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Items: 1 to 50 of 142

1.

Combination of a six microRNA expression profile with four clinicopathological factors for response prediction of systemic treatment in patients with advanced colorectal cancer.

Neerincx M, Poel D, Sie DLS, van Grieken NCT, Shankaraiah RC, van der Wolf-de Lijster FSW, van Waesberghe JTM, Burggraaf JD, Eijk PP, Verhoef C, Ylstra B, Meijer GA, van de Wiel MA, Buffart TE, Verheul HMW.

PLoS One. 2018 Aug 3;13(8):e0201809. doi: 10.1371/journal.pone.0201809. eCollection 2018.

2.

Identification and Validation of a 3-Gene Methylation Classifier for HPV-Based Cervical Screening on Self-Samples.

Verlaat W, Snoek BC, Heideman DAM, Wilting SM, Snijders PJF, Novianti PW, van Splunter AP, Peeters CFW, van Trommel NE, Massuger LFAG, Bekkers RLM, Melchers WJG, van Kemenade FJ, Berkhof J, van de Wiel MA, Meijer CJLM, Steenbergen RDM.

Clin Cancer Res. 2018 Jul 15;24(14):3456-3464. doi: 10.1158/1078-0432.CCR-17-3615. Epub 2018 Apr 9.

PMID:
29632006
3.

Improved high-dimensional prediction with Random Forests by the use of co-data.

Te Beest DE, Mes SW, Wilting SM, Brakenhoff RH, van de Wiel MA.

BMC Bioinformatics. 2017 Dec 28;18(1):584. doi: 10.1186/s12859-017-1993-1.

4.

Blood-based metabolic signatures in Alzheimer's disease.

de Leeuw FA, Peeters CFW, Kester MI, Harms AC, Struys EA, Hankemeier T, van Vlijmen HWT, van der Lee SJ, van Duijn CM, Scheltens P, Demirkan A, van de Wiel MA, van der Flier WM, Teunissen CE.

Alzheimers Dement (Amst). 2017 Sep 6;8:196-207. doi: 10.1016/j.dadm.2017.07.006. eCollection 2017.

5.

Prognostic modeling of oral cancer by gene profiles and clinicopathological co-variables.

Mes SW, Te Beest D, Poli T, Rossi S, Scheckenbach K, van Wieringen WN, Brink A, Bertani N, Lanfranco D, Silini EM, van Diest PJ, Bloemena E, Leemans CR, van de Wiel MA, Brakenhoff RH.

Oncotarget. 2017 Jul 26;8(35):59312-59323. doi: 10.18632/oncotarget.19576. eCollection 2017 Aug 29.

6.

Methods for significance testing of categorical covariates in logistic regression models after multiple imputation: power and applicability analysis.

Eekhout I, van de Wiel MA, Heymans MW.

BMC Med Res Methodol. 2017 Aug 22;17(1):129. doi: 10.1186/s12874-017-0404-7.

7.

A Strategy to Find Suitable Reference Genes for miRNA Quantitative PCR Analysis and Its Application to Cervical Specimens.

Babion I, Snoek BC, van de Wiel MA, Wilting SM, Steenbergen RDM.

J Mol Diagn. 2017 Sep;19(5):625-637. doi: 10.1016/j.jmoldx.2017.04.010.

PMID:
28826607
8.

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes.

van den Broek E, van Lieshout S, Rausch C, Ylstra B, van de Wiel MA, Meijer GA, Fijneman RJA, Abeln S.

Version 2. F1000Res. 2016 Sep 19 [revised 2017 Jan 1];5:2340. doi: 10.12688/f1000research.9259.2. eCollection 2016.

9.

Gene Network Reconstruction using Global-Local Shrinkage Priors.

Leday GG, de Gunst MC, Kpogbezan GB, van der Vaart AW, van Wieringen WN, van de Wiel MA.

Ann Appl Stat. 2017 Mar;11(1):41-68.

10.

An empirical Bayes approach to network recovery using external knowledge.

Kpogbezan GB, van der Vaart AW, van Wieringen WN, Leday GGR, van de Wiel MA.

Biom J. 2017 Sep;59(5):932-947. doi: 10.1002/bimj.201600090. Epub 2017 Apr 10.

11.

COGITA network has constructed a glossary of diagnostic reasoning terms.

Barais M, Hauswaldt J, Dinant GJ, van de Wiel M, Stolper CF, Van Royen P.

Eur J Gen Pract. 2017 Dec;23(1):53-56. doi: 10.1080/13814788.2016.1242569.

12.

Better diagnostic signatures from RNAseq data through use of auxiliary co-data.

Novianti PW, Snoek BC, Wilting SM, van de Wiel MA.

Bioinformatics. 2017 May 15;33(10):1572-1574. doi: 10.1093/bioinformatics/btw837.

PMID:
28073760
13.

Neoadjuvant systemic therapy in breast cancer: Challenges and uncertainties.

Van de Wiel M, Dockx Y, Van den Wyngaert T, Stroobants S, Tjalma WAA, Huizing MT.

Eur J Obstet Gynecol Reprod Biol. 2017 Mar;210:144-156. doi: 10.1016/j.ejogrb.2016.12.014. Epub 2016 Dec 14. Review.

PMID:
28039758
14.

Erratum to: Assessment of predictive performance in incomplete data by combining internal validation and multiple imputation.

Wahl S, Boulesteix AL, Zierer A, Thorand B, van de Wiel MA.

BMC Med Res Methodol. 2016 Dec 5;16(1):170. No abstract available.

15.

Cachexia in cancer: what is in the definition?

Vanhoutte G, van de Wiel M, Wouters K, Sels M, Bartolomeeussen L, De Keersmaecker S, Verschueren C, De Vroey V, De Wilde A, Smits E, Cheung KJ, De Clerck L, Aerts P, Baert D, Vandoninck C, Kindt S, Schelfhaut S, Vankerkhoven M, Troch A, Ceulemans L, Vandenbergh H, Leys S, Rondou T, Dewitte E, Maes K, Pauwels P, De Winter B, Van Gaal L, Ysebaert D, Peeters M.

BMJ Open Gastroenterol. 2016 Oct 18;3(1):e000097. eCollection 2016.

16.

Assessment of predictive performance in incomplete data by combining internal validation and multiple imputation.

Wahl S, Boulesteix AL, Zierer A, Thorand B, van de Wiel MA.

BMC Med Res Methodol. 2016 Oct 26;16(1):144. Erratum in: BMC Med Res Methodol. 2016 Dec 5;16(1):170.

18.

Genomic profiling of stage II and III colon cancers reveals APC mutations to be associated with survival in stage III colon cancer patients.

van den Broek E, Krijgsman O, Sie D, Tijssen M, Mongera S, van de Wiel MA, Belt EJ, den Uil SH, Bril H, Stockmann HB, Ylstra B, Carvalho B, Meijer GA, Fijneman RJ.

Oncotarget. 2016 Nov 8;7(45):73876-73887. doi: 10.18632/oncotarget.12510.

19.

Reduced genomic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma.

Obulkasim A, Ylstra B, van Essen HF, Benner C, Stenning S, Langley R, Allum W, Cunningham D, Inam I, Hewitt LC, West NP, Meijer GA, van de Wiel MA, Grabsch HI.

Oncotarget. 2016 Jul 12;7(28):44084-44095. doi: 10.18632/oncotarget.9857.

20.

Testing for association between RNA-Seq and high-dimensional data.

Rauschenberger A, Jonker MA, van de Wiel MA, Menezes RX.

BMC Bioinformatics. 2016 Mar 8;17:118. doi: 10.1186/s12859-016-0961-5.

21.

Calculating flux to predict future cave radon concentrations.

Rowberry MD, Martí X, Frontera C, Van De Wiel MJ, Briestenský M.

J Environ Radioact. 2016 Jun;157:16-26. doi: 10.1016/j.jenvrad.2016.02.023. Epub 2016 Mar 4.

PMID:
26950394
22.

Diagnostic reasoning and underlying knowledge of students with preclinical patient contacts in PBL.

Diemers AD, van de Wiel MW, Scherpbier AJ, Baarveld F, Dolmans DH.

Med Educ. 2015 Dec;49(12):1229-38. doi: 10.1111/medu.12886.

PMID:
26611188
23.

A prognostic classifier for patients with colorectal cancer liver metastasis, based on AURKA, PTGS2 and MMP9.

Goos JA, Coupé VM, van de Wiel MA, Diosdado B, Delis-Van Diemen PM, Hiemstra AC, de Cuba EM, Beliën JA, Menke-van der Houven van Oordt CW, Geldof AA, Meijer GA, Hoekstra OS, Fijneman RJ; DeCoDe PET Group.

Oncotarget. 2016 Jan 12;7(2):2123-34. doi: 10.18632/oncotarget.6188.

24.

MiR expression profiles of paired primary colorectal cancer and metastases by next-generation sequencing.

Neerincx M, Sie DL, van de Wiel MA, van Grieken NC, Burggraaf JD, Dekker H, Eijk PP, Ylstra B, Verhoef C, Meijer GA, Buffart TE, Verheul HM.

Oncogenesis. 2015 Oct 5;4:e170. doi: 10.1038/oncsis.2015.29.

25.

Molecular imaging of aurora kinase A (AURKA) expression: Synthesis and preclinical evaluation of radiolabeled alisertib (MLN8237).

Goos JACM, Verbeek J, Geldof AA, Hiemstra AC, van de Wiel MA, Adamzek KA, Delis-Van Diemen PM, Stroud SG, Bradley DP, Meijer GA, Hoekstra OS, Fijneman RJA, Windhorst AD.

Nucl Med Biol. 2016 Jan;43(1):63-72. doi: 10.1016/j.nucmedbio.2015.08.007. Epub 2015 Sep 11.

PMID:
26432753
26.

High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer.

van den Broek E, Dijkstra MJ, Krijgsman O, Sie D, Haan JC, Traets JJ, van de Wiel MA, Nagtegaal ID, Punt CJ, Carvalho B, Ylstra B, Abeln S, Meijer GA, Fijneman RJ.

PLoS One. 2015 Sep 16;10(9):e0138141. doi: 10.1371/journal.pone.0138141. eCollection 2015.

27.

Better prediction by use of co-data: adaptive group-regularized ridge regression.

van de Wiel MA, Lien TG, Verlaat W, van Wieringen WN, Wilting SM.

Stat Med. 2016 Feb 10;35(3):368-81. doi: 10.1002/sim.6732. Epub 2015 Sep 13.

PMID:
26365903
28.

HCsnip: An R Package for Semi-supervised Snipping of the Hierarchical Clustering Tree.

Obulkasim A, van de Wiel MA.

Cancer Inform. 2015 Mar 22;14:1-19. doi: 10.4137/CIN.S22080. eCollection 2015. Review.

29.

Incorporating anti-VEGF pathway therapy as a continuum of care in metastatic colorectal cancer.

Papadimitriou K, Rolfo C, Dewaele E, Van De Wiel M, Van den Brande J, Altintas S, Huizing M, Specenier P, Peeters M.

Curr Treat Options Oncol. 2015 Apr;16(4):18. doi: 10.1007/s11864-015-0333-9. Review.

PMID:
25813037
30.

Semi-supervised adaptive-height snipping of the hierarchical clustering tree.

Obulkasim A, Meijer GA, van de Wiel MA.

BMC Bioinformatics. 2015 Jan 16;16:15. doi: 10.1186/s12859-014-0448-1.

31.

FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations.

Krijgsman O, Benner C, Meijer GA, van de Wiel MA, Ylstra B.

Cancer Inform. 2014 Dec 1;13:153-6. doi: 10.4137/CIN.S19519. eCollection 2014.

32.

Genomic landscape of metastatic colorectal cancer.

Haan JC, Labots M, Rausch C, Koopman M, Tol J, Mekenkamp LJ, van de Wiel MA, Israeli D, van Essen HF, van Grieken NC, Voorham QJ, Bosch LJ, Qu X, Kabbarah O, Verheul HM, Nagtegaal ID, Punt CJ, Ylstra B, Meijer GA.

Nat Commun. 2014 Nov 14;5:5457. doi: 10.1038/ncomms6457.

33.

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities.

Miok V, Wilting SM, van de Wiel MA, Jaspers A, van Noort PI, Brakenhoff RH, Snijders PJ, Steenbergen RD, van Wieringen WN.

BMC Bioinformatics. 2014 Oct 2;15:327. doi: 10.1186/1471-2105-15-327.

34.

Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas.

van Thuijl HF, Scheinin I, Sie D, Alentorn A, van Essen HF, Cordes M, Fleischeuer R, Gijtenbeek AM, Beute G, van den Brink WA, Meijer GA, Havenith M, Idbaih A, Hoang-Xuan K, Mokhtari K, Verhaak RG, van der Valk P, van de Wiel MA, Heimans JJ, Aronica E, Reijneveld JC, Wesseling P, Ylstra B.

Genome Biol. 2014 Sep 23;15(9):471. doi: 10.1186/s13059-014-0471-6.

35.

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.

Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B.

Genome Res. 2014 Dec;24(12):2022-32. doi: 10.1101/gr.175141.114. Epub 2014 Sep 18.

36.

How do gut feelings feature in tutorial dialogues on diagnostic reasoning in GP traineeship?

Stolper CF, Van de Wiel MW, Hendriks RH, Van Royen P, Van Bokhoven MA, Van der Weijden T, Dinant GJ.

Adv Health Sci Educ Theory Pract. 2015 May;20(2):499-513. doi: 10.1007/s10459-014-9543-3. Epub 2014 Sep 4.

37.

RNA sequencing of creatine transporter (SLC6A8) deficient fibroblasts reveals impairment of the extracellular matrix.

Nota B, Ndika JD, van de Kamp JM, Kanhai WA, van Dooren SJ, van de Wiel MA, Pals G, Salomons GS.

Hum Mutat. 2014 Sep;35(9):1128-35. doi: 10.1002/humu.22609. Epub 2014 Jul 15.

PMID:
24962355
38.

M-CSF priming of osteoclast precursors can cause osteoclastogenesis-insensitivity, which can be prevented and overcome on bone.

De Vries TJ, Schoenmaker T, Aerts D, Grevers LC, Souza PP, Nazmi K, van de Wiel M, Ylstra B, Lent PL, Leenen PJ, Everts V.

J Cell Physiol. 2015 Jan;230(1):210-25. doi: 10.1002/jcp.24702.

PMID:
24962140
39.

stepwiseCM: An R Package for Stepwise Classification of Cancer Samples Using Multiple Heterogeneous Data Sets.

Obulkasim A, van de Wiel MA.

Cancer Inform. 2014 Jan 2;13:1-11. doi: 10.4137/CIN.S13075. eCollection 2014. Review.

40.

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs.

van de Wiel MA, Neerincx M, Buffart TE, Sie D, Verheul HM.

BMC Bioinformatics. 2014 Apr 26;15:116. doi: 10.1186/1471-2105-15-116.

41.

Penalized differential pathway analysis of integrative oncogenomics studies.

van Wieringen WN, van de Wiel MA.

Stat Appl Genet Mol Biol. 2014 Apr 1;13(2):141-58. doi: 10.1515/sagmb-2013-0020.

PMID:
24552967
42.

[Are postgraduate courses for GPs relevant to diagnostics?].

Stolper CF, van de Wiel MW, Dinant GJ.

Ned Tijdschr Geneeskd. 2013;157(52):A6923. Dutch.

PMID:
24382043
43.

DNA copy number aberrations in endobronchial lesions: a validated predictor for cancer.

van Boerdonk RA, Daniels JM, Snijders PJ, Grünberg K, Thunnissen E, van de Wiel MA, Ylstra B, Postmus PE, Meijer CJ, Meijer GA, Smit EF, Sutedja TG, Heideman DA.

Thorax. 2014 May;69(5):451-7. doi: 10.1136/thoraxjnl-2013-203821. Epub 2013 Nov 13.

PMID:
24227199
44.

EBM and gut feelings.

Stolper CF, van de Wiel MW.

Med Teach. 2014 Jan;36(1):87-8. doi: 10.3109/0142159X.2013.835390. Epub 2013 Sep 16. No abstract available.

PMID:
24040750
45.

General power and sample size calculations for high-dimensional genomic data.

van Iterson M, van de Wiel MA, Boer JM, de Menezes RX.

Stat Appl Genet Mol Biol. 2013 Aug;12(4):449-67. doi: 10.1515/sagmb-2012-0046.

PMID:
23934609
46.

Methotrexate normalizes up-regulated folate pathway genes in rheumatoid arthritis.

Blits M, Jansen G, Assaraf YG, van de Wiel MA, Lems WF, Nurmohamed MT, van Schaardenburg D, Voskuyl AE, Wolbink GJ, Vosslamber S, Verweij CL.

Arthritis Rheum. 2013 Nov;65(11):2791-802. doi: 10.1002/art.38094.

47.

Analysis of small-sample clinical genomics studies using multi-parameter shrinkage: application to high-throughput RNA interference screening.

van de Wiel MA, de Menezes RX, Siebring-van Olst E, van Beusechem VW.

BMC Med Genomics. 2013;6 Suppl 2:S1. doi: 10.1186/1755-8794-6-S2-S1. Epub 2013 May 7.

48.

DNA copy number profiling reveals extensive genomic loss in hereditary BRCA1 and BRCA2 ovarian carcinomas.

Kamieniak MM, Muñoz-Repeto I, Rico D, Osorio A, Urioste M, García-Donas J, Hernando S, Robles-Díaz L, Ramón Y Cajal T, Cazorla A, Sáez R, García-Bueno JM, Domingo S, Borrego S, Palacios J, van de Wiel MA, Ylstra B, Benítez J, García MJ.

Br J Cancer. 2013 Apr 30;108(8):1732-42. doi: 10.1038/bjc.2013.141. Epub 2013 Apr 4.

49.

Regional differences in gene expression and promoter usage in aged human brains.

Pardo LM, Rizzu P, Francescatto M, Vitezic M, Leday GG, Sanchez JS, Khamis A, Takahashi H, van de Berg WD, Medvedeva YA, van de Wiel MA, Daub CO, Carninci P, Heutink P.

Neurobiol Aging. 2013 Jul;34(7):1825-36. doi: 10.1016/j.neurobiolaging.2013.01.005. Epub 2013 Feb 19.

50.

PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data.

Leday GG, van de Wiel MA.

Bioinformatics. 2013 Apr 15;29(8):1081-2. doi: 10.1093/bioinformatics/btt082. Epub 2013 Feb 17.

PMID:
23419375

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