 2019.
10.1101/706994
Y. Ge, A. Atefi, H. Zhang, C. Miao, R. K. Ramamurthy, B. Sigmon, J. Yang, J. C. Schnable, High-throughput analysis of leaf physiological and chemical traits with VIS-NIR-SWIR spectroscopy: A case study with a maize diversity panel, Plant Methods, 2019.
166 citations
H. Liu, Q. Wang, M. Chen, Y. Ding, X. Yang, J. Liu, X. Li, C. Zhou, Q. Tian, Y. Lu, D. Fan, J. Shi, L. Zhang, C. Kang, M. Sun, F. Li, Y. Wu, Y. Zhang, B. Liu, X.Y. Zhao, Q. Feng, J. Yang, B. Han, J. Lai, X.S. Zhang, X. Huang, Genome-wide identification and analysis of heterotic loci in three maize hybrids, Plant Biotechnology Journal, 2019.
49 citations
C. Miao, J. Yang, J. C. Schnable, Optimizing the identification of causal variants across varying genetic architectures in crops, Plant Biotechnology Journal, 2019.
Preprint | 45 citations
R. Shao, H. Zheng, J. Yang, S. Jia, T. Liu, Y. Wang, J. Guo, Q. Yang, G. Kang, Proteomics Analysis Reveals That Nitric Oxide Regulates Photosynthesis of Maize Seedlings under Water Deficiency, Nitric Oxide, 2018.
8 citations
J. Yang, C. E. Yeh, R. K. Ramamurthy, X. Qi, R. L. Fernando, J. C.M. DekkersD. J. Garrick, D. Nettleton and P. S. Schnable, Empirical Comparisons of Different Statistical Models to Identify and Validate Kernel Row Number-Associated Variants from Structured Multiparent Mapping Populations of Maize, G3: Genes Genomes Genetics, 2018.
Github | Figshare | 16 citations
Z. Liang, S. K. Gupta, C. T. Yeh, Y. Zhang, D. W. Ngu, R. Kumar, H. T. Patil, K. D. Mungra, D. V. Yadav, A. Rathore, R. K. Srivastava, R. Gupkta, J. Yang, R. K. Varshney, P. S. Schnable, J. C. Schnable, Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids, G3: Genes Genomes Genetics, 2018.
55 citations
C. Miao, J. Fang, D. Li, P. Liang, X. Zhang, J. Yang, J. C. Schnable, H. Tang, Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations, Scientific Reports, 2018.
Github | 28 citations
M. Bezrutczyk, T. Hartwig, M. Horschman, S. N. Char, J. Yang, B. Yang, D. Sosso, W. Frommer, Impaired phloem loading in genome-edited triple knock-out mutants of SWEET13 sucrose transporters, New Phytologist, 2018.
Preprint | 150 citations
P. Bilinski, P. S. Albert, J. J. Berg, J. A. Birchler, M. N. Grote, A. Lorant, J. Quezada, K. Swarts, J. Yang, J. Ross-Ibarra, Parallel altitudinal clines reveal adaptive evolution of genome size in Zea mays, PLOS Genetics, 2018.
Preprint | Github | 133 citations
H.-Y. Lin, Q. Liu, X. Li, J. Yang, S. Liu, Y. Huang, M. J. Scanlon, D. Nettleton, P. S. Schnable, Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS, Genome Biology, 2017.
61 citations
J. Yang, S. Mezmouk, A. Baumgarten, E. S. Buckler, K. E. Guill, M. D. McMullen, R. H. Mumm, J. Ross-Ibarra, Incomplete dominance of deleterious alleles contribute substantially to trait variation and heterosis in maize, PLOS Genetics, 2017.
Preprint | Github | 148 citations
Z. Dong, W. Li, E. Unger-Wallace, J. Yang, E. Vollbrecht, G. S. Chuck., Ideal crop plant architecture is mediated by tassels replace upper ears1, a BTB/POZ ankyrin repeat gene 5 targeted by TEOSINTE BRANCHED1, PNAS, 2017.
96 citations
J. Hao, J. Yang, J. Dong, S-Z. Fei, Characterization of BdCBF genes and Genome-wide Transcriptome Profiling of BdCBF3-dependent and -independent Cold Stress Responses in Brachypodium Distachyon, Plant Science, 2017.
19 citations
J. Yang, H. Jiang, C. T. Yeh, J. Yu, J. A. Jeddeloh, D. Nettleton, and P. S. Schnable, 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, 2015.
Github | 119 citations
D. Sosso, D. Luo, Q. Li, J. Sasse, J. Yang, G. Gendrot, M. Suzuki, K. E. Koch, D. R. McCarty, P. S. Chourey, P. M. Rogowsky, J. Ross-Ibarra, B. Yang, and W. B. Frommer, Seed filling in domesticated maize and rice depends on SWEET-mediated hexose transport, Nature Genetics, 2015.
427 citations
S. Leiboff, X. Li, H.-C. Hu, N. Todt, J. Yang, X. Li, X. Yu, G. J. Muehlbauer, M. C. P. Timmermans, J. Yu, P. S. Schnable, and M. J. Scanlon, Genetic control of morphometric diversity in the maize shoot apical meristem, Nature Communications, 2015.
104 citations
S. Liu, K. Ying, C.-T. Yeh, J. Yang, R. Swanson-Wagner, W. Wu, T. Richmond, D. J. Gerhardt, J. Lai, N. Springer, D. Nettleton, J. A. Jeddeloh, and P. S. Schnable, Changes in genome content generated via segregation of non-allelic homolog, The Plant Journal, 2012.
29 citations
L. Koesterke, D. Stanzione, M. Vaughn, S. M. Welch, W. Kusnierczyk, J. Yang, C.-T. Yeh, D. Nettleton, and P. S. Schnable, An Efficient and Scalable Implementation of SNP-Pair Interaction Testing for Genetic Association Studies, 2011 IEEE Int. Symp. Parallel Distrib. Process. Work. Phd Forum, pp. 523–530, May 2011.
9 citations
P. S. Schnable, A. OTT, J. Yang, Intercrossed ex-PVP lines. 2014. PENDING.
P. S. Schnable, J. Yang, Identification of QTLs and trait-associated SNPs controlling six yield component traits in maize. 2013. PENDING.
P. S. Schnable, J. Yang, R. A. Swanson-Wagner, D. Nettleton, QTL regulating ear productivity traits in maize. U.S. Patent No. US8779233B1. granted July 15, 2014.