Publications by authors named "Stijn van Dongen"

40Publications

Comparison of visualization tools for single-cell RNAseq data.

NAR Genom Bioinform 2020 Sep 29;2(3):lqaa052. Epub 2020 Jul 29.

Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.

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September 2020

Visualization and analysis of RNA-Seq assembly graphs.

Nucleic Acids Res 2019 08;47(14):7262-7275

Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK.

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August 2019

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

Nucleic Acids Res 2017 Dec;45(21):e177

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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December 2017

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

Nucleic Acids Res 2017 02;45(3):1079-1090

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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February 2017

Exploring regulatory networks of miR-96 in the developing inner ear.

Sci Rep 2016 Mar 18;6:23363. Epub 2016 Mar 18.

Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK.

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March 2016

Processive catalysis.

Angew Chem Int Ed Engl 2014 Oct 22;53(43):11420-8. Epub 2014 Sep 22.

Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen (The Netherlands).

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October 2014

Structure-delivery relationships of lysine-based gemini surfactants and their lipoplexes.

Soft Matter 2014 Aug 27;10(31):5702-14. Epub 2014 Jun 27.

Radboud University Nijmegen, Institute for Molecules and Materials, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.

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August 2014

A reagent-based dynamic trigger for cell adhesion, shape change, or cocultures.

Methods Cell Biol 2014 ;120:171-84

Systems Cell Biology of Cell Division and Cell Polarity, UMR144, Institut Curie, CNRS, Paris, France.

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September 2014

A clamp-like biohybrid catalyst for DNA oxidation.

Nat Chem 2013 Nov 22;5(11):945-51. Epub 2013 Sep 22.

1] Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands [2].

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November 2013

Functional interlocked systems.

Chem Soc Rev 2014 Jan 26;43(1):99-122. Epub 2013 Sep 26.

Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.

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January 2014

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

Methods 2013 Sep 29;63(1):41-9. Epub 2013 Jun 29.

EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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September 2013

Triggering cell adhesion, migration or shape change with a dynamic surface coating.

Adv Mater 2013 Mar 27;25(12):1687-91. Epub 2013 Jan 27.

École Normale Supérieure, Department of chemistry, UMR 8640 CNRS-ENS-UPMC, Paris, France.

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March 2013

Using MCL to extract clusters from networks.

Methods Mol Biol 2012 ;804:281-95

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.

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March 2012

Messenger RNA and microRNA profiling during early mouse EB formation.

Gene Expr Patterns 2011 Jun-Jul;11(5-6):334-44. Epub 2011 Apr 1.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.

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September 2011

Cellular integration of an enzyme-loaded polymersome nanoreactor.

Angew Chem Int Ed Engl 2010 Sep;49(40):7213-6

Institute for Molecules and Materials, Department of Organic Chemistry, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.

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September 2010

Delivery of DNA and siRNA by novel gemini-like amphiphilic peptides.

J Control Release 2010 Jul 8;145(1):33-9. Epub 2010 Apr 8.

Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands.

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July 2010

Biohybrid polymer capsules.

Chem Rev 2009 Nov;109(11):6212-74

Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands.

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November 2009

Single-step azide introduction in proteins via an aqueous diazo transfer.

Bioconjug Chem 2009 Jan;20(1):20-3

Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands.

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January 2009

A three-enzyme cascade reaction through positional assembly of enzymes in a polymersome nanoreactor.

Chemistry 2009 ;15(5):1107-14

Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.

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February 2009

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

Nat Methods 2008 Dec 2;5(12):1023-5. Epub 2008 Nov 2.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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December 2008

miRBase: tools for microRNA genomics.

Nucleic Acids Res 2008 Jan 8;36(Database issue):D154-8. Epub 2007 Nov 8.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK.

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January 2008

RNA editing of human microRNAs.

Genome Biol 2006 4;7(4):R27. Epub 2006 Apr 4.

Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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September 2006

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

Science 2006 Apr 16;312(5770):75-9. Epub 2006 Feb 16.

Developmental Genetics Program, Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.

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April 2006

miRBase: microRNA sequences, targets and gene nomenclature.

Nucleic Acids Res 2006 Jan;34(Database issue):D140-4

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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January 2006

GeneMCL in microarray analysis.

Comput Biol Chem 2005 Oct 19;29(5):354-9. Epub 2005 Sep 19.

School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK.

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October 2005