Lucas van Dijk

Fast and exact gap-affine partial order alignment with POASTA post image

Partial order alignment is a common method to compute multiple sequence alignments through iterative sequence-to-graph alignment. In this paper, we introduce a new algorithm that accelerates alignment by exploiting graph topology and shared sequence between the query and the graph.

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.

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.

Publication

Microbiome

Software

Using locality sensitive hashing to compactly represent k-mers post image

By Lucas van Dijk

Mar 26, 2018

Using locality sensitive hashing to compactly represent k-mers

K-mers are frequently used in bioinformatics to profile and compare genomes. This article describes a technique for compactly representing long k-mers with locality-sensitive hashing.

Tutorial Bioinformatics

Visualizing the height of the Netherlands post image

By Lucas van Dijk

Feb 1, 2018

Visualizing the height of the Netherlands

Dataviz

Three circles that define a curved arrow.

By Lucas van Dijk

Jun 13, 2015

Drawing arbitrary shapes with OpenGL points

Tutorial GPU

Controlling a servo with an AVR microcontroller post image

By Lucas van Dijk

Oct 16, 2012

Controlling a servo with an AVR microcontroller

Servos are useful small motors with applications in robotics, RC cars, and others. Here, we describe how to use an ATTiny44 to control its position.

Tutorial Embedded Systems

Multithreading with C++11: protecting data post image

By Lucas van Dijk

Jun 14, 2012

Multithreading with C++11: protecting data

Tutorial Software Engineering

Introduction to threads with C++11 post image

By Lucas van Dijk

May 3, 2012

Introduction to threads with C++11

Tutorial Software Engineering

Hi, I'm Lucas! I write about computational biology and bioinformatic algorithms, from deep dives into the technical aspects behind a paper to explainers in simple language. Topics I find interesting include machine learning, sequence alignment algorithms, immunology, and the human microbiome.

I am a computational scientist at the Broad Institute of MIT and Harvard in the Long Reads Lab. My current projects include developing multi-omic data integration algorithms to improve our understanding of disease and writing novel sequence-to-graph alignment tools to reduce biases in genetic analyses.

Read the rest of my resume »

Fast and exact gap-affine partial order alignment with POASTA

Gut microbiome dysbiosis linked with recurrent UTIs

StrainGE: Strain Genome Explorer