Welcome to Ma Lab

We are group of people dedicated to Bioinformatics research and service provision.

What We Do

Within the fields of bioinformatics and systems biology, we seek to apply Big-Data technologies and methods to answer questions in plant biology, specifically in studies of crop genomics and genetics.

The main research interests include:

  • Artificial intelligence (AI) and Big-Data analysis,

  • Epitranscriptome: Bioinformatics approaches and regulation mechanisms,

  • Bioinformatics-based genotype-phenotype mapping,

  • Systems biology approaches-based plant stress research.

Recent Publications

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

MicroRNAs (miRNAs) are important regulators of gene expression. The large-scale detection and profiling of miRNAs has accelerated with …

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

RNA molecules are decorated with a variety of chemical modifications, which make up an epitranscriptome that extensively regulates gene …

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

Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same …

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

RNA N6-methyladenosine-modified genes exhibit biased subgenome fractionation, and their co-evolutionary relationship with transposable …

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

A widely used approach in transcriptome analysis is the alignment of short reads to a reference genome. However, owing to the …

Projects

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iwa-RNA

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

deepEA

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

deepTS

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

CAFU

A bioinformatics framework for comprehensive assembly and functional annotation

DeepGS

Deep learning-based genomic selection

Epitranscriptome

Bioinformatics approaches for epitranscriptome analysis and their applications

PEA

Plant epitranscriptome analysis

PEA-m5C

Machine learning-based m5C prediction

RAP

Gene prioritization for a pre-specific function

G2P

Bioinformatics approaches for genotype-to-phenotype mapping and their applications

miRLocator

mature miRNAs predictions from pre-miRNA sequences

BigData

Artificial intelligence (AI)-based Big-data analysis approaches and their applications

mlDNA

Machine learning-based differential network analysis

RSGCC

Gini-based transcriptiome analysis

KGBassembler

Karyotype-based genome assembly for Brassicaceae species

Meet the Team

Professor, Doctoral Supervisor

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Chuang Ma

Professor, Doctoral Supervisor

Associate Professor

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Zhaoxue Han

Associate Professor

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Zhenyan Miao

Associate Professor

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Beilei Lei

Associate Professor

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Yunjia Tang

Lecturer

PhD Candidates

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Jingjing Zhai

PhD Candidate

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Ting Zhang

PhD Candidate

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Siyuan Chen

PhD Candidate

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Yuhong Qi

PhD Candidate

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Zhixu Qiu

PhD Candidate

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Qian Cheng

PhD Candidate

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Shafy

PhD Candidate

Master Candidates

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Lei Ling

Master Candidate

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Shang Xie

Master Candidate

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Xiaorong Zhang

Master Candidate

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Bin Xie

Master Candidate

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Jiawen Zhao

Master Candidate

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Minggui Song

Master Candidate

Contact

  • The Ma Laboratory · School of Life Scieces, Northwest A&F University, Yangling, Shaanxi, 712100, China
  • Room NO.2216, State Key Laboratory of Crop Stress Biology for Arid Areas
  • Gmail
  • Google Scholar
  • Github