Publications

Dual-Extraction Modeling: A multimodal deep learning architecture for phenotypic prediction and functional gene mining of complex traits

Yanlin Ren, Chenhua Wu, He Zhou, Xiaona Hu, Zhenyan Miao

PDF Code DOI PubMed

PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants

Minggui Song, Jiawen Zhao, Chujun Zhang, Chengchao Jia, Jing Yang, Haonan Zhao, Jingjing Zhai, Beilei Lei, Shiheng Tao, Siqi Chen, Ran Su, Chuang Ma

PDF Code DOI PubMed

IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study

Wenyue Huang, Xiaona Hu, Yanlin Ren, Minggui Song, Chuang Ma, Zhenyan Miao

Project DOI PubMed

Changes in m6A RNA methylation are associated with male sterility in wolfberry

Jiawen Zhao, Chujun Zhang, Sifan Li, Mengmeng Yuan, Wenlan Mu, Jing Yang, Yutong Ma, Cuiping Guan, Chuang Ma

DOI PubMed

easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data

Wenlong Ma, Siyuan Chen, Yuhong Qi, Minggui Song, Jingjing Zhai, Ting Zhang, Shang Xie, Guifeng Wang, Chuang Ma

PDF Code DOI PubMed

Genome optimization via virtual simulation to accelerate maize hybrid breeding

Qian Cheng, Shuqing Jiang, Feng Xu, Qian Wang, Yingjie Xiao, Ruyang Zhang, Jiuran Zhao, Jianbing Yan, Chuang Ma, Xiangfeng Wang

Code Project DOI PubMed

SMART v1.0: A Database for Small Molecules with Functional Implications in Plants

Beilei Lei, Minggui Song, Xiyang Li, Xiaoxue Dang, Runwen Qin, Shuai Zhu, XiaoyanAn, Qinchang Liu, Xiaojun Yao, Yanming Nie, Chuang Ma

Project DOI PubMed

Evolutionary implications of the RNA N6-methyladenosine methylome in plants

Zhenyan Miao, Ting Zhang, Bin Xie, Yuhong Qi, Chuang Ma

Code DOI PubMed

Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA

Ting Zhang, Jingjing Zhai, Xiaorong Zhang, Lei Ling, Menghan Li, Shang Xie, Chuang Ma

Code Project DOI PubMed

deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data

Jingjing Zhai, Jie Song, Ting Zhang, Shang Xie, Chuang Ma

Code Project DOI PubMed

Exploring transcriptional switches from pairwise, temporal, and population RNA-Seq data using deepTS

Zhixu Qiu, Siyuan Chen, Yuhong Qi, Chunni Liu, Jingjing Zhai, Shang Xie, Chuang Ma

Code Project DOI PubMed

Evolution of the RNA N6-methyladenosine methylome mediated by genomic duplication

Zhenyan Miao, Ting Zhang, Yuhong Qi, Jie Song, Zhaoxue Han, Chuang Ma

DOI PubMed

CAFU: a Galaxy framework for exploring unmapped RNA-Seq data

Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jiantao Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma

Code Project DOI PubMed

miRLocator: A Python Implementation and Web Server for Predicting miRNAs from Pre-miRNA Sequences

Ting Zhang, Lie Ju, Jingjing Zhai, Yujia Song, Jie Song, Chuang Ma

Code DOI Springer

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat

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

DOI PubMed

Steroids-specific target library for steroids target prediction

Xiaoxue Dang, Zheng Liu, Yanzhuo Zhou, Peizi Chen, Jiyuan Liu, Xiaojun Yao, Beilei Lei

DOI PubMed

A deep convolutional neural network approach for predicting phenotypes from genotypes

Wenlong Ma, Zhixu Qiu, Jie Song, Jiajia Li, Qian Cheng, Jingjing Zhai, Chuang Ma

Code DOI PubMed

PEA: an Integrated R Toolkit for Plant Epitranscriptome Analysis

Jingjing Zhai, Song Jie, Qian Cheng, Yunjia Tang, Chuang Ma

Code DOI PubMed

Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm

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

DOI PubMed

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

Zhaoxue Han, Peter A. Crisp, Scott Stelpflug, Shawn M. Kaeppler, Qing Li, Nathan M. Springer

DOI PubMed

Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning

Song Jie, Jingjing Zhai, Bian Enze, Yujia Song, Jiantao Yu, Chuang Ma

Code DOI PubMed

Evolution of intron-poor clades and expression patterns of the glycosyltransferase family 47

Junfeng Tan, Zhenyan Miao, Chengzhi Ren, Ruxia Yuan, Yunjia Tang, Xiaorong Zhang, Zhaoxue Han, Chuang Ma

DOI PubMed

Evolutionary Origin, Gradual Accumulation and Functional Divergence of Heat Shock Factor Gene Family with Plant Evolution

Xiaoming Wang, Xue Shi, Siyuan Chen, Chuang Ma, Shengbao Xu

DOI PubMed

A systems approach to a spatio-temporal understanding of the drought stress response in maize

Zhenyan Miao, Zhaoxue Han, Ting Zhang, Siyuan Chen, Chuang Ma

DOI PubMed

An Effective Strategy for Trait Combinations in Multiple-Trait Genomic Selection

Zhixu Qiu, Yunjia Tang, Chuang Ma

DOI Springer

Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization

Xiaoming Wang, Ruochen Wang, Chuang Ma, Xue Shi, Zhenshan Liu, Zhonghua Wang, Qixin Sun, Jun Cao, Shengbao Xu

DOI PubMed

A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function

Jingjing Zhai, Yunjia Tang, Hao Yuan, Longteng Wang, Haoli Shang, Chuang Ma

Code DOI PubMed

Transcriptome Dynamics during Maize Endosperm Development

Jianzhou Qu, Chuang Ma, Jiaojiao Feng, Shutu Xu, Lei Wang, Feifei Li, Yibo Li, Renhe Zhang, Xinghua Zhang, Jiquan Xue, Dongwei Guo

DOI PubMed

Application of Machine Learning-Based Classification to Genomic Selection and Performance Improvement

Zhixu Qiu, Qian Cheng, Jie Song, Yunjia Tang, Chuang Ma

DOI Springer

miRLocator: Machine Learning-Based Prediction of Mature MicroRNAs within Plant Pre-miRNA Sequences

Haibo Cui, Jingjing Zhai, Chuang Ma

Code Project DOI PubMed

DNA sequence and structure properties analysis reveals similarities and differences to promoters of stress responsive genes in Arabidopsis thaliana

Pan Zhu, Yanhong Zhou, Libin Zhang, Chuang Ma

PubMed

RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation

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

DOI PubMed

Machine Learning for Big Data Analytics in Plants

Chuang Ma, Hao Helen Zhang, Xiangfeng Wang

DOI PubMed

Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis

Chuang Ma, Mingming Xin, Kenneth A. Feldmann, Xiangfeng Wang

Code DOI PubMed

Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development

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

DOI PubMed

Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis

Chuang Ma, Xiangfeng Wang

Code DOI PubMed

KGBassembler: A Karyotype-based Genome Assembler for Brassicaceae Species

Chuang Ma, Hao Chen, Mingming Xin, Ruolin Yang, Xiangfeng Wang

DOI PubMed