About Me

The About Me page has been rewrited! Now it uses tabs to collapse the content… to save space from being wasted too often~

Personal Profile

Self-proclaimed: Silen Wang / Sylens Wong, is a rosted egg that is gradually becoming happier!
Interests: Playing games, playing games, and still damn playing! Games! Anime is also watched, ~~but recently I’m less and less interested in series…~~, In 2024, I started chasing series again! ダンジョン飯 is really amazing! Go watch it!
Learning/Working Path: Public Health -> Molecular Epidemiology -> Bioinformatics -> Neoantigens -> All kinds of things
- emmmm… becoming more and more eclectic
- The word cloud below explains everything…

GitHub:

Education

2009.09-2014.06

School: Guangdong Pharmaceutical University (formerly Guangdong Pharmaceutical College)
College: School of Public Health
Major: Preventive Medicine
Degree: Bachelor

2014.09-2017.06

School: Southern Medical University
College: School of Public Health
Major: Epidemiology and Health Statistics
Degree: Master

Work Experience

Employment: Bioinformatics Analysis Engineer at a bioinformatics service company in Tianjin
Work Content:
1. Human genomic next-generation sequencing data (WES / WGS) quality control and analysis
  - Variant result screening based on frequency, gene region, pathogenicity software prediction, and family inheritance patterns
  - Localization of potentially harmful variants based on genome-wide association study (GWAS) results
  - Customization of screening plans and presentation of results according to customer requirements
2. Research on the current status of specific diseases
  - Research and learn the basic knowledge and current research status of specific diseases to prepare for the development of related analysis modules
3. Maintenance and upgrade of data delivery processes

Employment: Bioinformatics Engineer at a genetic technology company in Hangzhou
Work Content:
- Data Processing
  1. NGS data processing of cfDNA/FFPE/white blood cell samples
  2. Construction and testing of NGS analysis processes
  3. Development of tools for NGS analysis (Python / R / Julia / Shell) and quality control of cell sample sequencing data
  4. Alignment and quality control of raw sequencing data (fastq)
  5. Processing of UMI data / Molecular Barcode data
- Analysis Process Related
  1. Debugging of existing bioinformatics analysis processes
  2. Writing new analysis modules and integrating them into the existing pipeline
  3. Testing and debugging of analysis modules
  4. Deployment and dependency management of analysis software
  5. Performance testing of analysis software and comparison of analysis results
  6. Writing and maintaining process documentation
  7. Construction and testing of single-cell sequencing analysis processes
- Algorithm and Tool Development:
  1. Comparison and replication of UMI deduplication algorithms
  2. Development of tools for drawing quality control plots
  3. Development of variant result screening tools based on ML
  4. Performance optimization of existing tools (parallelization)

2019.07-2020.03 Bioinformatics Engineer at a biotechnology company in Hangzhou
1. Research on NGS-based cfDNA analysis plans and construction of analysis processes
2. Statistical analysis of neoantigen-related data
3. Maintenance of bioinformatics analysis programs
4. Maintenance of the database for medication guidance reports
2020.03-2024.04 Bioinformatics Supervisor at a biotechnology company in Hangzhou
1. Development of NGS-based HLA typing/quantification modules
2. Backend development of bioinformatics analysis tools based on flask
3. Development of neoantigen screening modules
4. Maintenance and upgrade of the main bioinformatics analysis process
5. Writing and revising materials as required

2024.05-Present Senior Bioinformatics Analysis Engineer at a medical technology company in Hangzhou
1. Development of WES/RNA-Seq/scRNA-Seq analysis processes
2. Research and execution of bioinformatics analysis plans
3. Operation and maintenance of bioinformatics databases

Common Languages and Tools

Programming Skills

Parallelization: Multiprocess, Ray
Next-Generation Sequencing Data Handling: Pysam, PyVCF, CyVCF, Biopython, Scanpy
Web Scraping:
- Scrapy: Experience with several small-scale web scraping projects, capable of using Scrapy for scraping static and unencrypted dynamic web pages, and data
- Capable of using splash, selenium in conjunction with Scrapy for scraping dynamic web page data
Data Processing/Statistical Computing: Pandas, numpy, math, scipy, statsmodels
Plotting: Plotly, altair
Data Interaction Display: Dash, Gradio, nicegui
Image Processing: pillow
WebUI/API Development: flask / FastAPI
Office Automation: docxtpl, openpyxl, python-docx
Single-Cell Data Analysis: Scanpy, Cellrank

Data Processing: base, dplyr
Parallelization: Parallel
Plotting: ggplot2, ggpubr, ggthemes, complexheatmap
Single-Cell Data Analysis: Seurat3, Monocle3

Linux System Installation/Configuration Management: Over a decade of experience in installing and using various Linux distributions, with a focus on designing Debian-based, Arch-based, and ChromiumOS-based distributions.
HPC Cluster Management System: Experience with SUN Grid Eengine usage, maintenance
Snakemake: Proficient in writing Snakefiles, proficient in using Snakemake for workflow construction and management, with rich practical experience in Snakemake
~~WDL: Abandoned due to the lack of a Python interpreter in WDL~~
Container Technology: Rich experience in container usage and deployment, capable of writing Dockerfiles and Def files to build Docker or Singularity containers (Example).
Conda/Mamba/Pixi: Sufficient practical experience, able to use conda to quickly deploy analysis software and workflows.
Git: Experience in using Git for project code/document management, understands basic methods of creation/pushing/merging, has used hooks to perform some automated task operations
DevOps: Understands the basic concepts of DevOps, capable of using Azure DevOps platform for code management, as well as automated testing and deployment work

Mastery of Bioinformatics Software/Modules

Well… I’ve used quite a few, and I haven’t used many of them in the past year… But I should be able to get reacquainted with them all within a week, hahahhahaha

Next-generation sequencing data splitting: bcl2fastq
BED file manipulation: bedtools
Data quality control: fastp/fastQC/MultiQC
Sequence alignment: bwa/bowtie/STAR
Expression quantification/analysis: DESeq2/DEXseq/Salmon/kallisto/htseq/Hisat2
Sequence processing: seqtk/seqkit
BAM/VCF file manipulation: Picard/Samtools/Bcftools/Sambamba/Pysam/Biogo
UMI processing: UMI-tools/fgbio

SNP/INDEL detection: Samtools/GATK(Mutect2)/Vardict/Vacscan/Strelka
DNA structural variation/fusion gene detection: CREAST/lumpy-sv/Smoove/SViCT/SvABA/Manta/Delly/GeneFuse/Factera/sv-tools
CNV detection: CNVkit/PyLOH
Variant annotation: ANNOVAR/snpEff/VEP

Clonality: PyClone/SciClone/FastClone
Genetic consistency screening of sequencing data: plink/NGSCheckMate
Mass spectrometry identification: pFind/maxquant

Other Work Experience

Patent draft writing experience
Software copyright writing experience
Research paper writing experience
Static blog/document writing
- hexo
- mkdocs
- gitbook

Displayable Projects

There’s not much to show after working… After all, writing is for survival, and playing games is the ultimate goal hhhhhhh

Github Projects

Published Articles

I generally only take responsibility for the bioinformatics related parts in following articles:

Ye Feng et al., “Multi-Epitope Vaccine Design Using an Immunoinformatic Approach for SARS-CoV-2” Pathogens 10 (June 11, 2021) 737.
Zheling Chen et al., “A Neoantigen-Based Peptide Vaccine for Patients With Advanced Pancreatic Cancer Refractory to Standard Treatment” Front. Immunol. 12 (2021) 691605.
Jiawei Shou et al., “Combination Treatment of Radiofrequency Ablation and Peptide Neoantigen Vaccination: Promising Modality for Future Cancer Immunotherapy” Front. Immunol. 13 (September 29, 2022) 1000681.