Variant Viewer | Streamlit
Variant viewer dashboard to browse annotated variant calling result for ACMG variant classification
🧬Zeo Choy
PhD / Bioinformatician / AI & ML
Highly motivated individual with a deep interest in leveraging artificial intelligence for precision medicine. My focus lies in applying bioinformatics & AI/ML techniques to analyze biological problems and next-generation sequencing (NGS) data.
My skillset combines technical expertise with hands on wet lab experience. I’m proficient in common AI/ML frameworks and possess a strong understanding of NGS data processing pipelines, variant calling, and functional genomics analysis. Additionally, I have a solid foundation in molecular biology techniques, cell culture, and in vitro drug assays.
I’m driven by the transformative potential of AI in the realm of precision medicine. I believe the synergy of deep learning and NGS data holds the key to unlocking novel diseases diagnoses and treatment strategies.
Experience
Chief Bioinformatician
GeneGuard Life Sciences- Lead the bioinformatics team to construct, prototype, deploy and maintain the AI-assisted next generation probiotics (NGP) design engine
- Prepare and draft research proposals to apply various government fundings in collaboration with academic collaborators
Founding CTO
Petcision- Develop technical aspects of the company’s strategy to ensure alignment with its business goals
- Build the AI models and bioinformatics reporting pipeline of gut microbiome analysis to reflect health status in companion animals
- Succesfully granted a Hong Kong short term patent within a year and filed 2 patents applications in China and US
MSc Thesis Project Suprevisor
HKU SPACESupervise MSc in Biomedical Sciences student to complete bioinformatics based thesis research projects.Senior Scientific Officer (Bioinformatics)
BioMed Technology Holdings Limited- In charge of the research logistics, coordination, timeline, manuscript preparation and bioinformatics analysis for microbiome research projects
- Leaded the R&D team and interns to prepare scientifically driven materials to support sales & marketing activities
Scientific Officer (Cancer Genome)
Hong Kong Genome Institute- Assisted the senior officers in planning and setting up a new molecular laboratory supporting population genome project
- Prepared reporting guidelines and internal training materials for data interpretation and genome analysis
Research Scientist
InSilico MedicineLecturer (Part Time)
HKU SPACE Po Leung Kuk Stanley Ho Community CollegeResearch Officer
Sanomics Limited- Provided bioinformatics support (including QA/QC, data analysis, management, and interpretation) for clinical reporting of NGS data
- Leaded and planned various cancer research projects ($10m funding)
Education
PhD in Medical Sciences
The Chinese University of Hong KongThesis on Advancing precision oncology with embedding and deep learning from chemoresistance forecast to therapeutic regimen proposalMPhil in Medical Sciences
The Chinese University of Hong KongThesis on To study the drug resistance in esophageal squamous cell carcinomaBEng in Biomedical Engineering
The Chinese University of Hong Kong
Skills
💻 Dry
Bioinformatics
➤ Data: WGS, WES, RNA-Seq, targeted resequencing, 16S/shotgun microbiome
➤ Database: GEO, TCGA, PCAWG, COSMIC, dbSNP, gnomAD, ClinVar, OncoKB, CCLE, LINCS, SILVA, Greengenes etc.
➤ Analysis: biological data mining, biomarkers discovery, molecular subtyping, survival analysis, differential abundance analysis, network inference etc.
➤ Pipeline: GATK, DRAGEN, QIIME2/PICRUSt, kneadData/MetaPhlAn/HUMAnN
➤ Experience in variant interpretation using ACGS, ACMG, AMP guidelines
Programming
➤ Lanuages: Python, R, Shell, SQL
➤ Frameworks: Django, Flask, Streamlit, HTML, Bootstrap, JavaScript, SQL, C++
➤ Platform: Linux, Mac, Windows, AWS and GCP
Data Science
Data wrangling, model training (scikit-learn), data visualisation (matplotlib, seaborn, ggplot), database managment (SQL)
🧫 Wet
Molecular Techniques
NGS, PCR (PCR, qPCR, dPCR), cloning, immunostaining (IF/ICC/IHC), western blotting, flow cytometry
Diagnostics
Clinical Validation (CAP, ISO)
Cell Culture & Drug Testing
Cell lines, Organoids, Mouse Xenograft
Recent Publications
(2024).
A Novel Multi-Strain E3 Probiotic Formula Improved the Gastrointestinal Symptoms and Quality of Life in Chinese Psoriasis Patients.
Microorganisms.
(2023).
A novel E3 probiotics formula restored gut dysbiosis and remodelled gut microbial network and microbiome dysbiosis index (MDI) in Southern Chinese Adult Psoriasis Patients.
International Journal of Molecular Sciences.
(2023).
Characterization of the Gut Microbiome in Healthy Dogs and Dogs with Diabetes Mellitus.
Animals.
Accomplishments
ESMO Congress 2018 Merit Award
European Society for Medical Oncology ∙
January 2018
Yeung Sau Hang Memorial Scholarship
The Chinese University of Hong Kong ∙
January 2018
Founding Master Gold Medal for Graduating Students
Lee Woo Sing College, The Chinese University of Hong Kong ∙
January 2014
Dean’s List
Faculty of Engineering, The Chinese University of Hong Kong ∙
January 2014
Selected Projects
DeepSAC
Deep learning framework to predict response towards sequential application of anti-cancer drugs
Gene Embedding
Using shallow neural network layer (embedding) to infer gene-gene/sample relationship from gene expression data
resim
A python package that simulates cancer chemoresistance dynamics based on a stochastic model. tags: