Publications

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. Brief Bioinform.

Code Project DOI PubMed

Beilei Lei, Minggui Song, Xiyang Li, Xiaoxue Dang, Runwen Qin, Shuai Zhu, XiaoyanAn, Qinchang Liu, Xiaojun Yao, Yanming Nie, Chuang Ma (2021). SMART v1.0: A Database for Small Molecules with Functional Implications in Plants. Interdiscip Sci.

Project DOI PubMed

Zhenyan Miao, Ting Zhang, Bin Xie, Yuhong Qi, Chuang Ma (2021). Evolutionary implications of the RNA N6-methyladenosine methylome in plants. Mol. Biol. Evol.

Code DOI PubMed

Ting Zhang, Jingjing Zhai, Xiaorong Zhang, Lei Ling, Menghan Li, Shang Xie, Chuang Ma (2021). Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA. Genomics Proteomics Bioinformatics.

Code Project DOI PubMed

Jingjing Zhai, Jie Song, Ting Zhang, Shang Xie, Chuang Ma (2020). deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data. Plant Physiol.

Code Project DOI PubMed

Zhixu Qiu, Siyuan Chen, Yuhong Qi, Chunni Liu, Jingjing Zhai, Shang Xie, Chuang Ma (2020). Exploring transcriptional switches from pairwise, temporal, and population RNA-Seq data using deepTS. Brief Bioinform.

Code Project DOI PubMed

Zhenyan Miao, Ting Zhang, Yuhong Qi, Jie Song, Zhaoxue Han, Chuang Ma (2019). Evolution of the RNA N6-methyladenosine methylome mediated by genomic duplication. Plant Physiol.

Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jiantao Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma (2019). CAFU: a Galaxy framework for exploring unmapped RNA-Seq data. Brief Bioinform.

Code Project DOI PubMed

Ting Zhang, Lie Ju, Jingjing Zhai, Yujia Song, Jie Song, Chuang Ma (2019). miRLocator: A Python Implementation and Web Server for Predicting miRNAs from Pre-miRNA Sequences. Plant MicroRNAs.

Code DOI Springer

Xiaoming Wang, Siyuan Chen, Xue Shi, Danni Liu, Peng Zhao, Yunze Lu, Yanbing Cheng, Zhenshan Liu, Xiaojun Nie, Weining Song, Qixin Sun, Shengbao Xu, Chuang Ma (2019). Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat. Plant J.

Xiaoxue Dang, Zheng Liu, Yanzhuo Zhou, Peizi Chen, Jiyuan Liu, Xiaojun Yao, Beilei Lei (2018). Steroids-specific target library for steroids target prediction. Steroids.

Wenlong Ma, Zhixu Qiu, Jie Song, Jiajia Li, Qian Cheng, Jingjing Zhai, Chuang Ma (2018). A deep convolutional neural network approach for predicting phenotypes from genotypes. Planta.

Code DOI PubMed

Jingjing Zhai, Song Jie, Qian Cheng, Yunjia Tang, Chuang Ma (2018). PEA: an Integrated R Toolkit for Plant Epitranscriptome Analysis. Bioinformatics.

Code DOI PubMed

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.

Zhaoxue Han, Peter A. Crisp, Scott Stelpflug, Shawn M. Kaeppler, Qing Li, Nathan M. Springer (2018). Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture. Genetics.

Song Jie, Jingjing Zhai, Bian Enze, Yujia Song, Jiantao Yu, Chuang Ma (2018). Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning. Front Plant Sci.

Code DOI PubMed

Junfeng Tan, Zhenyan Miao, Chengzhi Ren, Ruxia Yuan, Yunjia Tang, Xiaorong Zhang, Zhaoxue Han, Chuang Ma (2018). Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47. Planta.

Xiaoming Wang, Xue Shi, Siyuan Chen, Chuang Ma, Shengbao Xu (2018). Evolutionary Origin, Gradual Accumulation and Functional Divergence of Heat Shock Factor Gene Family with Plant Evolution. Front Plant Sci.

Zhenyan Miao, Zhaoxue Han, Ting Zhang, Siyuan Chen, Chuang Ma (2017). A systems approach to a spatio-temporal understanding of the drought stress response in maize. Sci Rep.

Zhixu Qiu, Yunjia Tang, Chuang Ma (2017). An Effective Strategy for Trait Combinations in Multiple-Trait Genomic Selection. ICIC.

Xiaoming Wang, Ruochen Wang, Chuang Ma, Xue Shi, Zhenshan Liu, Zhonghua Wang, Qixin Sun, Jun Cao, Shengbao Xu (2017). Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization. Sci Rep.

Jingjing Zhai, Yunjia Tang, Hao Yuan, Longteng Wang, Haoli Shang, Chuang Ma (2016). A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function. Front Plant Sci.

Code DOI PubMed

Jianzhou Qu, Chuang Ma, Jiaojiao Feng, Shutu Xu, Lei Wang, Feifei Li, Yibo Li, Renhe Zhang, Xinghua Zhang, Jiquan Xue, Dongwei Guo (2016). Transcriptome Dynamics during Maize Endosperm Development. PLoS One.

Zhixu Qiu, Qian Cheng, Jie Song, Yunjia Tang, Chuang Ma (2016). Application of Machine Learning-Based Classification to Genomic Selection and Performance Improvement. ICIC.

Haibo Cui, Jingjing Zhai, Chuang Ma (2015). miRLocator: Machine Learning-Based Prediction of Mature MicroRNAs within Plant Pre-miRNA Sequences. PLoS One.

Code Project DOI PubMed

Pan Zhu, Yanhong Zhou, Libin Zhang, Chuang Ma (2015). DNA sequence and structure properties analysis reveals similarities and differences to promoters of stress responsive genes in Arabidopsis thaliana. Int J Data Min Bioinform.

Junpeng Zhan, Dhiraj Thakare, Chuang Ma, Alan Lloyd, Neesha M. Nixon, 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 Plant Sci.

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.

Code DOI PubMed

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.

Chuang Ma, Xiangfeng Wang (2012). Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis. Plant Physiol.

Code DOI PubMed

Chuang Ma, Hao Chen, Mingming Xin, Ruolin Yang, Xiangfeng Wang (2012). KGBassembler: A Karyotype-based Genome Assembler for Brassicaceae Species. Bioinformatics.