I am a lecturer at College of Agronomy, Hunan Agricultural University (HUNAU), Changsha, China. My Ph.D research work covers a range of issues: Population Genetics Evolution and Ecotype Divergence Analysis of Brassica napus, Genome-wide Association Study (GWAS) of Agronomic Traits. Currently, I am interested in Transposable Elements Insertion Polymorphisms (TIPs) in Crop Population and genetic basis such as SV, CNV and TIPs etc. Now my research focus on Crop Stress and Improvement.

I am broadly interested in bioinformatics, data integration and visualization.

Interests

  • Python & R Program
  • Bioinformatics
  • Machine Learning
  • Data Science
  • Data Visualization
  • Open Source

Education

  • PhD Candidate in Crop Genetics and Breeding, 2016

    Zhejiang University (ZJU)

  • BSc in Crop Science, 2012

    The College of Agriculture and Biotechnology, Zhejiang University (ZJU)

From my blog

ShinyApp域名、端口、安全设置及代理

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简介

前面我将 ShinyApp部署在阿里云上，阿里云只提供ip，不方便记忆，需要我们自己购买域名，为了方便后续域名解析绑定，所以我在阿里云又购买了域名bnapus-zju.com。域名的解析以及绑定在阿里云上十分简单，这里就不细讲了。下面就是讲一下如何使用Nginx反向代理以及使用HTTPS来保护ShinyApp。

3 min read Shiny

基于SNP进行主成分分析PCA

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简介

主成分分析(PCA)是一种线性降维方法，通过线性变换简化数据集，提取关键信息对数据进行区分。群体重测序项目往往能得到百万乃至千万级别的SNP，基于SNP进行PCA的软件有很多，主流是下面三种：

1 min read bioinformatics

使用SNPhylo基于SNP构建群体系统发育树

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简介

系统发育树是一种推断各种生物之间进化关系的好方法，在进化研究中得到了广泛的应用，得益于测序技术的发展以及成本的不断下降，大量的物种以及群体被测序，产生了海量的基因型数据，在重测序项目中，基于SNP数据进行系统发育树的构建有利于更全面地囊括整个基因组层面的变异进行分析。 SNPhylo是基于SNP数据构建群体系统发育树的一个pipeline，可以接受主流的VCF文件以及HapMap文件，同时其内置了过滤功能，通过对低质量的SNP，连锁不平衡进行过滤，生成用于构建群体系统发育树的输入数据，SNPhylo会调用muscle进行对序列比对，DNAML构树，具体流程如下：

3 min read bioinformatics
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Recent Publications

Quickly discover relevant content by filtering publications.

BnaGVD: A Genomic Variation Database of Rapeseed (Brassica napus)

Rapeseed (Brassica napus L.) is a typical polyploid crop and one of the most important oilseed crops worldwide. With the rapid progress …
Tao Yan, Yao Yao, Dezhi Wu, Lixi Jiang
PDF

BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions

The rapid development of high-throughput sequencing technology and the decrease in sequencing costs provide valuable resources and …
Tao Yan, Qian Wang, Antony Maodzeka, Dezhi Wu, Lixi Jiang
PDF Code Dataset Video

Genome-wide association study reveals new genes involvedin leaf trichome formation in polyploid oilseed rape(Brassica napus L.)

Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in …
Lijie Xuan, Tao Yan, Lingzhi Lu, Xinze Zhao, Dezhi Wu, Shuijin Hua, Lixi Jiang
PDF Slides

Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype …
Dezhi Wu, Zhe Liang, Tao Yan, Ying Xu, Lijie Xuan, Juan Tang, Gang Zhou, Ulrike Lohwasser, Shuijin Hua, Haoyi Wang, Xiaoyang Chen, Qian Wang, Le Zhu, Antony Maodzeka, Nazim Hussain, Zhilan Li, Xuming L, Imran Haider Shamsi, Ghulam Jilani, Linde Wu, Hongkun Zheng, Guoping Zhang, Boulos Chalhoub, Lisha Shen, Hao Yu, Lixi Jiang
PDF Poster Slides

TRANSPARENT TESTA 4‐mediated flavonoids negatively affect embryonic fatty acid biosynthesis in Arabidopsis

Flavonoids are involved in many physiological processes in plants. TRANSPARENTTESTA 4 (TT4) acts at the first step of flavonoid …
Lijie Xuan, Cuicui Zhang, Tao Yan, Dezhi Wu, Nazim Hussain, Zhilan Li, Mingxun Chen, Jianwei Pan, Lixi Jiang
PDF
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Projects

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All r website software

BnaGWAS

A shinyapp for performing GWAS in rapeseed based on a core collection

BnaSNPDB

An interactive web portal for exploring SNPs among 1007 rapeseed germplasm accessions

ttplot

Tao Yan’s Plot Toolkit