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

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Differentiation of genome-wide DNA methylation between japonica and indica rice

Rice (Oryza sativa L.) subspecies japonica and indica show distinct morphological and genetic differentiation. However, the differences …
Tao Yan, Liuhui Kuang, Fei Gao, Jian Chen, Lin Li, Dezhi Wu
PDF

Transcriptome-wide m⁶A methylation and metabolomic analysis reveal regulatory networks in rice roots under manganese stress

Rice (Oryza sativa) has a higher tolerance to manganese (Mn) stress than other cereals. However, the regulatory mechanisms governing Mn …
Tingting Su, Jian Chen, Xing Huo, Liuhui Kuang, Tao Yan, Fei Gao, Dezhi Wu
PDF

Genomic and transcriptome analyses reveal potential contributors to erucic acid biosynthesis in seeds of rapeseed (Brassica napus)

Through comprehensive genomic and transcriptomic analyses, we identified a set of 23 genes that act up- or downstream of erucic acid …
Shiqi Xu, Shan Chen, Jialing Cai, Tao Yan, Mengxin Tu, Ruisen Wang, Shuijin Hua, Lixi Jiang
PDF

Multi-omics analysis reveals differential molecular responses to cadmium toxicity in rice root tip and mature zone

Cadmium (Cd) is a highly toxic heavy metal that can be readily absorbed by plants and enriched in human body. Rice (Oryza sativa L.) …
Liuhui Kuang, Tao Yan, Fei Gao, Wenbang Tang, Dezhi Wu
PDF

Transcriptomic Profiling of Cold Stress-Induced Differentially Expressed Genes in Seedling Stage of Indica Rice

Cold stress significantly constrains the growth, development, productivity, and distribution of rice, particularly the indica cultivar, …
Tao Yan, Meng Sun, Rui Su, Xiaozhong Wang, Xuedan Lu, Yunhua Xiao, Huabing Deng, Xiong Liu, Wenbang Tang, Guilian Zhang
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

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