Clinical Bioinformatics Scientist - NIPT & cfDNA (with clinical WGS and IVDR documentation)
On-siteLjubljana, Ljubljana, Slovenia
Job Summary
Develop and optimise cfDNA/NIPT algorithms for fetal signal detection, including aneuploidy, sex-chromosome abnormalities, sub-chromosomal CNVs, and fetal fraction estimation. Build and maintain normalization, calibration, and batch correction approaches while defining QC metrics and acceptance criteria using data-driven sensitivity and specificity evaluation. Investigate analytical artifacts and pipeline failures, perform root-cause analysis, and implement corrective actions to ensure reproducible, version-controlled analyses suitable for clinical and regulatory environments. Prepare analytical validation reports and technical documentation for audits, transferring validated methods into production environments while collaborating with molecular biology, clinical, software, QA, and regulatory teams.
Required Qualifications
- MSc or PhD in bioinformatics, computational biology, statistics, mathematics, computer science, genetics or related field
- Proven experience debugging and stabilising quantitative genomic pipelines (batch effects, bias correction, calibration, QC)
- Strong applied statistics: normalization, calibration, robust estimators, z-scores, ROC/performance evaluation and rare-event detection
- Strong Python skills (numpy/pandas/scipy/statsmodels or equivalent)
- R knowledge
- Hands-on NGS experience with genomic data formats (FASTQ/BAM/CRAM, VCF, coverage data, HDF5) and large-scale datasets
- Experience with reproducible Linux workflows, git, testing and structured documentation
- Ability to translate complex analyses into clear scientific and regulatory documentation
- Excellent scientific English
- Ability to work independently in interdisciplinary teams
Desired Qualifications
- Direct cfDNA/NIPT/prenatal genetics experience, including fetal fraction and aneuploidy/CNV detection
- Experience with cfDNA fragmentomics and bias-correction methods
- Experience in regulated IVD/clinical environments and knowledge of IVDR, ISO 13485, IEC 62304 or ISO 14971
- End-to-end clinical WGS pipeline experience
- Nextflow/Snakemake, Docker/containers, CI/CD
- HPC/cloud computing or parallel processing
- Statistical modelling or ML approaches with proven clinical performance benefits
- Experience with genomic data governance and sensitive clinical data
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