For the complete list, see google scholar (# equal contribution; * corresponding author).
Harnessing enviromics to predict climate-impacted high-profile traits to assist informed decisions in agriculture
Bosen Zhang, Amber L. Hauvermale, Zhiwu Zhang, Alison Thompson, Clark Neely, Aaron Esser, Michael Pumphrey, Kimberly Garland-Campbell, Jianming Yu, Camille Steber*, Xianran Li*
Food and Energy Security, 2024. (Article)
Evolutionary patterns of barley and rice genomes highlight the role of the environment in shaping the genome
Xiangjian Gou, Yang Shao, Haoran Shi, Jianming Yu, Xianran Li*, Tingting Guo*
Plant Genome, 2024. (Article)
Novel allelic variations in Tannin1 and Tannin2 contribute to tannin absence in sorghum
Wenbin Zhang, Ryan Benke, Xiao Zhang, Huawen Zhang, Cunyuan Zhao, Yu Zhao, Ying Xu, Hailian Wang, Shubing Liu, Xianran Li*, Yuye Wu*
Molecular Breeding, 2024. (Article)
Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa
Fan Zhang,Ruicai Long,Zhiyao Ma,Hua Xiao,Xiaodong Xu,Zhongjie Liu,Chunxue Wei,Yiwen Wang,Yanling Peng,Xuanwen Yang,Xiaoya Shi,Shuo Cao,Mingna Li,Ming Xu,Fei He,Xueqian Jiang,Tiejun Zhang,Zhen Wang,Xianran Li,Long-Xi Yu,Junmei Kang,Zhiwu Zhang,Yongfeng Zhou,Qingchuan Yang
Molecular Plant, 2024 (Article)
The role of artificial intelligence in crop improvement
Karlene Negus, Xianran Li, Stephen Welch, and Jianming Yu
Advances in Agronomy, 2024. (Book Chapter)
Environmental context of phenotypic plasticity in flowering time in sorghum and rice
Tingting Guo, Jialu Wei, Xianran Li, and Jianming Yu
Journal of Experimental Botany, 2023. (Article)
Streamline unsupervised machine learning to survey and graph indel-based haplotypes from pan-genomes
Bosen Zhang, Haiyan Huang, Laura E. Tibbs-Cortes, Adam Vanous, View ORCID ProfileZhiwu Zhang, Karen Sanguinet, Kimberly A. Garland-Campbell, Jianming Yu, Xianran Li*
Molecular Plant, 2023 (Article)
(BRIDGEcereal webapp)
(Press release by USDA ARS BRIDGEcereal: Self-Teaching Web App Improves Speed, Accuracy of Classifying DNA Variations Among Cereal Varieties)
Machine learning for predicting phenotype from genotype and environment
Tingting Guo*, Xianran Li*
Current Opinion in Biotechnology, 2023 (Review)
(Propose to expand the pan-genome concept into pan-phenome and pan-envirome)
Affordable High Throughput Field Detection of Wheat Stripe Rust Using Deep Learning with Semi-Automated Image Labeling
Zhou Tang, Meinan Wang, Michael Schirrmann, Karl-Heinz Dammer, Xianran Li, Robert Brueggeman, Sindhuja Sankaran, Arron H. Carter, Michael O. Pumphrey, Yang Hu, Xianming Chen, Zhiwu Zhang
Computers and Electronics in Agriculture, 2023 (Article)
Genetics-inspired data-driven approaches explain and predict crop performance fluctuations attributed to changing climatic conditions
Xianran Li*, Tingting Guo, Guihua Bai, Zhiwu Zhang, Juliet Marshall, Kimberly A. Garland-Campbell, Jianming Yu
Molecular Plant, 2022 (Article)
(Highlighted by a Spotlight Prediction of and for new environments: what’s your model?)
(Press release by USDA ARS Tellus Quantifying the Impact of Changing Climate Conditions on Elite Wheat Variety Performance)
Phenotypic plasticity in plant height shaped by interaction between genetic loci and diurnal temperature range
Qi Mu, Tingting Guo, Xianran Li*, Jianming Yu*
New Phytologist, 2022 (Article)
(News Press Under the hood: How environment and genomes interact in plant development)
Unraveling the sorghum domestication
Xianran Li and Jianming Yu
Molecular Plant, 2022 (Spotlight)
A integrated framework reinstating the environmental dimension for genome-wide association studies and genomic selection for crops
Xianran Li#, Tingting Guo#, Jinyu Wang Wubishet Bekele, Sivakumar Sukumaran, Adam E. Vanous, James P. McNellie, Laura Cortes, Marta Lopes, Kendall Lamkey, Mark Westgate, John McKay, Sotirios Archontoulis, Matthew Reynolds, Nicholas Tinker, Patrick Schnable, Jianming Yu
Molecular Plant, 2021 (Article)
(Highlighted by a Spotlight Prediction of and for new environments: what’s your model?)
Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize
Matthew Dzievit, Tingting Guo, Xianran Li, Jianming Yu
Plant Genome, 2021 (Article)
Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping
Jinyu Wang, Tingting Guo, Xianran Li, Jianming Yu
Plant Genome, 2021 (Article)
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I. Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H. O’Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia V. Krasileva, John L. Portwood II, Ethalinda K. S. Cannon, Carson M. Andorf, Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I. Gent, Candice N. Hirsch, Doreen Ware, R. Kelly Dawe.
Science, 2021 (Article)
High-efficiency plastome base-editing in rice with TAL cytosine deaminase
Riqing Li, Si Nian Char, Bo Liu, Hua Liu, Xianran Li, Bing Yang
Molecular Plant, 2021 (Article)
Retrofitting elites with ancestral alleles with different plasticity for sustainable agriculture
Xianran Li, Jianming Yu
Sci China Life Sci, 2021 (Research Highlight)
Dynamic effects of interacting genes underlying rice flowering-time phenotypic plasticity and global adaptation
Tingting Guo, Qi Mu, Jinyu Wang, Adam Vanous, Xianran Li*, and Jianming Yu*
Genome Research, 2020 (Article)
Peanut FAD2 genotype and growing location interactions significantly affect seed fatty acid composition
Brandon Tonnis, Ming Li Wang, Xianran Li, Jianping Wang, Naveen Puppala, Shyam Tallury, Jianming Yu
Journal of the American Oil Chemists’ Society, 2020
An Agrobacterium-delivered CRISPR/Cas9 system for targeted mutagenesis in sorghum
Si Nian Char, Jialu Wei, Qi Mu, Xianran Li, Zhuanyuan Zhang, Keith Edwards, Jianming Yu, Bing Yang
Plant Biotechnology Journal, 2020 (Article)
Genomic prediction of maize micro-phenotypes provides insights for optimizing selection and mining diversity
Xiaoqing Yu, Samuel Leiboff, Xianran Li, Tingting Guo, Natalie Ronning, Xiaoyu Zhang, Gary Muehlbauer, Marja Timmermans, Patrick Schnable, Michael Scanlon, Jianming Yu
Plant Biotechnology Journal, 2020 (Article)
A large transposon insertion in the Stiff1 promoter controls stalk strength in maize
Zhihai Zhang, Xuan Zhang, Zhelong Lin, Jian Wang, Hangqiu Liu, Leina Zhou, Shuyang Zhong Yan Li Can Zhu, Jinsheng Lai, Xianran Li, Jianming Yu, Zhongwei Lin
Plant Cell, 2020 (Article)
Allelochemicals targeted to balance competing selections in African agroecosystems
Yuyue Wu, Tingting Guo, Qi Mu, Jinyu Wang, Xin Li, Yun Wu, Bin Tian, Ming Li Wang, Guihua Bai, Ramasamy Perumal, Harold Trick, Scott Bean, Ismail Dweikat, Mitchell Tuinstra, Geoffrey Morris, Tesfaye Tesso, Jianming Yu*, Xianran Li*
Nature Plants, 2019 (Article)
(Highlighted by News & Views When bitter is better; Recommended in Faculty Opinions F1000)
Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean
Jinyu Wang, Xianran Li*, Kyung Do Kim, Michael Scanlon, Scott Jackson, Nathan Springer, Jianming Yu*
Genome Biology, 2019 (Article)
Optimal designs for genomic prediction in hybrid crops
Tingting Guo, Xiaoqin Yu, Xianran Li, Haozhe Zhang, Chengsong Zhu, Sherry Flint-Garcia, Michael McMullen, James Holland, Randall Wisser, Jianming Yu
Molecular Plant, 2019 (Article)
A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
Steffen Knauer, Marie Javelle, Lin Li, Xianran Li, Xiaoli Ma, Kokulapalan Wimalanathan, Sunita Kumari, Robyn Johnston, Samuel Leiboff, Robert Meeley, Patrick Schnable, Doreen Ware, Carolyn Lawrence-Dill, Jianming Yu, Gary Meuhlbauer, Michael Scanlon, Marja Timmermans
Genome Research, 2019 (Article)
Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice
Yongzhen Wu#, Shuangshuang Zhao#, Xianran Li#, Bosen Zhang, Liyun Jiang, Yanyan Tang, Jie Zhao, Xin Ma, Hongwei Cai, Chuanqing Sun, Lubin Tan
Nature Communications, 2018 (Article)
Genomic and environmental determinants and their interplay underlying phenotypic plasticity
Xin Li, Tingting Guo, Qi Mu, Xianran Li*, Jianming Yu*
PNAS, 2018 (Article)
Stability analysis of kernel quality traits in exotic derived maize doubled haploid lines
Adam Vanous, Candice Gardner, Michael Blanco, Adam Martin-Schwarze, Jinyu Wang, Xianran Li, Alexander Lipka, Sherry Flint-Garcia, Martin Bohn, Jode Edwards, Thomas Lübberstedt
Plant Genome, 2018 (Article)
Dissection of leaf angle variation in maize through genetic mapping and meta-analysis
Matthew Dzievit, Xianran Li, Jianming Yu
Plant Genome, 2018 (Article)
Genetic mapping of foliar and tassel heat stress tolerance in field grown maize
James McNellie, Junping Chen, Xianran Li, Jianming Yu
Crop Science, 2018 (Article)