Register for Postdocs & Researchers - EPIGENICA- Internship project VT 2026

EPIGENICA AB

Cell Composition Modeling and Pipeline Standardization for Multiplex Epigenomic Data

Target Group 

Postdoctoral Researchers (3 months)

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
Bulk epigenomic assays capture signals from heterogeneous cell populations, which can confound biological interpretation. At the same time, increasing data volume and multiplexed experimental design require standardized, production-ready computational workflows. This project combines methodological development and pipeline standardization to strengthen the analytical framework supporting MINUTE-ChIP.

The Work Will Include

1. Cell Composition Modeling

• Evaluating and benchmarking deconvolution approaches using simulated and synthetic
  datasets
• Applying selected methods to internal MINUTE-ChIP data
• Assessing feasibility of integrating cell-type estimates into downstream analyses

2. Pipeline Development and Standardization

• Reviewing and restructuring the current MINUTE-ChIP workflow
• Converting and optimizing the pipeline within a modular Nextflow framework
• Integrating relevant best practices from nf-core/chipseq

Expected Outcome

• Proof-of-concept validation of a cell composition estimation workflow
• A standardized, containerized, and reproducible multiplex ChIP-seq pipeline
• Improved scalability and robustness of data processing
• Clear recommendations for integration into future projects

Location
Hybrid (Stockholm)

Time Period
March – May (3 months project)

Candidate Profile

• PhD in bioinformatics, computational biology, genomics, or related field
• Strong experience with omics data analysis (ChIP-seq, epigenomics)
• Proficiency in workflow managers (Nextflow required; Snakemake advantageous)
• Strong programming skills in R and/or Python
• Experience with Linux, containerization (Docker/Singularity), and version control
• Familiarity with nf-core standards and statistical modeling is highly desirable

Contact Information 

Name: Nima Rafati 

Email: nima.rafati@epigenica.se