Jeroen de Ridder

Jeroen de Ridder

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Jeroen de Ridder

Jeroen de Ridder

Publications by authors named "Jeroen de Ridder"

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Three-dimensional analysis of single molecule FISH in human colon organoids.

Biol Open 2019 Aug 9;8(8). Epub 2019 Aug 9.

Oncode Institute and Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, The Netherlands

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http://dx.doi.org/10.1242/bio.042812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6737975PMC
August 2019

Value pluralism in research integrity.

Res Integr Peer Rev 2019 22;4:18. Epub 2019 Aug 22.

1Philosophy Department, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s41073-019-0076-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706923PMC
August 2019

TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors.

PLoS One 2018 29;13(11):e0208002. Epub 2018 Nov 29.

Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208002PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6264523PMC
April 2019

A lentiviral vector-based insertional mutagenesis screen identifies mechanisms of resistance to MAPK inhibitors in melanoma.

Pigment Cell Melanoma Res 2019 03 19;32(2):332-335. Epub 2018 Oct 19.

Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1111/pcmr.12737DOI Listing
March 2019

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction.

PLoS Comput Biol 2019 02 6;15(2):e1006657. Epub 2019 Feb 6.

Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1006657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380593PMC
February 2019

Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development.

Br J Cancer 2019 Feb 11;120(4):444-452. Epub 2019 Feb 11.

Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1038/s41416-019-0381-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461884PMC
February 2019

A Single Complex Allele in a Patient With Partial Lipodystrophy.

Front Physiol 2018 26;9:1363. Epub 2018 Sep 26.

Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, Netherlands.

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http://dx.doi.org/10.3389/fphys.2018.01363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168662PMC
September 2018

From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.

Genome Biol 2018 07 13;19(1):90. Epub 2018 Jul 13.

Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584, CG, Utrecht, The Netherlands.

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http://dx.doi.org/10.1186/s13059-018-1462-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045860PMC
July 2018

Predicting treatment benefit in multiple myeloma through simulation of alternative treatment effects.

Nat Commun 2018 07 27;9(1):2943. Epub 2018 Jul 27.

Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/s41467-018-05348-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063966PMC
July 2018

Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics.

PLoS One 2016 20;11(4):e0154070. Epub 2016 Apr 20.

MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154070PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838236PMC
September 2016

ECCB 2016: The 15th European Conference on Computational Biology.

Bioinformatics 2016 09;32(17):i389-i392

University Medical Centre Utrecht, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btw481DOI Listing
September 2016

Genome wide DNA methylation profiles provide clues to the origin and pathogenesis of germ cell tumors.

PLoS One 2015 10;10(4):e0122146. Epub 2015 Apr 10.

Department of Pathology, Erasmus MC Cancer Institute-University Medical Center Rotterdam, Rotterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122146PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479500PMC
December 2015

FERAL: network-based classifier with application to breast cancer outcome prediction.

Bioinformatics 2015 Jun;31(12):i311-9

Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btv255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765883PMC
June 2015

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.

PLoS Comput Biol 2015 May 12;11(5):e1004221. Epub 2015 May 12.

Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1004221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429121PMC
May 2015

Applications of DNA integrating elements: Facing the bias bully.

Mob Genet Elements 2014 Nov-Dec;4(6):1-6. Epub 2015 Mar 9.

Division of Molecular Genetics; The Netherlands Cancer Institute ; Amsterdam, The Netherlands.

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http://dx.doi.org/10.4161/2159256X.2014.992694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588226PMC
March 2015

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.

Nat Commun 2015 Feb 27;6:6381. Epub 2015 Feb 27.

Delft Bioinformatics Lab, Faculty of Electrical Engineering Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://www.nature.com/articles/ncomms7381
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http://dx.doi.org/10.1038/ncomms7381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351571PMC
February 2015

The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

PLoS Comput Biol 2013 7;9(11):e1003350. Epub 2013 Nov 7.

Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1003350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820508PMC
July 2014

Soft skills: an important asset acquired from organizing regional student group activities.

PLoS Comput Biol 2014 Jul 3;10(7):e1003708. Epub 2014 Jul 3.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America; VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium.

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http://dx.doi.org/10.1371/journal.pcbi.1003708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080995PMC
July 2014

Scale-space measures for graph topology link protein network architecture to function.

Bioinformatics 2014 Jun;30(12):i237-45

Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628CD Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btu283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058939PMC
June 2014

Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.

Proc Natl Acad Sci U S A 2014 Apr 2;111(15):5747-52. Epub 2014 Apr 2.

Department of Biological Sciences, Columbia University, New York, NY 10027.

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http://dx.doi.org/10.1073/pnas.1309293111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992641PMC
April 2014

Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis.

PLoS Genet 2014 Feb 27;10(2):e1004167. Epub 2014 Feb 27.

Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937229PMC
February 2014

Pattern recognition in bioinformatics.

Brief Bioinform 2013 Sep 4;14(5):633-47. Epub 2013 Apr 4.

Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty of Electrical Engineering, Mathematics & Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands. Tel.: +31 15 2785114; Fax: +31 15 2787022;

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http://dx.doi.org/10.1093/bib/bbt020DOI Listing
September 2013

Enthalpy and entropy barriers explain the effects of topology on the kinetics of zeolite-catalyzed reactions.

Chemistry 2013 Aug 29;19(35):11568-76. Epub 2013 Jul 29.

Center for Molecular Modeling (CMM), Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium-QCMM Alliance, Ghent-Brussels, Belgium.

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http://dx.doi.org/10.1002/chem.201301272DOI Listing
August 2013

Chromatin position effects assayed by thousands of reporters integrated in parallel.

Cell 2013 Aug;154(4):914-27

Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.

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http://dx.doi.org/10.1016/j.cell.2013.07.018DOI Listing
August 2013

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.

BMC Bioinformatics 2013 Jan 23;14:29. Epub 2013 Jan 23.

Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-14-29DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626877PMC
January 2013

Computational identification of insertional mutagenesis targets for cancer gene discovery.

Nucleic Acids Res 2011 Aug 7;39(15):e105. Epub 2011 Jun 7.

Bioinformatics and Statistics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkr447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159484PMC
August 2011

Inferring combinatorial association logic networks in multimodal genome-wide screens.

Bioinformatics 2010 Jun;26(12):i149-57

Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btq211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881395PMC
June 2010

HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data.

BMC Bioinformatics 2010 May 21;11:275. Epub 2010 May 21.

Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, the Netherlands.

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http://dx.doi.org/10.1186/1471-2105-11-275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892465PMC
May 2010

Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes.

Bioinformatics 2007 Jul;23(13):i133-41

Information and Communication Theory Group, Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btm202DOI Listing
July 2007

Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens.

PLoS Comput Biol 2006 Dec 24;2(12):e166. Epub 2006 Oct 24.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, The Netherlands.

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http://dx.plos.org/10.1371/journal.pcbi.0020166
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.0020166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1676030PMC
December 2006