AmsterdamUMC · University of Amsterdam · OmiQuant

Andrew
Yung Fong
Li Yim

Tenure-track Assistant Professor in immuno-informatics, applying computational and machine learning approaches to unravel immune-mediated inflammatory diseases with a focus on translating multi-omics findings into clinical application towards precision medicine.

By identifying shared molecular pathways across immune-mediated inflammatory diseases - including inflammatory bowel disease, rheumatoid arthritis, and atopic dermatitis - I aim to identify conserved disease mechanisms that can be leveraged for drug repurposing, accelerating the translation of existing therapeutics into new indications.

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Andrew Y.F. Li Yim
35+
Publications
3
Major Grants

Focus Areas

Research

Epigenomics

DNA methylation profiling (450k/EPIC/EPICv2 BeadChip, targeted/whole genome bisulfite sequencing), ChIP-seq, and ATAC-seq analysis to map regulatory landscapes in immune and intestinal cells.

Single-Cell Transcriptomics

scRNA-seq and CITE-seq using 10X Genomics platform, with Seurat/scater pipelines, to resolve cellular heterogeneity in inflammatory bowel disease and rheumatoid arthritis.

Multi-omics Integration

Integrating transcriptomics, proteomics (Olink, mass cytometry), metabolomics, and methylomics for a systems-level understanding of mechanisms underlying immune-mediated inflammatory disease.

Biomarker Discovery

Machine learning (random forests, elastic net, gradient boosting) applied to high-dimensional omics data for disease stratification and therapy response prediction.

Reproducible Pipelines

Development of scalable Snakemake workflows for omics data processing (RNA-seq, ChIP-seq, ATAC-seq, bisulfite-seq), deployable on HPC and cloud infrastructure.

Industry Translation

Proven academic–industry track record spanning a GSK-partnered EU-funded Marie-Skłodowska Curie PhD and OmiQuant, a bioinformatics consultancy serving biotech and pharma clients.

Output

Publications

Loading publications…

Funding

Grants

2025
Predicting and understanding response to biological therapy at single cell level
Litwin IBD Pioneers — Crohn's and Colitis Foundation · Ref: 1289785 · Principal Investigator
$130,000
2023
Characterizing the single cell DNA methylome of treatment response in inflammatory bowel disease
AmsterdamUMC Starter Grant · Ref: 23.02.278 · Principal Investigator · 2023–2029
€315,000
2022
METHYLOMIC — DNA methylation as biomarker and therapeutic target in immune-mediated inflammatory diseases
EU Horizon Research & Innovation Actions · Ref: 101095449 · Work Package Leader · 2023–2026
€9.4M

Career & Education

Experience

Positions

2022 – Present
Assistant Professor Immuno-informatics (Tenure Track)
AmsterdamUMC - Tytgat Institute for Liver and Intestinal Research
AmsterdamUMC - Dept. of Gastroenterology & Hepatology
University of Amsterdam
Research programme on therapy response in immune-mediated inflammatory diseases.
2019 – Present
Founder & Bioinformatics Consultant
OmiQuant
Consultancy, omics data analysis, pipeline development, guest lecturing and PhD co-supervision for life science and pharma clients.
2021 – 2022
Postdoctoral Researcher
AmsterdamUMC — Paediatric Surgery
AmsterdamUMC - Dept. of Human Genetics
Transcriptomics and proteomics of anastomotic leakage and necrotising enterocolitis; scRNA-seq and CITE-seq in Crohn's disease.

Education

2015 – 2022
PhD — Epigenetics in Inflammatory Disease
AmsterdamUMC - Dept. of Human Genetics
GSK - Epinova DPU
EU H2020 Marie Skłodowska-Curie Actions EPIMAC project. Multi-omics integration for understanding the role of epigenetics in immune cells in inflammatory bowel disease.
2012 – 2015
MSc Molecular & Cellular Life Sciences
Utrecht University
Prokaryotic Microbiology & Theoretical Biology and Bioinformatics.
2009 – 2012
BSc Liberal Arts & Sciences
University College Utrecht
Major in Molecular Cell Biology & Mathematics. Minor in Law.
2011 - 2011
Exchange semester
Chinese University of Hong Kong
Plant Biotechnology. Programming in Java. Mandarin Language Course.

Technical Expertise

Skills

Core Languages

R Python Snakemake Bash Perl MATLAB

Omics Providers

Illumina Oxford Nanopore MGI 10X Genomics Methylation BeadChip Olink CyTOF

Analysis Methods

NGS scRNA-seq DNBSEQ CITE-seq ChIP-seq ATAC-seq Bisulfite-seq Spatial transcriptomics Mass Cytometry

Machine Learning/Data Analysis

Random Forests Elastic Net Gradient Boosting scipy pandas tidyverse

Infrastructure

GNU/UNIX HPC (Helios/SURFsara LISA) AWS Azure DigitalOcean Git

Bioinformatics Tools

DESeq2 edgeR limma Seurat scater minfi MAFFT RAxML

Get in Touch

Contact

I welcome enquiries from prospective BSc, MSc, and PhD students, academic collaborators, and industry partners interested in computational approaches to inflammatory disease. Feel free to reach out.

Affiliation

Tytgat Institute for Liver and Intestinal Research
Department of Gastroenterology & Hepatology
Amsterdam University Medical Center
University of Amsterdam
Meibergdreef 69, 1105 BK Amsterdam, the Netherlands