Work
–now
Production pipeline for nanopore sequencing in an accredited clinical laboratory
Department of Clinical Genetics, Erasmus MC
Nanopore sequencing requires extensive data engineering. I took the first version of a pipeline from the research team and extended and formalized it as a Nextflow pipeline for clinical use. With a colleague I built the automation around it. I also administer the PromethION data towers (Ubuntu) and I am the first on call when they fail. The laboratory is ISO 15189 accredited.
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Creator and coordinator of three MSc courses
Genomics in Society MSc, Erasmus MC
I developed and coordinated the Statistics for Genomics course (year 2, 5 ECTS) and co-developed and co-coordinated Research Design (year 1, 8 ECTS) and the fourth period of Genomics and the City (year 1, 5 of its 20 ECTS). All courses ran every year. For Statistics for Genomics I also built statistics4genomics, the course's capstone: a website of R-programming puzzles.
–now
Creator of QDECR: open-source structural MRI analysis in R
Generation R
As MRI was introduced into large population cohorts, new analysis approaches were needed. Based on an idea by Ryan Muetzel I built the QDECR package, which allows for large-scale analysis of structural MRI data with R's own formula syntax. I still maintain it.
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Lead PhD of the ORACLE study
Generation R
I co-designed the ORACLE study and coordinated it from protocol to data analysis: building systems for data administration, writing the study and MRI protocols, inviting participants and coordinating their visits, training students and staff to run the visits and QC the data, and ensuring ETL of all data. We collected data from about 2,000 parents in Generation R. I am first author of its design paper.
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Lead PhD neuroimaging data collection
Generation R
I led the first part of Generation R's third wave of neuroimaging. I wrote part of the protocols, helped train students/staff to run them, wrote code for automated QC of the MRI data, and coordinated the procedure for incidental findings. The full third wave included ~3,000 children.