de Ridder J - Search Results

1

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. Dorssers LCJ, et al. Among authors: de ridder j. Br J Cancer. 2019 Feb;120(4):444-452. doi: 10.1038/s41416-019-0381-1. Epub 2019 Feb 11. Br J Cancer. 2019. PMID: 30739914 Free PMC article.

2

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. Rijlaarsdam MA, et al. Among authors: de ridder j. PLoS One. 2015 Apr 10;10(4):e0122146. doi: 10.1371/journal.pone.0122146. eCollection 2015. PLoS One. 2015. PMID: 25859847 Free PMC article.

3

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. Cretu Stancu M, et al. Among authors: de ridder j, de bruijn e, de ligt j. Nat Commun. 2017 Nov 6;8(1):1326. doi: 10.1038/s41467-017-01343-4. Nat Commun. 2017. PMID: 29109544 Free PMC article.

4

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

Nieboer MM, Dorssers LCJ, Straver R, Looijenga LHJ, de Ridder J. Nieboer MM, et al. Among authors: de ridder j. PLoS One. 2018 Nov 29;13(11):e0208002. doi: 10.1371/journal.pone.0208002. eCollection 2018. PLoS One. 2018. PMID: 30496231 Free PMC article.

5

svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning.

Nieboer MM, de Ridder J. Nieboer MM, et al. Among authors: de ridder j. Bioinformatics. 2020 Dec 30;36(Suppl_2):i692-i699. doi: 10.1093/bioinformatics/btaa802. Bioinformatics. 2020. PMID: 33381833

6

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

Nieboer MM, Nguyen L, de Ridder J. Nieboer MM, et al. Among authors: de ridder j. Sci Rep. 2021 Jul 13;11(1):14411. doi: 10.1038/s41598-021-93917-y. Sci Rep. 2021. PMID: 34257393 Free PMC article.

7

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

de Jong AC, Danyi A, van Riet J, de Wit R, Sjöström M, Feng F, de Ridder J, Lolkema MP. de Jong AC, et al. Among authors: de ridder j. Nat Commun. 2023 Apr 8;14(1):1968. doi: 10.1038/s41467-023-37647-x. Nat Commun. 2023. PMID: 37031196 Free PMC article.

8

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group; Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris QD, Stein LD; PCAWG Consortium. Jiao W, et al. Among authors: de ridder j. Nat Commun. 2020 Feb 5;11(1):728. doi: 10.1038/s41467-019-13825-8. Nat Commun. 2020. PMID: 32024849 Free PMC article.

9

Gene Networks Constructed Through Simulated Treatment Learning can Predict Proteasome Inhibitor Benefit in Multiple Myeloma.

Ubels J, Sonneveld P, van Vliet MH, de Ridder J. Ubels J, et al. Among authors: de ridder j. Clin Cancer Res. 2020 Nov 15;26(22):5952-5961. doi: 10.1158/1078-0432.CCR-20-0742. Epub 2020 Sep 10. Clin Cancer Res. 2020. PMID: 32913136

10

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. Allahyar A, et al. Among authors: de laat w, de ridder j, de wit e. Nat Genet. 2018 Aug;50(8):1151-1160. doi: 10.1038/s41588-018-0161-5. Epub 2018 Jul 9. Nat Genet. 2018. PMID: 29988121

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