Junyu Chen

Timeline

Contact

Address: Floor 14, Block F, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, P. R. China
Phone: 0086-13602696421
E-mail: jy.chen1@siat.ac.cn

Research interest

Education

Chinese Academy of Sciences Jul. 2019 ‑ Jul. 2020
Visiting Student | Shenzhen Institute of Synthetic Biology
Shenzhen University Sep. 2016 ‑ Jul. 2020
Bioengineering | College of Life and Ocean Sciences

Professional Experience

Shenzhen Institute of Synthetic Biology(iSynBio)

Research Assistant | Advisor: Prof. Lei Dai

Established the LD Lab GitHub group and maintained 8 project repository.
Chaired the release and deployment of pipelines in High-Performance Computing(HPC) cluster.
cooperated with 3 main research project and taught at least 5 research assistants for pipeline and software usage
Participated in the pipeline design and test for the analysis of 16S rRNA gene amplicon sequence and metagenomics data.

Research Experience

Meta‑analysis of microbiome data

Research Assistant | Advisor: Prof. Tong Si, Prof. Lei Dai

Customized the Virulence Factors Database(VFDB) for HUMAnN2 Pipeline and analyzed the virulence genes abundance in different dataset.
Developed the pipeline for the analysis of gene abundance based on pure translated search for CAZy and other database.
Mined the biosynthetic gene clusters(BGC) of interest in metagenomics data and evaluated the differential expression in paired metatranscriptomics data.

Whole genome sequencing(WGS) data analysis for culturomics

Research Assistant | Advisor: Prof. Lei Dai

Worked collaboratively with experimental scientists and provided the analysis and interpretation of comparative and functional genomics for synthetic microbiome.
Constructed the pipeline to inspect the taxonomy and phylogeny of gut microbe based on consensus vsearch and multiple sequence alignment, tremendously reduced the time based on commercial software.
Developed and deploy robust data processing and analysis pipelines both for gut microbe and bacteriophage isolates WGS data.

Primer-Coverage for Amplicon-Sequencing(PCAS) Database

Visiting Student | Advisor: Prof. Lei Dai

Statistically analyzed the conservation of 23S rRNA by using R and Python.
Designed the amplicon primers for 23S rRNA based on the conserved region and utilized in silico PCR to evaluate the performance of primers.
Participated in the construction and matainence of the Primer’s Scientific Names(DPSN) Database and PCAS Database.

International Genetically Engineered Machine(iGEM) competition

Team Member | SZU‑China

Choose the insect‑infected fungus as chassis to tackle the cockroach’s problem, by enhancing its adhesion, pene‑tration, and immune‑avoidance ability through synthetic biology, which will continuously infect and spread in the group.
Chaired the up stream design, InterLab experiments,Wikiconstruction and communication with iGEM Headquarters.
Achieved the 2nd Runner UpPrize(343 teams), Gold medal, two special prizes; Best Wiki, Best Modeling, Best SocialPractice, and Best Education and Public Participation Awards nomination.

The analysis of selenoproteins in deer

Undergraduate Research Assistant | Advisor: Prof. Yan Zhang

Deployed, optimized and applied the pipeline and algorithm for the recognition of selenoprotein coding genes in cervidae's Whole-genome sequencing data.
Utilized the OrhoMCL workflow to cluster the orthologous groups of selenoproteins.
Applied RAN‑Seq data to analyze the differential expression of selenoprotein genes in transcriptome‑level.

Skill

Programming: Python, R, Shell script, C, SQL, LATEX
Pipelines: QIIME2, HUMAnN2, MetaBGC, Snakemake, Nextflow
Platforms: Linux/Unix, WSL, Windows, HPC cluster, Google Cloud Platform
Applications: Docker, Git, Conda, Bioconductor, Jupyter notebook/Lab, RStudio, etc.
Web development: HTML, CSS, JavaScript, XAMPP, WordPress, Hexo
Languages: Mandarin(native ),English (IELTS: 7.0)

Honors & Awards

International

2nd Runner Up Prize, International Genetically Engineered Machine competition, 2018
Best Manufacturing Project, International Genetically Engineered Machine competition, 2018
Best Product Design, International Genetically Engineered Machine competition, 2018
Final List, International Genetically Engineered Machine competition, 2018

Domestic(full list)

Outstanding Graduates, Shenzhen University, 2020
Star of self‑improvement, Shenzhen University, 2020
Dean Scholarship, Shenzhen University, 2019
First Prize, Star of Double Innovations Group, Shenzhen University, 2019
3rd Award, Star of Learning, Shenzhen University, 2017

Publications:

[1] Tan, Y., Chen, J., Cai, R., Yang, H., Yin, Z. (2020). PCAS: check the coverage of your primer pair before putting on amplicon sequencing. Drafting

[2] Tan, Y., Tian, Y., Chen, J., Yin, Z., & Yang, H. (2020). DPSN: Standardizing the short names of amplicon-sequencing primers to avoid ambiguity. BioRxiv

[3] Zhang, Y., Xiao, Z., He, Z., Chen, J., Wang, X., & Jiang, L. (2020). Dendritic complexity change in the triple transgenic mouse model of Alzheimer’s disease. PeerJ

[4] Beal, J., Farny, N.G., Haddock-Angelli, T., Selvarajah, V., Baldwin, G.S., Buckley-Taylor, R., Gershater, M., Kiga, D., Marken, J., Sanchania, V., Sison, A., Workman, C.T., & iGEM Interlab Study Contributors. (2020). Robust estimation of bacterial cell count from optical density. Communications Biology