马闯

基本信息

马闯，西北农林科技大学教授，博导。

工作经历

2014- 西北农林科技大学生命科学学院，教授，博导

2011-2014 美国亚利桑那大学农业与生命科学学院，博士后

2010-2011 美国南加州大学洛杉矶儿童医院，博士后

荣誉获奖

陕西省“创新人才推进计划（青年科技新星）”

陕西省人才计划入选者

国家青年人才项目入选者

科学研究

1）人工智能与生物学大数据分析

2）生物信息学与植物功能基因组学

3）农作物智能育种理论、方法与应用

主要学术成果

1)研发软件

· deepEA:表观转录组数据整合分析软件 (https://github.com/cma2015/deepEA)

· deepTS:转录水平的基因表达数据分析软件 (https://github.com/cma2015/deepTS)

· CAFU: unmapped转录组数据分析软件 (https://github.com/cma2015/cafu)

· DeepGS: 基于深度学习技术的全基因组选择分子育种分析软件(https://github.com/cma2015/DeepGS;  软件著作版权登记号: 2017SR318612)

· G2P: 全基因组选择预测软件评估与推荐系统

（https://github.com/cma2015/G2P; 软件著作版权登记号: 2017SR034534）

· PEA: 植物表观转录组学数据整合分析软件

(https://github.com/cma2015/PEA; 软件著作版权登记号: 2017SR658481)

· RAP: 基于机器学习技术的基因功能预测软件

(https://github.com/cma2015/RAP; 软件著作版权登记号: 2016SR318029)

· miRLocator: 基于机器学习技术的植物miRNA预测软件

(https://github.com/cma2015/miRLocator; 软件著作版权登记号: 2015SR102323)

· KGBassembler：植物十字花科基因组序列拼接软件

· rsgcc：基因调控关系挖掘软件 ( http://cran.r-project.org/web/packages/rsgcc)

· mlDNA: 大规模转录组学数据智能分析软件 (http://cran.r-project.org/web/packages/mlDNA)

2)学术论文

1. Zhai JJ, Song J, Zhang T, …, Ma C. deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data.  Plant Physiology , 2020, doi: 10.1093/plphys/kiaa008

2. Miao ZY, Zhang T, Qi YH, …, Ma C. Evolution of the RNA N⁶-methyladenosine methylome mediated by genomic duplication.  Plant Physiology , 2020, 182, 345-360.

3. Qiu ZX, Chen SY, Qi YH, …, Ma C. Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS.  Briefings in Bioinformatics , doi: 10.1093/bib/bbaa137.

4. Chen SY, Ren CZ, Zhai JJ, …, Ma C. CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.  Briefings in Bioinformatics , 2020, 21(2): 676-686.

5. Wang X, Chen S, Shi X, …, Ma C. Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat.  Plant Journal , 2019, 98(6): 1015-1032.

6. Zhai JJ, Song J, Cheng Q, …, Ma C. PEA: an integrated R toolkit for plant epitranscriptome analysis.  Bioinformatics , 2018, 34(21): 3747-3749.

7. Song J, Zhai JJ, Bian EZ, …, Ma C. Transcriptome-wide annotation of m⁵C modifications using machine learning.  Frontiers in Plant Science , 2018, 9: 519.

8. Ma WL, Qiu ZX, Song J, …, Ma C. A deep convolutional neural network approach for predicting phenotypes from genotypes.  Planta , 2018, 248(5): 1307-1318.

9. Miao ZY, Han ZX, Zhang T,…, Ma C. A systems approach to a spatio-temporal understanding of the drought stress response in maize.  Scientific Reports , 2017, 7: 6590.

10. Zhai JJ, Tang YJ, Yuan H, …, Ma C. A meta-analysis based method for prioritizing candidate genes in a pre-specific function.  Frontiers in Plant Science , 2016, 7: 1914.

11. Zha JP, Thakare D, Ma C, …, Yadegari R. RNA sequencing of laser-capture microdissected compartments of the maize kernel identified regulatory modules associated with endosperm cell differentiation.  Plant Cell , 2015, 27, 513-531.

12. Ma C, Zhang HH, Wang XF. Machine learning for big data analytics in plants.  Trends in Plant Science,  2014, 19: 798-808

13. Ma C, Xin MM, Feldmann KA, Wang XF. Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in  Arabidopsis thaliana. Plant Cell , 2014, 26: 520-537

14. Ma C, Wang XF. Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis.  Plant Physiology , 2012, 160(1): 192-203.

15. Ma C, Chen H, Xin MM, …, Wang XF. KGBassembler: A karyotype-based genome assembler for  Brassicaceae species.  Bioinformatics , 2012, 28(23): 3141-3143.

更多信息

· MaLab：https://bioinfo.nwafu.edu.cn

· GitHub: https://github.com/cma2015