Dr Stijn van Dongen | Senior Software Developer

van Dongen, Stijn

I work in the Cellular Genetics Informatics lab at the Wellcome Sanger institute, providing pipeline development and analysis services for RNA-seq, Chip-Seq, ATAC-seq and others. Currently our pipelines run under Nextflow, an elegant and powerful language to express and manage process dependencies and parallellisation.

Publications

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

    Vitsios DM, Davis MP, van Dongen S and Enright AJ

    Nucleic acids research 2017;45;3;1079-1090

  • Kraken: a set of tools for quality control and analysis of high-throughput sequence data.

    Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N and Enright AJ

    Methods (San Diego, Calif.) 2013;63;1;41-9

  • Using MCL to extract clusters from networks.

    van Dongen S and Abreu-Goodger C

    Methods in molecular biology (Clifton, N.J.) 2012;804;281-95

  • Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets.

    Palmer RD, Murray MJ, Saini HK, van Dongen S, Abreu-Goodger C et al.

    Cancer research 2010;70;7;2911-23

  • Detecting microRNA binding and siRNA off-target effects from expression data.

    van Dongen S, Abreu-Goodger C and Enright AJ

    Nature methods 2008;5;12;1023-5

  • miRBase: tools for microRNA genomics.

    Griffiths-Jones S, Saini HK, van Dongen S and Enright AJ

    Nucleic acids research 2008;36;Database issue;D154-8

  • Construction, visualisation, and clustering of transcription networks from microarray expression data.

    Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P et al.

    PLoS computational biology 2007;3;10;2032-42

  • Requirement of bic/microRNA-155 for normal immune function.

    Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P et al.

    Science (New York, N.Y.) 2007;316;5824;608-11

  • Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs.

    Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S et al.

    Science (New York, N.Y.) 2006;312;5770;75-9

  • An efficient algorithm for large-scale detection of protein families.

    Enright AJ, Van Dongen S and Ouzounis CA

    Nucleic acids research 2002;30;7;1575-84

van Dongen, Stijn
Stijn's Timeline
2018

Joined the Cellular Genetics Informatics lab under Vladimir Kiselev as senior software developer

2014

Release of mcl-14-137, the still-current and stable mcl release

2009

Wrote my first R code

2008

The Sylamer paper with Cei-Abreu Goodger and Anton Enright was published.

The Enright lab moved to the EBI, myself included.

2004

Joined the Anton Enright lab as a senior software developer

2002

Published the TribeMCL paper with Anton Enright and Christos Ouzounis whilst working at the software company diff in Amsterdam

2001

Initial relase of the mcl software

2000

PhD Graph clustering by flow simulation under Michiel Hazewinkel and Jan van Eijck in Utrecht

1997

Wrote my first C code

1995

Wrote my first Perl code

Civiliian duty at the Centre for Mathematics and Computing Science in Amsterdam

1994

Graduated at Technical University Eindhoven under Arjeh Cohen on the subject of exact computation of the sign of a real algebraic number