Zgłoszenie na PhD Students - EPIGENICA- Internship project VT 2026

EPIGENICA AB

Experimental Design Optimization and Cross-Platform Valid

Target Group 

PhD student

About the Company
Epigenica AB is a Stockholm-based biotechnology company developing advanced epigenomic
technologies. Our proprietary platform, MINUTE-ChIP, enables multiplexed profiling of histone
modifications and DNA methylation from limited biological material. We focus on building robust,
scalable, and reproducible com

Project Overview
Reliable epigenomic analysis requires both optimized sequencing depth and validated
measurement strategies. This PhD project combines simulation-based experimental design
optimization with cross-platform DNA methylation validation, aiming to strengthen both the
technical and biological robustness of our assays. 

The Work Will Include
1. Simulation-Based Sequencing Depth Estimation

• Modeling genome equivalents and expected read coverage in cfDNA ChIP-seq
• Simulating varying sequencing depths under realistic duplication rates
• Evaluating peak detection sensitivity and signal saturation

2. Cross-Platform DNA Methylation Comparison

• Comparing global methylation levels between EPIC array and MBD-seq
• Evaluating CpG island–level trends across samples
• Relating enrichment-based sequencing signals to EPIC beta/M-values
• Assessing reproducibility and concordance between platforms

Expected Outcome

• Data-driven guidelines for optimal sequencing depth under cfDNA conditions
• Quantitative assessment of agreement between EPIC array and MBD-seq
• Improved understanding of enrichment-based versus array-based measurements
• Recommendations to strengthen experimental design and interpretation

Location
Hybrid (Stockholm)

Time Period
May – June (1-month project)

Candidate Profile

• Master’s degree (PhD track) in bioinformatics, computational biology, genomics,
  biostatistics, or related field
•  Experience with NGS data analysis (ChIP-seq, methylation, epigenomics)
• Strong programming skills in R and/or Python
• Solid understanding of statistical modeling and data normalization
• Experience with sequencing depth analysis or DNA methylation platforms is
  advantageous.

Contact Information 

Name: Nima Rafati 

Email: nima.rafati@epigenica.se