Torsten Houwaart

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

Complete sequences of six Major Histocompatibility Complex haplotypes, including all the major MHC class II structures

The paper completes six MHC haplotypes, including DR1, DR4, and structurally variable C4 regions, improving reference panels for immunogenomics analysis.

Pangenome-based genome inference

PanGenie improves variant calling by using a pangenome reference and k-mer counts, achieving higher accuracy and speed compared to traditional methods.

GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering

GraphClust2 improves RNA clustering and annotation by integrating sequence and structural data, revealing conserved structures in long non-coding RNAs and targets of Roquin-1.

Community-driven data analysis training for biology

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.

Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter

The paper describes a hybrid platform integrating predefined workflows with ad hoc analytics to simplify and reproduce the raw data-to-publication process in biomedical research.