Works matching AU de Ridder, Jeroen

Results: 72

Direct detection of 8-oxo-dG using nanopore sequencing.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60391-3

By:

Pagès-Gallego, Marc;
van Soest, Daan M. K.;
Besselink, Nicolle J. M.;
Straver, Roy;
Keijer, Janneke P.;
Vermeulen, Carlo;
Marcozzi, Alessio;
van Roosmalen, Markus J.;
van Boxtel, Ruben;
Burgering, Boudewijn M. T.;
Dansen, Tobias B.;
de Ridder, Jeroen

Publication type:

Article

ReQuant: improved base modification calling by k-mer value imputation Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 9, p. 1, doi. 10.1093/nar/gkaf323

By:

Straver, Roy;
Vermeulen, Carlo;
Verity-Legg, Joe R;
Pagès-Gallego, Marc;
Stoker, Dieter G G;
van Oudenaarden, Alexander;
de Ridder, Jeroen

Publication type:

Article

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

Published in:

2016

By:

Heringa, Jaap;
Reinders, Marcel;
Abeln, Sanne;
de Ridder, Jeroen

Publication type:

Proceeding

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

Published in:

Bioinformatics, 2014, v. 30, n. 12, p. i237, doi. 10.1093/bioinformatics/btu283

By:

Hulsman, Marc;
Dimitrakopoulos, Christos;
de Ridder, Jeroen

Publication type:

Article

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

Published in:

Bioinformatics, 2010, v. 26, n. 12, p. i149, doi. 10.1093/bioinformatics/btq211

By:

De Ridder, Jeroen;
Gerrits, Alice;
Bot, Jan;
De Haan, Gerald;
Reinders, Marcel;
Wessels, Lodewyk

Publication type:

Article

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

Published in:

Bioinformatics, 2007, v. 23, n. 13, p. i133, doi. 10.1093/bioinformatics/btm202

By:

Jeroen de Ridder;
Jaap Kool;
Anthony Uren;
Jan Bot;
Lodewyk Wessels;
Marcel Reinders

Publication type:

Article

Author Correction: Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-35518-w

By:

Taskesen, Erdogan;
Huisman, Sjoerd M. H.;
Mahfouz, Ahmed;
Krijthe, Jesse H.;
de Ridder, Jeroen;
van de Stolpe, Anja;
van den Akker, Erik;
Verhaegh, Wim;
Reinders, Marcel J. T.

Publication type:

Article

In Defense of the Netherlands Code of Conduct for Research Integrity: Response to Radder.

Published in:

Accountability in Research: Policies & Quality Assurance, 2023, v. 30, n. 5, p. 276, doi. 10.1080/08989621.2023.2167599

By:

de Ridder, Jeroen;
Bouter, Lex;
Haven, Tamarinde;
Peels, Rik;
Tijdink, Joeri;
Zeegers, Maurice P.

Publication type:

Article

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

Published in:

PLoS ONE, 2018, v. 13, n. 11, p. 1, doi. 10.1371/journal.pone.0208002

By:

Nieboer, Marleen M.;
Dorssers, Lambert C. J.;
Straver, Roy;
Looijenga, Leendert H. J.;
de Ridder, Jeroen

Publication type:

Article

Online and Offline Battles: Usage of Different Political Conflict Frames.

Published in:

International Journal of Press/Politics, 2024, v. 29, n. 1, p. 26, doi. 10.1177/19401612221096633

By:

van der Goot, Emma;
Kruikemeier, Sanne;
de Ridder, Jeroen;
Vliegenthart, Rens

Publication type:

Article

Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis.

Published in:

Nature Genetics, 2011, v. 43, n. 12, p. 1202, doi. 10.1038/ng.990

By:

March, H Nikki;
Rust, Alistair G;
Wright, Nicholas A;
ten Hoeve, Jelle;
de Ridder, Jeroen;
Eldridge, Matthew;
van der Weyden, Louise;
Berns, Anton;
Gadiot, Jules;
Uren, Anthony;
Kemp, Richard;
Arends, Mark J;
Wessels, Lodewyk F A;
Winton, Douglas J;
Adams, David J

Publication type:

Article

Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-93917-y

By:

Nieboer, Marleen M.;
Nguyen, Luan;
de Ridder, Jeroen

Publication type:

Article

IS THERE EPISTEMIC JUSTIFICATION FOR SECRECY IN SCIENCE?

Published in:

Episteme (Cambridge University Press), 2013, v. 10, n. 2, p. 101, doi. 10.1017/epi.2013.18

By:

DE RIDDER, JEROEN

Publication type:

Article

A Single Complex Agpat2 Allele in a Patient With Partial Lipodystrophy.

Published in:

Frontiers in Physiology, 2018, p. N.PAG, doi. 10.3389/fphys.2018.01363

By:

Broekema, Marjoleine F.;
Massink, Maarten P. G.;
De Ligt, Joep;
Stigter, Edwin C. A.;
Monajemi, Houshang;
De Ridder, Jeroen;
Burgering, Boudewijn M. T.;
van Haaften, Gijs W.;
Kalkhoven, Eric

Publication type:

Article

Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling.

Published in:

Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02903-2

By:

Pagès-Gallego, Marc;
de Ridder, Jeroen

Publication type:

Article

Genome Wide DNA Methylation Profiles Provide Clues to the Origin and Pathogenesis of Germ Cell Tumors.

Published in:

PLoS ONE, 2015, v. 10, n. 4, p. 1, doi. 10.1371/journal.pone.0122146

By:

Rijlaarsdam, Martin A.;
Tax, David M. J.;
Gillis, Ad J. M.;
Dorssers, Lambert C. J.;
Koestler, Devin C.;
de Ridder, Jeroen;
Looijenga, Leendert H. J.

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006657

By:

Allahyar, Amin;
Ubels, Joske;
de Ridder, Jeroen

Publication type:

Article

The Online Battlefield: How Conflict Frames in Political Advertisements Affect Political Participation in a Multiparty Context.

Published in:

Political Studies, 2024, v. 72, n. 3, p. 1112, doi. 10.1177/00323217231178105

By:

van der Goot, Emma;
Kruikemeier, Sanne;
Vliegenthart, Rens;
de Ridder, Jeroen

Publication type:

Article

Enthalpy and Entropy Barriers Explain the Effects of Topology on the Kinetics of Zeolite-Catalyzed Reactions.

Published in:

Chemistry - A European Journal, 2013, v. 19, n. 35, p. 11568, doi. 10.1002/chem.201301272

By:

Van der Mynsbrugge, Jeroen;
De Ridder, Jeroen;
Hemelsoet, Karen;
Waroquier, Michel;
Van Speybroeck, Veronique

Publication type:

Article

Predicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37647-x

By:

de Jong, Anouk C.;
Danyi, Alexandra;
van Riet, Job;
de Wit, Ronald;
Sjöström, Martin;
Feng, Felix;
de Ridder, Jeroen;
Lolkema, Martijn P.

Publication type:

Article

Unsafe Assertions.

Published in:

Australasian Journal of Philosophy, 2012, v. 90, n. 4, p. 797, doi. 10.1080/00048402.2011.641573

By:

Blaauw, Martijn;
de Ridder, Jeroen

Publication type:

Article

Integration of gene expression and DNAmethylation profiles improves molecular subtype classification in acute myeloid leukemia.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/1471-2105-16-S4-S5

By:

Taskesen, Erdogan;
Babaei, Sepideh;
Reinders, Marcel M. J.;
de Ridder, Jeroen

Publication type:

Article

Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 12, p. 1530, doi. 10.1371/journal.pcbi.0020166

By:

Ridder, Jeroen de;
Uren, Anthony;
Kool, Jaap;
Reinders, Marcel;
Wessels, Lodewyk

Publication type:

Article

Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics.

Published in:

Scientific Reports, 2016, p. 24949, doi. 10.1038/srep24949

By:

Taskesen, Erdogan;
Huisman, Sjoerd M. H.;
Mahfouz, Ahmed;
Krijthe, Jesse H.;
de Ridder, Jeroen;
van de Stolpe, Anja;
van den Akker, Erik;
Verheagh, Wim;
Reinders, Marcel J. T.

Publication type:

Article

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

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-05348-5

By:

Ubels, Joske;
Sonneveld, Pieter;
van Beers, Erik H.;
Broijl, Annemiek;
van Vliet, Martin H.;
de Ridder, Jeroen

Publication type:

Article

Multi-country metabolic signature discovery for chicken health classification.

Published in:

Metabolomics, 2023, v. 19, n. 2, p. 1, doi. 10.1007/s11306-023-01973-4

By:

Wolthuis, Joanna C.;
Magnúsdóttir, Stefanía;
Stigter, Edwin;
Tang, Yuen Fung;
Jans, Judith;
Gilbert, Myrthe;
van der Hee, Bart;
Langhout, Pim;
Gerrits, Walter;
Kies, Arie;
de Ridder, Jeroen;
van Mil, Saskia

Publication type:

Article

MetaboShiny: interactive analysis and metabolite annotation of mass spectrometry-based metabolomics data.

Published in:

Metabolomics, 2020, v. 16, n. 9, p. N.PAG, doi. 10.1007/s11306-020-01717-8

By:

Wolthuis, Joanna C.;
Magnusdottir, Stefania;
Pras-Raves, Mia;
Moshiri, Maryam;
Jans, Judith J. M.;
Burgering, Boudewijn;
van Mil, Saskia;
de Ridder, Jeroen

Publication type:

Article

sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data.

Published in:

PeerJ, 2020, p. 1, doi. 10.7717/peerj.8214

By:

Kuzniar, Arnold;
Maassen, Jason;
Verhoeven, Stefan;
Santuari, Luca;
Shneider, Carl;
Kloosterman, Wigard P.;
Ridder, Jeroen de

Publication type:

Article

Pattern recognition in bioinformatics.

Published in:

Briefings in Bioinformatics, 2013, v. 14, n. 5, p. 633, doi. 10.1093/bib/bbt020

By:

de Ridder, Dick;
de Ridder, Jeroen;
Reinders, Marcel J. T.

Publication type:

Article

Kunnen goed geïnformeerde burgers wel betrokken burgers zijn?

Published in:

Algemeen Nederlands Tijdschrift voor Wijsbegeerte, 2024, v. 116, n. 1, p. 74, doi. 10.5117/ANTW2024.1.006.RIDD

By:

de Ridder, Jeroen

Publication type:

Article

Wetenschap en sciëntisme in de populaire wetenschap.

Published in:

Algemeen Nederlands Tijdschrift voor Wijsbegeerte, 2015, v. 107, n. 3, p. 233, doi. 10.5117/ANTW2015.3.RIDD

By:

de Ridder, Jeroen

Publication type:

Article

Group belief reconceived.

Published in:

Synthese, 2022, v. 200, n. 2, p. 1, doi. 10.1007/s11229-022-03633-x

By:

de Ridder, Jeroen

Publication type:

Article

Scientism: The New Orthodoxy.

Published in:

2016

By:

de Ridder, Jeroen

Publication type:

Book Review

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

Published in:

PLoS Computational Biology, 2015, v. 11, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004221

By:

Babaei, Sepideh;
Mahfouz, Ahmed;
Hulsman, Marc;
Lelieveldt, Boudewijn P. F.;
de Ridder, Jeroen;
Reinders, Marcel

Publication type:

Article

Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 7, p. 1, doi. 10.1371/journal.pcbi.1003708

By:

de Ridder, Jeroen;
Meysman, Pieter;
Oluwagbemi, Olugbenga;
Abeel, Thomas

Publication type:

Article

The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

Published in:

2013

By:

de Ridder, Jeroen;
Bromberg, Yana;
Michaut, Magali;
Satagopam, Venkata P.;
Corpas, Manuel;
Macintyre, Geoff;
Alexandrov, Theodore

Publication type:

Opinion

Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pcbi.1002834

By:

de Ridder, Jeroen;
Abeel, Thomas;
Michaut, Magali;
Satagopam, Venkata P.;
Gehlenborg, Nils

Publication type:

Article

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

Published in:

Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1462-9

By:

Rang, Franka J.;
Kloosterman, Wigard P.;
de Ridder, Jeroen

Publication type:

Article

The epistemology of groups.

Published in:

2023

By:

de Ridder, Jeroen

Publication type:

Book Review

The Epistemic Status of Evolutionary Theory.

Published in:

Theology & Science, 2017, v. 15, n. 4, p. 454, doi. 10.1080/14746700.2017.1369759

By:

Brink, Gijsbert van den;
de Ridder, Jeroen;
Woudenberg, René van

Publication type:

Article

Cancer Type Classification in Liquid Biopsies Based on Sparse Mutational Profiles Enabled through Data Augmentation and Integration.

Published in:

Life (2075-1729), 2022, v. 12, n. 1, p. 1, doi. 10.3390/life12010001

By:

Danyi, Alexandra;
Jager, Myrthe;
de Ridder, Jeroen

Publication type:

Article

Evidence of survival bias in the association between APOE-Є4 and age at ischemic stroke onset.

Published in:

Frontiers in Genetics, 2024, p. 1, doi. 10.3389/fgene.2024.1392061

By:

von Berg, Joanna;
McArdle, Patrick F.;
Häppölä, Paavo;
Haessler, Jeffrey;
Kooperberg, Charles;
Lemmens, Robin;
Pezzini, Alessandro;
Thijs, Vincent;
Pulit, Sara L.;
Kittner, Steven J.;
Mitchell, Braxton D.;
de Ridder, Jeroen;
van der Laan, Sander W.

Publication type:

Article

Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 1, p. e3, doi. 10.1093/nar/gkac931

By:

Pedersen, Brent S;
de Ridder, Jeroen

Publication type:

Article

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01343-4

By:

Stancu, Mircea Cretu;
van Roosmalen, Markus J.;
Renkens, Ivo;
Nieboer, Marleen M.;
Middelkamp, Sjors;
de Ligt, Joep;
Pregno, Giulia;
Giachino, Daniela;
Mandrile, Giorgia;
Valle-Inclan, Jose Espejo;
Korzelius, Jerome;
de Bruijn, Ewart;
Cuppen, Edwin;
Talkowski, Michael E.;
Marschall, Tobias;
de Ridder, Jeroen;
Kloosterman, Wigard P.

Publication type:

Article

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

Published in:

Nature Communications, 2015, v. 6, n. 2, p. 6381, doi. 10.1038/ncomms7381

By:

Babaei, Sepideh;
Akhtar, Waseem;
de Jong, Johann;
Reinders, Marcel;
de Ridder, Jeroen

Publication type:

Article

Online Illusions of Understanding.

Published in:

Social Epistemology, 2024, v. 38, n. 6, p. 727, doi. 10.1080/02691728.2022.2151331

By:

de Ridder, Jeroen

Publication type:

Article

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

Published in:

Pigment Cell & Melanoma Research, 2019, v. 32, n. 2, p. 332, doi. 10.1111/pcmr.12737

By:

Ranzani, Marco;
Alifrangis, Constantine;
Thompson, Nicola A.;
Rust, Alistair G.;
Allahyar, Amin;
Iyer, Vivek;
Price, Stacey;
Ellis, Peter;
Turner, Gemma;
de Ridder, Jeroen;
McDermott, Ultan;
Adams, David J.

Publication type:

Article

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

Published in:

PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0154070

By:

Gilroy, Kathryn L.;
Terry, Anne;
Naseer, Asif;
de Ridder, Jeroen;
Allahyar, Amin;
Wang, Weiwei;
Carpenter, Eric;
Mason, Andrew;
Wong, Gane K-S.;
Cameron, Ewan R.;
Kilbey, Anna;
Neil, James C.

Publication type:

Article

Value pluralism in research integrity.

Published in:

2019

By:

Peels, Rik;
de Ridder, Jeroen;
Haven, Tamarinde;
Bouter, Lex

Publication type:

Letter

The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models.

Published in:

Genome Biology, 2013, v. 14, n. 10, p. 3, doi. 10.1186/gb-2013-14-10-r113

By:

Yen, Jennifer;
White, Richard M.;
Wedge, David C.;
Loo, Peter Van;
Ridder, Jeroen de;
Capper, Amy;
Richardson, Jennifer;
Jones, David;
Raine, Keiran;
Watson, Ian R.;
Chang-Jiun Wu;
Jiqiu Cheng;
Martincorena, Iñigo;
Nik-Zainal, Serena;
Mudie, Laura;
Moreau, Yves;
Marshall, John;
Ramakrishna, Manasa;
Tarpey, Patrick;
Shlien, Adam

Publication type:

Article