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

Genome optimization via virtual simulation to accelerate maize hybrid breeding

The employment of doubled-haploid (DH) technology in maize has vastly accelerated the efficiency of developing inbred lines. The …
Code Project DOI PubMed

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

We developed SMART v1.0 (http://smart.omicstudio.cloud), the first database for small molecules with functional implications in plants. …
Project DOI PubMed

Evolutionary implications of the RNA N6-methyladenosine methylome in plants

Epigenetic modifications play important roles in genome evolution and innovation. However, most analyses have focused on the …
Code DOI PubMed

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 …
Code Project DOI PubMed

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 …
Code Project DOI PubMed

Projects

*
All Machine Learning Databases Software Algorithms

GOVS

Genome optimization via virtual simulation to accelerate maize hybrid breeding

SMART

A Database for Small Molecules with Functional Implications in Plants

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

Avatar

Chuang Ma

Professor, Doctoral Supervisor

Associate Professor

Avatar

Beilei Lei

Associate Professor

Avatar

Zhenyan Miao

Associate Professor

Avatar

Zhaoxue Han

Associate Professor

Avatar

Yunjia Tang

Lecturer

PhD Candidates

Avatar

Yuhong Qi

PhD Candidate

Avatar

Zhixu Qiu

PhD Candidate

Avatar

Jing Yang

PhD Candidate

Master Candidates

Avatar

Minggui Song

Master Candidate

Avatar

Chengchao Jia

Master Candidate

Avatar

Chenhua Wu

Master Candidate

Avatar

Chujun Zhang

Master Candidate

Avatar

Jiawen Zhao

Master Candidate

Avatar

Liyuan Guo

Master Candidate

Avatar

Meihua Xu

Master Candidate

Avatar

Mengmeng Yuan

Master Candidate

Avatar

Pengjun Ding

Master Candidate

Avatar

Shuang Zhao

Master Candidate

Avatar

Wen Sun

Master Candidate

Avatar

Wenyue Huang

Master Candidate

Avatar

Yanlin Ren

Master Candidate

Avatar

Yifan Bu

Master Candidate

Avatar

Yishui Han

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