Koen van der Heide

Developer on the EndoPredict and Prolaris Report Generators (IVDD): Java/Tomcat apps turning gene-expression data into risk-of-recurrence reports for breast and prostate cancer patients. • Lead developer on the EndoPredict 4.2.2/4.2.3 and Prolaris 1.1.3/1.1.4 Report Generator releases: • Helped produce the DHF/DMR each release; author/co-author of QMS documents under IEC 62304 and ISO 13485. • Added support for the Maxwell extraction kit to EndoPredict and helped validate its score calculation.

• Enabled genotyping of Swine Leukocyte Antigen (SLA) and Leukocyte Immunoglobulin-like Receptors/ Leukocyte-Associated Immunoglobulin-like Receptors (LILR/LAIR) loci in NGSengine. • Identified 100+ novel LILR/LAIR alleles from samples sequenced on Oxford Nanopore (ONT) and PacBio platforms. • Expanded the KIR allele database included with NGSengine for Research Use Only (RUO) applications.

• Built AquaValidator, an R Shiny app that flags out-of-range results and plots calculated water-quality ratios over time, helping analysts validate measurements quickly and consistently. Scoped and built end to end. Open-sourced with Aqualysis's permission: github.com/koenvdheide/AquaValidator • Performed statistical analysis of historical water-quality measurements to surface patterns that could form the basis of new validation criteria.

• Integrated an advanced phylogenetics suite (forester / Archaeopteryx) into Jalview, the open-source multiple-sequence-alignment viewer used widely in academic biology. • Worked in Java on a large pre-existing codebase, in an agile team using JIRA, in the Barton Group at the University of Dundee.