Work
–now
Bioinformatician
Department of Clinical Genetics, Erasmus MC
Production data pipelines in an ISO 15189-accredited laboratory
I build the pipelines that process the laboratory's sequencing data. The nanopore pipeline is one: I took the research team's first version, extended and formalised it as a Nextflow pipeline for clinical use, and with a colleague built the automation around it.
Sysadmin and DevOps for the team
Beyond the pipelines, I administer the PromethION data towers (Ubuntu) and am first on call when they fail. I also build the team's GitLab CI components: pre-commit hooks, static code analysis and git-flow tooling.
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Postdoctoral researcher
Department of Clinical Genetics, Erasmus MC
SumRank and ctar: cross-trait genetics methods, benchmarked and packaged in R
I developed SumRank, a method that finds genetic variants shared between traits, and benchmarked it against the existing methods. My R package ctar offers standardised versions of these methods, with continuous integration and test coverage.
Three MSc courses, developed and run every year · –
In the Genomics in Society MSc, I developed and coordinated Statistics for Genomics, and co-developed and co-coordinated Research Design and part of Genomics and the City. For Statistics for Genomics I also built statistics4genomics, a website of R-programming puzzles that serves as the course's capstone.
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PhD candidate
Department of Epidemiology, Erasmus MC
QDECR: open-source MRI analysis at cohort scale, in R · since
From an idea by Ryan Muetzel, I built QDECR, an R package for large-scale analysis of structural MRI data with R's own formula syntax. I still maintain it.
ORACLE: data collection for nearly 2,000 parents, from protocol to ETL · –
I co-designed ORACLE, a brain-health study within Generation R, and coordinated it: data administration, the study and MRI protocols, the participants' visits, training the students and staff, and the ETL of all its data. I am first author of its design paper.
MRI data collection in a population cohort, with automated quality control · –
I led the first part of Generation R's third wave of neuroimaging, which scanned some 3,000 children in all. I wrote part of its protocols, helped train the students and staff who ran it, wrote the code for automated quality control of its MRI data, and coordinated the procedure for incidental findings.
Education
MSc in Genetic Epidemiology
Erasmus MC
MSc in Neuroscience
Erasmus MC
BSc in Psychology
Erasmus University Rotterdam
39 publications: sanderlamballais.com/publications