Jose Ramon Jeronimo Liñan
Bridging biology and computation to turn biological data into decisions
As a bioprocess engineer, I bring the biological understanding behind the data — along with laboratory and industrial experience — to my computational biology work
Vienna, Austria EU national, no sponsorship needed Part-time now, full-time from November 2026
Get in touchBridge
Bioprocess engineering taught me to read biological systems under pressure — optimizing fermentation runs, designing controlled experiments, and translating batch data into process decisions. That training built a skill most computational pipelines lack: the ability to look at a statistical output and ask what it means for the organism, not just the model. I build workflows with that lens built in, so the results translate into actions, not just plots.
What I bring:
- Experimental design experience that catches data quality problems before they reach the pipeline
- The biological grounding to interpret computational outputs in context — not just report them
- Industrial and research exposure across fermentation, microbial systems, and omics
Projects
gemAGT
Manually discovering where a metabolic pathway is broken is painful. GemAGT provides the reactions that are causing the model to fail, shortening the discovery time from hours of manual search to minutes of automatic computing
biopipes
Set of sequencing data pipelines that converge into a multiomics integration pipeline and plot generation. Currently supporting RNAseq, ATACseq and WGS.
Single-cell data analysis
Notebook used to analyze a given single-cell sequencing data set provided as an assignment for a lecture
Dark proteome analysis using Machine Learning
Comparative ML pipeline on the A. thaliana PeptideAtlas dataset, classifying protein detectability from three sequence-derived and two transcript-level properties
Skills
Single-cell analysis
scanpy scVI CellTypist Scrublet Leiden UMAP HVG selection batch integration AnnData / .h5adMachine learning
scikit-learn PCA stratified & nested CV pipeline preprocessing class imbalance ROC & threshold tuning model interpretationMetabolic modelling
COBRApy gapseq genome-scale models model curationSequencing pipelines
bash R samtools bowtie2 fastqc fastp RNAseq / ATACseq / WGS multiomics integrationData handling & visualisation
Python pandas numpy SciPy matplotlib seaborn streamlitEnvironments
GitHub JupyterLab server remote Linux server HPCContact
Bioinformatics, computational biology and life-science data science roles. Also open to PhD positions and industry internships.
- Based in
- Vienna, Austria
- Work eligibility
- Spanish citizen, EU national - no visa or sponsorship required
- Availability
- Available part-time now. Full-time from November 2026.
- Studying
- M.Sc. OMICs Technologies and Data Science in Biomedicine, IMC Krems. Master Thesis project at the University of Vienna until November 2026.
- Languages
- Spanish (native), English (professional), German (B1)