About

I am a scientist and research software engineer with 7+ years of experience, passionate about developing high-performance tools and machine learning systems to accelerate research. My tools and algorithms have enabled new insights into human disease and enabled genome analyses previously impossible.

Areas of Expertise

  • Languages & Frameworks. Python, C++, Rust, JavaScript, scikit-learn, TensorFlow, Jax, Pandas, NumPy
  • Bioinformatics. Sequence Alignment, Variant Calling, Pangenomics, Genome Assembly, Phylogenetics.
  • Machine Learning. Deep Learning, Hidden Markov Models, Logistic Regression, Linear Models
  • Software Engineering. Git, Docker, CI/CD, Unit Testing, Google Cloud Platform, PostgreSQL, Linux

Professional experience

Pacific Biosciences, Remote

  • Senior Software Engineer, Bioinformatics, Nov 2025 - Current

Broad Institute of MIT and Harvard, Cambridge, MA

  • Computational Scientist II, Data Sciences Platform, Sep 2024 - Jul 2025
    • Developed a Google Cloud-based data pre-processing pipeline, curating disease phenotypes from electronic health records (EHR) for 10,000 participants in the “All of Us” biobank and assessing the quality of associated terabyte-scale next-generation sequencing (NGS) data.
    • Led the design of interpretable machine learning models integrating genomic (PacBio HiFi, Illumina), transcriptomic, and proteomic data to predict disease onset and identify novel biomarkers.
    • Redesigned and optimized an implementation of a hidden markov model for recombination-aware DNA sequence alignment using Cython and C++, resulting in 360x faster inference.
GitHub - castcollab/tesserae2: Tesserae2: Fast recombination-aware global and local alignment.
Tesserae2: Fast recombination-aware global and local alignment. - castcollab/tesserae2
GitHubcastcollab
  • Computational Associate II, Bacterial Genomics Lab, Nov 2017 - Aug 2024
    • Designed and implemented a new optimal partial order alignment algorithm in Rust, which was, on average, 4.1x faster than similar tools, enabling DNA sequence-to-graph alignments previously impossible.
    • Led the development of Python and C++-based software specifically designed to track low-abundance (>0.1%) bacterial strains in complex microbial communities (e.g., the human gut microbiome) using whole metagenome sequencing data.
    • Developed a cloud-based pipeline using the Workflow Description Language (WDL) and Docker to enable fast and reproducible characterization of thousands of metagenomic samples.
    • Obtained detailed insight into the E. coli strain-level dynamics in a year-long longitudinal microbiome study of women with recurrent urinary tract infections (UTIs), revealing unexpected similarities with a healthy control group and that the UTI-causing strain is rarely cleared from the gut after antibiotics.
StrainGE: Strain Genome Explorer
StrainGE is a toolkit for tracking and characterizing low-abundance strains in complex microbial communities. It enables detailed insights into the bacterial strain-level diversity of whole metagenomic sequencing samples.
Lucas van DijkLucas van Dijk
Gut microbiome dysbiosis linked with recurrent UTIs
More than half of the women in the US get a urinary tract infection (UTI) in their lifetime, which frequently becomes recurrent. In this paper, we investigated the role of the gut microbiome in facilitating recurrence.
Lucas van DijkLucas van Dijk

DSM-firmenich, Delft, The Netherlands

  • Intern, Jun 2016 - Oct 2016
    • Reviewed literature and proposed a plan to analyze a large-scale protein production problem with Bacillus subtilis using genome-scale metabolic models.

Studio bereikbaar, Rotterdam, The Netherlands

  • Software Engineer, May 2013 - Jun 2016
    • Led the development of web-based geographic information systems (GIS) tools using Django and PostgreSQL, securing multi-million euro infrastructure contracts with the government through improved collaborative project planning and design.
    • Enabled local analysis and modification of GIS data in the open-source desktop application QGIS by developing a custom Python-based plugin, communicating with a central server through a REST API.

Thales, Delft, The Netherlands

  • Intern, Sep 2012 - Nov 2012
    • Developed a GPU-accelerated tool to analyze the radar reflectivity of navy ships using nVidia's OptiX CUDA ray tracing library.

Extracurricular Projects

Python Software Foundation (VisPy Google Summer of Code 2015)

  • Implemented a high-performance graph visualization system in Python and OpenGL, including several automatic graph layout algorithms.
  • Contributed the open-source code upstream to VisPy, a high-performance scientific data visualization software
    library.
Drawing arbitrary shapes with OpenGL points
Part of my Google Summer of Code project involves porting several arrow heads from Glumpy to Vispy. I also want to make a slight change to them: the arrow heads in Glumpy include an arrow body, I want to remove that to make sure you can put an arrow head
Lucas van DijkLucas van Dijk
Home — VisPy
VisPy - Home

Delft University of Technology, "Helios 3D team"

  • Built a large 3x3x1 meter 3D RGB LED cube display as part of a student team.
  • Architected and implemented the C++ embedded software responsible for receiving the image to display over Wi-Fi and driving individual LEDs to the correct color.

Education

  • PhD Bioinformatics. Delft University of Technology. 2025.
    • Research conducted at Broad Institute’s Bacterial Genomics Lab in collaboration with the Delft Bioinformatics Lab. Courses: Immunology, Bayesian Methods for Machine Learning, Deep Learning
  • MSc Computer Science. Delft University of Technology. 2017.
  • BEng Electrical Engineering. The Hague University of Applied Sciences. 2013.