Stijn van Dongen

Comparison of visualization tools for single-cell RNAseq data

Vladimir Yu Kiselev, Ni Huang, Batuhan Cakir, 2020, NAR genomics and bioinformatics.

Comparison of visualisation tools for single-cell RNAseq data

Ni Huang, Pınar Pir, Martin Prete, 2020, bioRxiv.

Using MCL to extract clusters from networks.

Stijn van Dongen, Cei Abreu-Goodger, S. van Dongen, 2012, Methods in molecular biology.

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench

Vladimir Yu Kiselev, Martin Hemberg, Stijn van Dongen, 2020, bioRxiv.

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

Anton J. Enright, Stijn van Dongen, Cei Abreu-Goodger, 2013, Methods.

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis

Anton J. Enright, Dimitrios M. Vitsios, Stijn van Dongen, 2016, Nucleic acids research.

RNA editing of human microRNAs

Anton J. Enright, Richard Wooster, Michael R Stratton, 2006, Genome Biology.

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests

Anton J. Enright, Dimitrios M. Vitsios, Stijn van Dongen, 2017, Nucleic acids research.