Ziwei Xue

Ziwei Xue

Major in Biomedical science, ZJU-UoE Institute, Zhejiang University

📧 ziwei.17@intl.zju.edu.cn

About

I am a PhD student major in bioinformatics in Zhejiang University - University of Edinburgh joint institute. I am currently working in labW led by Dr. Wanlu Liu. I am currently working on genomic algorithm development, multi-omics analysis, and front-end visualization.

Education Experience

2017 - Present

Bachelor, Medical School, Zhejiang University

Publications

Wu, L.† , Xue, Z.† , Jin, S., Zhang, J., Bai, Y., Jin, X., Wang, C., Wang, L., Wang, J.Q., Lu, L. & Liu, W.#. huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level. Nucleic Acid Research (Under revision)

Guo, Y.†, Xue, Z., Yuan, R., Li, J., Pastor, W. & Liu, W.# , 2021. RAD: a web application to identify region associated differentially expressed genes. Bioinformatics, btab075. The webtool is available in here.

†, first or co-first author; #, corresponding author.

Portfolio at a Glance

CRISPRTE

Bioinformatics
In-progress
Designing Transposable element specific guide RNAs.

HUARC

Bioinformatics
In-progress
Visualization of Single Cell VDJ sequencing data from various publications. Available at https://huarc.net. Currently under peer-review.

Wu, L.† , Xue, Z.† , Jin, S., Zhang, J., Bai, Y., Jin, X., Wang, C., Wang, L., Wang, J.Q., Lu, L. & Liu, W.#. huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level. Nucleic Acid Research (Under revision)

TRIBECaller

Bioinformatics
In-progress
Calling RNA Editing Sites using RNA-seq data. Currently under development and testing.

RAD - A web to to identify region associated differentially expressed genes (DEGs)

Bioinformatics

RAD is a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes. RAD maps the up- and down-regulated genes associated with any genomic regions of interest (gROI) and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance.
The webpage is designed and developed by PhD candidate student Yixin and me, using JQuery.js, Angular.js and Flask Framework. The algorithm and its visualization is written in Python by my another undergraduate student Ruihong and I am responsible for maintaining and improving its performance.

Guo, Y.†, Xue, Z., Yuan, R., Li, J., Pastor, W. & Liu, W.# , 2021. RAD: a web application to identify region associated differentially expressed genes. Bioinformatics, btab075.

Transcription Factors - Transposable Element network

Bioinformatics
In-progress
TF-TE network is build according to ChIP-Seq data mainly from ENCODE database. We focus on binding of transcription factors to knowned transposable element regions, and analysis the significance of the interaction. Our goal is to predict interaction between TFs and TEs and their functions in embryogenesis and cancer progression.
The visualization of the data is highly interactive using Plotly
The visualization is development under Plotly & Dash, is the most downloaded, trusted framework for building ML & data science web apps.