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Value pluralism in research integrity.

Peels R, de Ridder J, Haven T, Bouter L.

Res Integr Peer Rev. 2019 Aug 22;4:18. doi: 10.1186/s41073-019-0076-4. eCollection 2019.


Activation of human monocytes by colloidal aluminium salts.

Vrieling H, Kooijman S, de Ridder J, Thies-Weesie D, Soema P, Jiskoot W, van Riet E, Heck A, Philipse A, Kersten G, Meiring H, Pennings J, Metz B.

J Pharm Sci. 2019 Aug 23. pii: S0022-3549(19)30511-8. doi: 10.1016/j.xphs.2019.08.014. [Epub ahead of print]


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

Omerzu M, Fenderico N, de Barbanson B, Sprangers J, de Ridder J, Maurice MM.

Biol Open. 2019 Aug 9;8(8). pii: bio042812. doi: 10.1242/bio.042812.


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

Dorssers LCJ, Gillis AJM, Stoop H, van Marion R, Nieboer MM, van Riet J, van de Werken HJG, Oosterhuis JW, de Ridder J, Looijenga LHJ.

Br J Cancer. 2019 Feb;120(4):444-452. doi: 10.1038/s41416-019-0381-1. Epub 2019 Feb 11.


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

Allahyar A, Ubels J, de Ridder J.

PLoS Comput Biol. 2019 Feb 6;15(2):e1006657. doi: 10.1371/journal.pcbi.1006657. eCollection 2019 Feb.


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

Nieboer MM, Dorssers LCJ, Straver R, Looijenga LHJ, de Ridder J.

PLoS One. 2018 Nov 29;13(11):e0208002. doi: 10.1371/journal.pone.0208002. eCollection 2018.


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

Taskesen E, Huisman SMH, Mahfouz A, Krijthe JH, de Ridder J, van de Stolpe A, van den Akker E, Verhaegh W, Reinders MJT.

Sci Rep. 2018 Nov 23;8(1):17304. doi: 10.1038/s41598-018-35518-w.


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

Broekema MF, Massink MPG, De Ligt J, Stigter ECA, Monajemi H, De Ridder J, Burgering BMT, van Haaften GW, Kalkhoven E.

Front Physiol. 2018 Sep 26;9:1363. doi: 10.3389/fphys.2018.01363. eCollection 2018.


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

Ranzani M, Alifrangis C, Thompson NA, Rust AG, Allahyar A, Iyer V, Price S, Ellis P, Turner G, de Ridder J, McDermott U, Adams DJ.

Pigment Cell Melanoma Res. 2019 Mar;32(2):332-335. doi: 10.1111/pcmr.12737. Epub 2018 Oct 19. No abstract available.


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

Ubels J, Sonneveld P, van Beers EH, Broijl A, van Vliet MH, de Ridder J.

Nat Commun. 2018 Jul 27;9(1):2943. doi: 10.1038/s41467-018-05348-5.


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

Rang FJ, Kloosterman WP, de Ridder J.

Genome Biol. 2018 Jul 13;19(1):90. doi: 10.1186/s13059-018-1462-9. Review.


Enhancer hubs and loop collisions identified from single-allele topologies.

Allahyar A, Vermeulen C, Bouwman BAM, Krijger PHL, Verstegen MJAM, Geeven G, van Kranenburg M, Pieterse M, Straver R, Haarhuis JHI, Jalink K, Teunissen H, Renkens IJ, Kloosterman WP, Rowland BD, de Wit E, de Ridder J, de Laat W.

Nat Genet. 2018 Aug;50(8):1151-1160. doi: 10.1038/s41588-018-0161-5. Epub 2018 Jul 9.


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

Cretu Stancu M, van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, de Ligt J, Pregno G, Giachino D, Mandrile G, Espejo Valle-Inclan J, Korzelius J, de Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP.

Nat Commun. 2017 Nov 6;8(1):1326. doi: 10.1038/s41467-017-01343-4.


Specific Contributions of Age of Onset, Callous-Unemotional Traits and Impulsivity to Reactive and Proactive Aggression in Youths with Conduct Disorders.

Urben S, Habersaat S, Pihet S, Suter M, de Ridder J, Stéphan P.

Psychiatr Q. 2018 Mar;89(1):1-10. doi: 10.1007/s11126-017-9506-y.


The association between seven-day objectively measured habitual physical activity and 24 h ambulatory blood pressure: the SABPA study.

Hamer M, Bruwer EJ, de Ridder JH, Swanepoel M, Kengne AP, Cockeran M, Malan L.

J Hum Hypertens. 2017 Jun;31(6):409-414. doi: 10.1038/jhh.2016.93. Epub 2017 Jan 26.


Incidence and origin of histologically confirmed liver metastases: an explorative case-study of 23,154 patients.

de Ridder J, de Wilt JH, Simmer F, Overbeek L, Lemmens V, Nagtegaal I.

Oncotarget. 2016 Aug 23;7(34):55368-55376. doi: 10.18632/oncotarget.10552.


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

Taskesen E, Huisman SM, Mahfouz A, Krijthe JH, de Ridder J, van de Stolpe A, van den Akker E, Verheagh W, Reinders MJ.

Sci Rep. 2016 Apr 25;6:24949. doi: 10.1038/srep24949. Erratum in: Sci Rep. 2018 Nov 23;8(1):17304.


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

Gilroy KL, Terry A, Naseer A, de Ridder J, Allahyar A, Wang W, Carpenter E, Mason A, Wong GK, Cameron ER, Kilbey A, Neil JC.

PLoS One. 2016 Apr 20;11(4):e0154070. doi: 10.1371/journal.pone.0154070. eCollection 2016.


Association between objectively measured physical activity, chronic stress and leukocyte telomere length.

von Känel R, Bruwer EJ, Hamer M, de Ridder JH, Malan L.

J Sports Med Phys Fitness. 2017 Oct;57(10):1349-1358. doi: 10.23736/S0022-4707.16.06426-4. Epub 2016 Apr 13.


Management of liver metastases in colorectal cancer patients: A retrospective case-control study of systemic therapy versus liver resection.

de Ridder JAM, van der Stok EP, Mekenkamp LJ, Wiering B, Koopman M, Punt CJA, Verhoef C, de Wilt JH.

Eur J Cancer. 2016 May;59:13-21. doi: 10.1016/j.ejca.2016.02.003. Epub 2016 Mar 16.


Comparison of anthropometric measurements of adiposity in relation to cancer risk: a systematic review of prospective studies.

De Ridder J, Julián-Almárcegui C, Mullee A, Rinaldi S, Van Herck K, Vicente-Rodríguez G, Huybrechts I.

Cancer Causes Control. 2016 Mar;27(3):291-300. doi: 10.1007/s10552-015-0709-y. Epub 2016 Jan 13. Review.


Liver Resection for Metastatic Disease; A Population-Based Analysis of Trends.

de Ridder JA, Lemmens VE, Overbeek LI, Nagtegaal ID, de Wilt JH; Dutch Liver Surgery Group.

Dig Surg. 2016;33(2):104-13. doi: 10.1159/000441802. Epub 2016 Jan 6.


Gender Differences in at Risk Versus Offender Adolescents: A Dimensional Approach of Antisocial Behavior.

Urben S, Habersaat S, Suter M, Pihet S, De Ridder J, Stéphan P.

Psychiatr Q. 2016 Dec;87(4):619-631.


Diagnostic yield and accuracy of CT angiography, MR angiography, and digital subtraction angiography for detection of macrovascular causes of intracerebral haemorrhage: prospective, multicentre cohort study.

van Asch CJ, Velthuis BK, Rinkel GJ, Algra A, de Kort GA, Witkamp TD, de Ridder JC, van Nieuwenhuizen KM, de Leeuw FE, Schonewille WJ, de Kort PL, Dippel DW, Raaymakers TW, Hofmeijer J, Wermer MJ, Kerkhoff H, Jellema K, Bronner IM, Remmers MJ, Bienfait HP, Witjes RJ, Greving JP, Klijn CJ; DIAGRAM Investigators.

BMJ. 2015 Nov 9;351:h5762. doi: 10.1136/bmj.h5762.


Applications of DNA integrating elements: Facing the bias bully.

de Jong J, Wessels LF, van Lohuizen M, de Ridder J, Akhtar W.

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


Time-scales of hydrological forcing on the geochemistry and bacterial community structure of temperate peat soils.

Nunes FL, Aquilina L, de Ridder J, Francez AJ, Quaiser A, Caudal JP, Vandenkoornhuyse P, Dufresne A.

Sci Rep. 2015 Oct 6;5:14612. doi: 10.1038/srep14612.


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

Allahyar A, de Ridder J.

Bioinformatics. 2015 Jun 15;31(12):i311-9. doi: 10.1093/bioinformatics/btv255.


Lymphatic Invasion is an Independent Adverse Prognostic Factor in Patients with Colorectal Liver Metastasis.

de Ridder JA, Knijn N, Wiering B, de Wilt JH, Nagtegaal ID.

Ann Surg Oncol. 2015 Dec;22 Suppl 3:S638-45. doi: 10.1245/s10434-015-4562-8. Epub 2015 May 19.


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

Babaei S, Mahfouz A, Hulsman M, Lelieveldt BP, de Ridder J, Reinders M.

PLoS Comput Biol. 2015 May 12;11(5):e1004221. doi: 10.1371/journal.pcbi.1004221. eCollection 2015 May.


[A woman with acute pain and swelling of her wrist].

de Ridder JA, Koning GG.

Ned Tijdschr Geneeskd. 2015;159:A8623. Dutch.


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

Rijlaarsdam MA, Tax DM, Gillis AJ, Dorssers LC, Koestler DC, de Ridder J, Looijenga LH.

PLoS One. 2015 Apr 10;10(4):e0122146. doi: 10.1371/journal.pone.0122146. eCollection 2015. Erratum in: PLoS One. 2015;10(7):e0132981.


PAX5 is a tumor suppressor in mouse mutagenesis models of acute lymphoblastic leukemia.

Dang J, Wei L, de Ridder J, Su X, Rust AG, Roberts KG, Payne-Turner D, Cheng J, Ma J, Qu C, Wu G, Song G, Huether RG, Schulman B, Janke L, Zhang J, Downing JR, van der Weyden L, Adams DJ, Mullighan CG.

Blood. 2015 Jun 4;125(23):3609-17. doi: 10.1182/blood-2015-02-626127. Epub 2015 Apr 8.


Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia.

Taskesen E, Babaei S, Reinders MM, de Ridder J.

BMC Bioinformatics. 2015;16 Suppl 4:S5. doi: 10.1186/1471-2105-16-S4-S5. Epub 2015 Feb 23.


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

Babaei S, Akhtar W, de Jong J, Reinders M, de Ridder J.

Nat Commun. 2015 Feb 27;6:6381. doi: 10.1038/ncomms7381.


The challenges of underweight and overweight in South African children: are we winning or losing the battle? A systematic review.

Monyeki MA, Awotidebe A, Strydom GL, de Ridder JH, Mamabolo RL, Kemper HC.

Int J Environ Res Public Health. 2015 Jan 22;12(2):1156-73. doi: 10.3390/ijerph120201156. Review.


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

de Ridder J, Meysman P, Oluwagbemi O, Abeel T.

PLoS Comput Biol. 2014 Jul 3;10(7):e1003708. doi: 10.1371/journal.pcbi.1003708. eCollection 2014 Jul.


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

Hulsman M, Dimitrakopoulos C, de Ridder J.

Bioinformatics. 2014 Jun 15;30(12):i237-45. doi: 10.1093/bioinformatics/btu283.


Chromatin landscapes of retroviral and transposon integration profiles.

de Jong J, Akhtar W, Badhai J, Rust AG, Rad R, Hilkens J, Berns A, van Lohuizen M, Wessels LF, de Ridder J.

PLoS Genet. 2014 Apr 10;10(4):e1004250. doi: 10.1371/journal.pgen.1004250. eCollection 2014 Apr.


Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.

Lee E, de Ridder J, Kool J, Wessels LF, Bussemaker HJ.

Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5747-52. doi: 10.1073/pnas.1309293111. Epub 2014 Apr 2.


Implicit attitudes and self-concepts towards transgression and aggression: differences between male community and offender adolescents, and associations with psychopathic traits.

Suter M, Pihet S, de Ridder J, Zimmermann G, Stephan P.

J Adolesc. 2014 Jul;37(5):669-80. doi: 10.1016/j.adolescence.2014.03.004. Epub 2014 Mar 25.


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

Huser CA, Gilroy KL, de Ridder J, Kilbey A, Borland G, Mackay N, Jenkins A, Bell M, Herzyk P, van der Weyden L, Adams DJ, Rust AG, Cameron E, Neil JC.

PLoS Genet. 2014 Feb 27;10(2):e1004167. doi: 10.1371/journal.pgen.1004167. eCollection 2014 Feb.


Preoperative FDG-PET-scan in patients with resectable colorectal liver metastases does not improve overall survival: a retrospective analyses stratified by clinical risk score.

Ayez N, de Ridder J, Wiering B, Oyen WJ, de Wilt JH, Verhoef C.

Dig Surg. 2013;30(4-6):451-8. doi: 10.1159/000357351. Epub 2014 Jan 18.


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

de Ridder J, Bromberg Y, Michaut M, Satagopam VP, Corpas M, MacIntyre G, Alexandrov T.

PLoS Comput Biol. 2013;9(11):e1003350. doi: 10.1371/journal.pcbi.1003350. Epub 2013 Nov 7. No abstract available.


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

Yen J, White RM, Wedge DC, Van Loo P, de Ridder J, Capper A, Richardson J, Jones D, Raine K, Watson IR, Wu CJ, Cheng J, Martincorena I, Nik-Zainal S, Mudie L, Moreau Y, Marshall J, Ramakrishna M, Tarpey P, Shlien A, Whitmore I, Gamble S, Latimer C, Langdon E, Kaufman C, Dovey M, Taylor A, Menzies A, McLaren S, O'Meara S, Butler A, Teague J, Lister J, Chin L, Campbell P, Adams DJ, Zon LI, Patton EE, Stemple DL, Futreal PA.

Genome Biol. 2013;14(10):R113.


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

Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LF, van Lohuizen M, van Steensel B.

Cell. 2013 Aug 15;154(4):914-27. doi: 10.1016/j.cell.2013.07.018.


Structural vascular disease in Africans: Performance of ethnic-specific waist circumference cut points using logistic regression and neural network analyses: The SABPA study.

Botha J, de Ridder JH, Potgieter JC, Steyn HS, Malan L.

Exp Clin Endocrinol Diabetes. 2013 Oct;121(9):515-20. doi: 10.1055/s-0033-1351289. Epub 2013 Aug 9.


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

Van der Mynsbrugge J, De Ridder J, Hemelsoet K, Waroquier M, Van Speybroeck V.

Chemistry. 2013 Aug 26;19(35):11568-76. doi: 10.1002/chem.201301272. Epub 2013 Jul 29.


Histopathological evaluation of resected colorectal cancer liver metastases: what should be done?

Knijn N, de Ridder JA, Punt CJ, de Wilt JH, Nagtegaal ID.

Histopathology. 2013 Aug;63(2):149-56. doi: 10.1111/his.12124. Epub 2013 Jun 13. Review.


Pattern recognition in bioinformatics.

de Ridder D, de Ridder J, Reinders MJ.

Brief Bioinform. 2013 Sep;14(5):633-47. doi: 10.1093/bib/bbt020. Epub 2013 Apr 4. Review.


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

Babaei S, Hulsman M, Reinders M, de Ridder J.

BMC Bioinformatics. 2013 Jan 23;14:29. doi: 10.1186/1471-2105-14-29.

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