Projects
Open Source Contributions
Iām passionate about developing tools and algorithms that make bioinformatics more accessible and reproducible. Here are some of my key projects:
vcf-reformatter
Rust Package for VCF to TSV Conversion
High-performance VCF file parser and reformatter with VEP annotation support. Converts complex VCF files to analyzable TSV format with intelligent transcript handling. Reduces preprocessing time by 90%.
Rust Genomics VCF TSV Variant annotation
drugsens
CRAN Package for Drug Sensitivity Analysis
A comprehensive R package providing a user-friendly workflow for analyzing drug sensitivity from high-content imaging data. Features automated image processing, dose-response curve fitting, and statistical analysis.
R Image Analysis Statistics CRAN
CRAN | GitHub | Documentation
Research Projects
Current Focus
Leading a multi-institutional effort to identify novel biomarkers in rare gynecological cancers using integrated multi-omics approaches. This project combines:
- Whole genome sequencing
- Single-cell RNA sequencing
- Spatial transcriptomics
- Clinical proteomics
- Advanced machine learning
Goal: Develop a clinical decision support system for personalized treatment selection.
Past Projects
Developed an innovative platform combining microfluidics and electrical impedance spectroscopy for high-throughput drug screening. This work resulted in a patent application and multiple publications.
Technologies: Arduino, Python, COMSOL, Microfluidics
Mathematical modeling of praziquantel prodrugs to improve treatment options for schistosomiasis. Used population PK/PD approaches to optimize dosing regimens.
Technologies: R, NONMEM, Monolix
Collaborative Initiatives
BioData Basel
Founder of a meetup community for data scientists and bioinformaticians in the Basel life sciences hub, bringing together computational biologists for knowledge sharing and collaboration. We organize monthly meetups and workshops.
Resources
š Educational Materials
- SIB course cancer variant analysis - Comprehensive tutorial on how to analyze genomic mutations in cancer genomics
Iām always open to collaborating on interesting bioinformatics projects! If you have an idea or need help with computational biology challenges, feel free to reach out.