Ziwei Xue

Major in Bioinformatics, ZJU-UoE Institute, Zhejiang University 📧 ziwei.21@intl.zju.edu.cn

Personal email: xueziweisz@gmail.com

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/multi-omics algorithm development, analysis, and front-end visualization.

I am currently is exploring the multi-omics data analysis in the field of bioinformatics and developing algorithms/tools for better understanding of transcriptome dynamics and clonal enrichment of antigen-receptors in cancers and autoimmune diseases. I am also developing methods for the integration of increasing amount and variety of next-generation sequnecing data for bioinformatics and biologist.

Pinned

In preparation

scAtlasVAE

A deep learning model for integration of scRNA-seq.

In preparation

TCR-DeepInsight

A deep learning model for antigen receptor clonotype-transcriptome analysis.

publication

huARdb

The human antigen receptor database.

publication

RAD

The Region Associated DEG Web tool.

Tool

AnnData-Tensorstore

Efficiently store and access AnnData objects.

You can also find me at

Education Experience

2021 - Present

PhD Student major in Bioinformatics, ZJE institute, Zhejiang University

2017 - 2021

Bachelor major in Biomedical science, ZJE institute, Zhejiang University

2014 - 2017

Shenzhen Middle School

Publications

Guo, Y.†, Xue, Z.†, Gong, M., Jin, S., Wu, X. & Liu, W.# , (2024). CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements. Mobile DNA, (link). The webtool is available in here.

Su, Y. , Yu, Z. , Jin, S. , Ai, Z. Yuan, R. , Chen, X. , Xue, Z. , Guo, Y. , Chen, D., Liang, H., Liu, Z., Liu, W. (2024) Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data. Nature Communications, 15, 3972 (link

Tian, R.†, Xue, Z.†, Ruan, D., Chen, P., Xu, Y., Dai, C., Shen, W., Ouyang, H., Liu, W., and Lin, J. (2023). MSdb: An integrated expression atlas of human musculoskeletal system. iScience, 26, 106933. (link). The webtool is available in here.

Wu, L.† , Xue, Z.† , Jin, S., Zhang, J., Bai, Y., Jin, X., Wang, C., Wang, L., Wang, J.Q., Lu, L. & Liu, W.#. (2022) huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level. Nucleic Acid Research, 50(D1), D1244-D1254 (link). The webtool is available in here.

Xiang, X., Tao, Y., DiRusso, J., Hsu, F.-M., Zhang, J., Xue, Z., Pontis, J., Trono, D., Liu, W., and Clark, A.T. (2022). Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nature Communications, 13, 463. link.

Jin, S.† , Xue, Z.† , Zhang, J. , Wang, Z., Zhang, J., Chen, D.#, Liu, W.# , Lin, J.# (2021). Identification of SRSF3 target mRNAs using inducible TRIBE. Biochemical and Biophysical Research Communications. link.

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 (link). The webtool is available in here.

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