Publications

Feng Xu, Tianhao Wu, Qian Cheng, Xiangfeng Wang, Jun Yan (2025). Foundation models in plant molecular biology: advances, challenges, and future directions. Frontiers in Plant Science.

Feng Xu, Qian Cheng, Songyu Liu, Shuqin Jiang, Jianan Zhang, Xiaowei Mao, Xiangfeng Wang, Jinsheng Lai, Jun Yan (2025). MRBIGR: A versatile toolbox for genetic regulation inference from population-scale multi-omics data. Plant Communications.

Qian Cheng, Xiangfeng Wang (2024). Machine Learning for AI Breeding in Plants. Genomics, Proteomics & Bioinformatics.

Feng Xu, Songyu Liu, Anwen Zhao, Meiqi Shang, Qian Wang, Shuqin Jiang, Qian Cheng, Xingming Chen, Xiaoguang Zhai, Jianan Zhang, Xiangfeng Wang, Jun Yan (2024). iFLAS: positive-unlabeled learning facilitates full-length transcriptome-based identification and functional exploration of alternatively spliced isoforms in maize. New Phytologist.

Qian Wang, Shan Jiang, Tong Li, Zhixu Qiu, Jun Yan, Ran Fu, Chuang Ma, Xiangfeng Wang, Shuqin Jiang, Qian Cheng (2023). G2P Provides an Integrative Environment for Multi-model genomic selection analysis to improve genotype-to-phenotype prediction. Frontiers in Plant Science.

Ran Fu, Xiangfeng Wang (2023). Modeling the influence of phenotypic plasticity on maize hybrid performance. Plant Communications.

Tong Li, Shan Jiang, Ran Fu, Xiangfeng Wang, Qian Cheng, Shuqin Jiang (2023). IP4GS:Bringing genomic selection analysis to breedersBringing genomic selection analysis to breeders. Plant J.

Jun Yan, Xiangfeng Wang (2022). Machine learning bridges omics sciences and plant breeding. Trends in Plant Science.

Jun Yan, Xiangfeng Wang (2022). Unsupervised and semi-supervised learning: the next frontier in machine learning for plant systems biology. The Plant Journal.

Songyu Liu, Feng Xu, Yuetong Xu, Qian Wang, Jun Yan, Jinyu Wang, Xianbing Wang, Xiangfeng Wang (2022). MODAS: exploring maize germplasm with multi-omics data association studies. Science Bulletin.

Matthew McGowan, Jiabo Wang, Haixiao Dong, Xiaolei Liu, Yi Jia, Xiangfeng Wang, Hiroyoshi Iwata, Yutao Li, Alexander E. Lipka, Zhiwu Zhang (2021). Ideas in Genomic Selection with the Potential to Transform Plant Molecular Breeding: A Review. Plant Breeding Reviews.

Qian Cheng, Shuqing Jiang, Feng Xu, Qian Wang, Yingjie Xiao, Ruyang Zhang, Jiuran Zhao, Jianbing Yan, Chuang Ma, Xiangfeng Wang (2021). Genome optimization via virtual simulation to accelerate maize hybrid breeding. Briefings in Bioinformatics.

Yuetong Xu, John D. Laurie, Xiangfeng Wang (2021). CropGBM: An Ultra-Efficient Machine Learning Toolbox for Genomic Selection-Assisted Breeding in Crops. Springer Protocols Handbooks.

Jun Yan, Yuetong Xu, Qian Cheng, Shuqin Jiang, Qian Wang, Yingjie Xiao, Chuang Ma, Jianbing Yan, Xiangfeng Wang (2021). LightGBM: accelerated genomically designed crop breeding through ensemble learning. Genome Biol.

Fengchao Cui, Geli Taier, Manli Li, Xiaoxia Dai, Nan Hang, Xunzhong Zhang, Xiangfeng Wang, Kehua Wang (2021). The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis). Hortic Res.

Xiaoyan Liang, Songyu Liu, Tao Wang, Fenrong Li, Jinkui Cheng, Jinsheng Lai, Feng Qin, Zhen Li, Xiangfeng Wang, Caifu Jiang (2021). Metabolomics-driven gene mining and genetic improvement of tolerance to salt-induced osmotic stress in maize. New Phytol.

Chunming Yang, Jun Yan, Shuqin Jiang, Xia Li, Haowei Min, Xiangfeng Wang, Dongyun Hao (2021). Resequencing 250 soybean accessions: new insights into genes associated with agronomic traits and genetic networks. Genomics, Proteomics & Bioinformatics.

Shi-Jian Zhang, Lei Liu, Ruolin Yang, Xiangfeng Wang (2020). Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae. Genomics, Proteomics & Bioinformatics.

Jun Yan, Dong Zou, Chen Li, Zhang Zhang, Shuhui Song, Xiangfeng Wang (2020). SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice. Genomics, Proteomics & Bioinformatics.

Zhipeng Zhou, Guoliang Li, Siyu Tan, Dongdong Li, Thea Mi Weiß, Xiangfeng Wang, Shaojiang Chen, Tobias Würschum, Wenxin Liu (2020). A QTL atlas for grain yield and its component traits in maize ( Zea mays ). Plant Breed.

Huan Zhang, Qian Zhang, Hong Zhai, Shaopei Gao, Li Yang, Zhen Wang, Yuetong Xu, Jinxi Huo, Zhitong Ren, Ning Zhao, Xiangfeng Wang, Jigang Li, Qingchang Liu, Shaozhen He (2020). IbBBX24 Promotes the Jasmonic Acid Pathway and Enhances Fusarium Wilt Resistance in Sweet Potato. Plant Cell.

Zechuan Lin, Peng Qin, Xuanwen Zhang, Chenjian Fu, Hanchao Deng, Xingxue Fu, Zhen Huang, Shuqin Jiang, Chen Li, Xiaoyan Tang, Xiangfeng Wang, Guangming He, Yuanzhu Yang, Hang He, Xing Wang Deng (2020). Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice. Proc Natl Acad Sci USA.

Hong Li, Shuqin Jiang, Chen Li, Lei Liu, Zechuan Lin, Hang He, Xing Wang Deng, Ziding Zhang, Xiangfeng Wang (2019). The hybrid protein interactome contributes to rice heterosis as epistatic effects. Plant J.

Shuqin Jiang, Qian Cheng, Jun Yan, Ran Fu, Xiangfeng Wang (2019). Genome optimization for improvement of maize breeding. Theor Appl Genet.

Peng Liang, Songyu Liu, Feng Xu, Shuqin Jiang, Jun Yan, Qiguang He, Wenbo Liu, Chunhua Lin, Fucong Zheng, Xiangfeng Wang, Weiguo Miao (2019). Corrigendum: Powdery Mildews Are Characterized by Contracted Carbohydrate Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic Lifestyle. Front. Microbiol..

Peng Liang, Songyu Liu, Feng Xu, Shuqin Jiang, Jun Yan, Qiguang He, Wenbo Liu, Chunhua Lin, Fucong Zheng, Xiangfeng Wang, Weiguo Miao (2018). Powdery Mildews Are Characterized by Contracted Carbohydrate Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic Lifestyle. Front. Microbiol..

Shi-Jian Zhang, Peiqi Meng, Jieni Zhang, Peizeng Jia, Jiuxiang Lin, Xiangfeng Wang, Feng Chen, Xiaoxing Wei (2018). Machine Learning Models for Genetic Risk Assessment of Infants with Non-syndromic Orofacial Cleft. Genomics, Proteomics & Bioinformatics.

Junpeng Zhan, Guosheng Li, Choong-Hwan Ryu, Chuang Ma, Shanshan Zhang, Alan Lloyd, Brenda G. Hunter, Brian A. Larkins, Gary N. Drews, Xiangfeng Wang, Ramin Yadegari (2018). Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm. Plant Cell.

Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q Zhang, Xiangfeng Wang, Zhongfu Ni (2017). CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. Bioinformatics.

Yuange Wang, Haopeng Yu, Caihuan Tian, Muhammad Sajjad, Caixia Gao, Yiping Tong, Xiangfeng Wang, Yuling Jiao (2017). Transcriptome Association Identifies Regulators of Wheat Spike Architecture. Plant Physiol..

Shi-Jian Zhang, Chenqu Wang, Shouyu Yan, Aisi Fu, Xuke Luan, Yumei Li, Qing Sunny Shen, Xiaoming Zhong, Jia-Yu Chen, Xiangfeng Wang, Bertrand Chin-Ming Tan, Aibin He, Chuan-Yun Li (2017). Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events. Molecular Biology and Evolution.

Huan Zhang, Qian Zhang, Hong Zhai, Yan Li, Xiangfeng Wang, Qingchang Liu, Shaozhen He (2017). Transcript profile analysis reveals important roles of jasmonic acid signalling pathway in the response of sweet potato to salt stress. Sci Rep.

Jun Yan, Shuwei Lv, Min Hu, Zhaoxu Gao, Hang He, Qingwei Ma, Xing~Wang Deng, Zuofeng Zhu, Xiangfeng Wang (2016). Single-Molecule Sequencing Assists Genome Assembly Improvement and Structural Variation Inference. Molecular Plant.

Xuanli Yao, Herbert N. Arst, Xiangfeng Wang, Xin Xiang (2015). Discovery of a vezatin-like protein for dynein-mediated early endosome transport. MBoC.

(2015). Information Commons for Rice (IC4R). Nucleic Acids Res.

Mingming Xin, Guanghui Yang, Yingyin Yao, Huiru Peng, Zhaorong Hu, Qixin Sun, Xiangfeng Wang, Zhongfu Ni (2015). Temporal small RNA transcriptome profiling unraveled partitioned miRNA expression in developing maize endosperms between reciprocal crosses. Front. Plant Sci..

Junpeng Zhan, Dhiraj Thakare, Chuang Ma, Alan Lloyd, Neesha M. Nixon, Angela M. Arakaki, William J. Burnett, Kyle O. Logan, Dongfang Wang, Xiangfeng Wang, Gary N. Drews, Ramin Yadegari (2015). RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation. Plant Cell.

Chuang Ma, Hao Helen Zhang, Xiangfeng Wang (2014). Machine learning for Big Data analytics in plants. Trends in Plant Science.

Mingming Xin, Ruolin Yang, Yingyin Yao, Chuang Ma, Huiru Peng, Qixin Sun, Xiangfeng Wang, Zhongfu Ni (2014). Dynamic parent-of-origin effects on small interfering RNA expression in the developing maize endosperm. BMC Plant Biol.

G. Li, D. Wang, R. Yang, K. Logan, H. Chen, S. Zhang, M. I. Skaggs, A. Lloyd, W. J. Burnett, J. D. Laurie, B. G. Hunter, J. M. Dannenhoffer, B. A. Larkins, G. N. Drews, X. Wang, R. Yadegari (2014). Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing. Proceedings of the National Academy of Sciences.

Chuang Ma, Mingming Xin, Kenneth A. Feldmann, Xiangfeng Wang (2014). Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis. Plant Cell.

Yuliang Zhang, Naitong Yu, Qixing Huang, Guohua Yin, Anping Guo, Xiangfeng Wang, Zhongguo Xiong, Zhixin Liu (2014). Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing. Virus Genes.

Mingming Xin, Ruolin Yang, Guosheng Li, Hao Chen, John Laurie, Chuang Ma, Dongfang Wang, Yingyin Yao, Brian A. Larkins, Qixin Sun, Ramin Yadegari, Xiangfeng Wang, Zhongfu Ni (2013). Dynamic Expression of Imprinted Genes Associates with Maternally Controlled Nutrient Allocation during Maize Endosperm Development. Plant Cell.

Xiaoxing Wei, Xiangfeng Wang (2013). A Computational Workflow to Identify Allele-specific Expression and Epigenetic Modification in Maize. Genomics, Proteomics & Bioinformatics.

Hao Chen, Xiangfeng Wang (2013). CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species. Plant Physiol..

Ruolin Yang, David E. Jarvis, Hao Chen, Mark A. Beilstein, Jane Grimwood, Jerry Jenkins, ShengQiang Shu, Simon Prochnik, Mingming Xin, Chuang Ma, Jeremy Schmutz, Rod A. Wing, Thomas Mitchell-Olds, Karen S. Schumaker, Xiangfeng Wang (2013). The Reference Genome of the Halophytic Plant Eutrema salsugineum. Front. Plant Sci..

Ruolin Yang, Xiangfeng Wang (2013). Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns. The Plant Cell.

C. Ma, H. Chen, M. Xin, R. Yang, X. Wang (2012). KGBassembler: a karyotype-based genome assembler for Brassicaceae species. Bioinformatics.

Mingming Xin, Xiangfeng Wang, Huiru Peng, Yingyin Yao, Chaojie Xie, Yao Han, Zhongfu Ni, Qixin Sun (2012). Transcriptome Comparison of Susceptible and Resistant Wheat in Response to Powdery Mildew Infection. Genomics, Proteomics & Bioinformatics.

Xiangfeng Wang, John D. Laurie, Tao Liu, Jacqueline Wentz, X. Shirley Liu (2011). Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. Genomics.

Xiangfeng Wang, X. Shirley Liu (2011). Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila. Front. Gene..

Huiyong Zhang, Hang He, Xuncheng Wang, Xiangfeng Wang, Xiaozeng Yang, Lei Li, Xing W. Deng (2010). Genome-wide mapping of the HY5-mediated genenetworks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. The Plant Journal.

Hang He, Huiyong Zhang, Xiangfeng Wang, Nicholas Wu, Xiaozeng Yang, Runsheng Chen, Yi Li, Xing Wang Deng, Lei Li (2010). Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. Genomics.

Guangming He, Xiaopeng Zhu, Axel A. Elling, Liangbi Chen, Xiangfeng Wang, Lan Guo, Manzhong Liang, Hang He, Huiyong Zhang, Fangfang Chen, Yijun Qi, Runsheng Chen, Xing Wang Deng (2010). Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids. The Plant Cell.

Junli Zhou, Xiangfeng Wang, Kun He, Jean-Benoit F. Charron, Axel A. Elling, Xing Wang Deng (2010). Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. Plant Mol Biol.

Xiangfeng Wang, Axel A. Elling, Xueyong Li, Ning Li, Zhiyu Peng, Guangming He, Hui Sun, Yijun Qi, X. Shirley Liu, Xing Wang Deng (2009). Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize. The Plant Cell.

Xiangfeng Wang, Zhihui Yu, Xiaozeng Yang, Xing Wang Deng, Lei Li (2009). Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. Bioinformatics.

Zhi-Yu Peng, Huiyong Zhang, Tingting Liu, Katherine M. Dzikiewicz, Songgang Li, Xiangfeng Wang, Guocheng Hu, Zhengge Zhu, Xinghua Wei, Qi-Hui Zhu, Zongxiu Sun, Song Ge, Ligeng Ma, Lei Li, Xing Wang Deng (2009). Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. Genomics.

Ben-Liang Yin, Lan Guo, Dong-Fen Zhang, William Terzaghi, Xiang-Feng Wang, Ting-Ting Liu, Hang He, Zhu-Kuan Cheng, Xing Wang Deng (2008). Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4. Molecular Plant.

Hui-Yong Zhang, Hang He, Liang-Bi Chen, Lei Li, Man-Zhong Liang, Xiang-Feng Wang, Xi-Gang Liu, Guang-Ming He, Run-Sheng Chen, Li-Geng Ma, Xing Wang Deng (2008). A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids. Molecular Plant.

Xueyong Li, Xiangfeng Wang, Kun He, Yeqin Ma, Ning Su, Hang He, Viktor Stolc, Waraporn Tongprasit, Weiwei Jin, Jiming Jiang, William Terzaghi, Songgang Li, Xing Wang Deng (2008). High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression. The Plant Cell.

Lei Li, Hang He, Juan Zhang, Xiangfeng Wang, Sulan Bai, Viktor Stolc, Waraporn Tongprasit, Nevin D Young, Oliver Yu, Xing Wang Deng (2008). Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol.

Lei Li, Xiangfeng Wang, Rajkumar Sasidharan, Viktor Stolc, Wei Deng, Hang He, Jan Korbel, Xuewei Chen, Waraporn Tongprasit, Pamela Ronald, Runsheng Chen, Mark Gerstein, Xing Wang Deng (2007). Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome. PLoS ONE.

Junli Zhou, Xiangfeng Wang, Yuling Jiao, Yonghua Qin, Xigang Liu, Kun He, Chen Chen, Ligeng Ma, Jian Wang, Lizhong Xiong, Qifa Zhang, Liumin Fan, Xing Wang Deng (2007). Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol.

X. Wang, H. He, L. Li, R. Chen, X. W. Deng, S. Li (2006). NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics.

Lei Li, Xiangfeng Wang, Viktor Stolc, Xueyong Li, Dongfen Zhang, Ning Su, Waraporn Tongprasit, Songgang Li, Zhukuan Cheng, Jun Wang, Xing Wang Deng (2005). Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet.

Viktor Stolc, Lei Li, Xiangfeng Wang, Xueyong Li, Ning Su, Waraporn Tongprasit, Bin Han, Yongbiao Xue, Jiayang Li, Michael Snyder, Mark Gerstein, Jun Wang, Xing Wang Deng (2005). A Pilot Study of Transcription Unit Analysis in Rice Using Oligonucleotide Tiling-path Microarray. Plant Mol Biol.

L. Ma (2005). A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Research.

Yuling Jiao, Peixin Jia, Xiangfeng Wang, Ning Su, Shuliang Yu, Dongfen Zhang, Ligeng Ma, Qi Feng, Zhaoqing Jin, Lei Li, Yongbiao Xue, Zhukuan Cheng, Hongyu Zhao, Bin Han, Xing Wang Deng (2005). A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription. The Plant Cell.

Lei Li, Xiangfeng Wang, Mian Xia, Viktor Stolc, Ning Su, Zhiyu Peng, Songgang Li, Jun Wang, Xiping Wang, Xing Deng (2005). Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol.