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Items: 1 to 50 of 153

1.

MEXPRESS update 2019.

Koch A, Jeschke J, Van Criekinge W, van Engeland M, De Meyer T.

Nucleic Acids Res. 2019 Jul 2;47(W1):W561-W565. doi: 10.1093/nar/gkz445.

2.

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms.

Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S126-S140. doi: 10.1074/mcp.RA118.001218. Epub 2019 Apr 30.

3.

Multicenter Optimization and Validation of a 2-Gene mRNA Urine Test for Detection of Clinically Significant Prostate Cancer before Initial Prostate Biopsy.

Haese A, Trooskens G, Steyaert S, Hessels D, Brawer M, Vlaeminck-Guillem V, Ruffion A, Tilki D, Schalken J, Groskopf J, Van Criekinge W.

J Urol. 2019 Aug;202(2):256-263. doi: 10.1097/JU.0000000000000293. Epub 2019 Jul 8.

PMID:
31026217
4.

MGMT Promoter Methylation Cutoff with Safety Margin for Selecting Glioblastoma Patients into Trials Omitting Temozolomide: A Pooled Analysis of Four Clinical Trials.

Hegi ME, Genbrugge E, Gorlia T, Stupp R, Gilbert MR, Chinot OL, Nabors LB, Jones G, Van Criekinge W, Straub J, Weller M.

Clin Cancer Res. 2019 Mar 15;25(6):1809-1816. doi: 10.1158/1078-0432.CCR-18-3181. Epub 2018 Dec 4.

PMID:
30514777
5.

A comprehensive overview of genomic imprinting in breast and its deregulation in cancer.

Goovaerts T, Steyaert S, Vandenbussche CA, Galle J, Thas O, Van Criekinge W, De Meyer T.

Nat Commun. 2018 Oct 8;9(1):4120. doi: 10.1038/s41467-018-06566-7. Review.

6.

Exploratory analysis of the human breast DNA methylation profile upon soymilk exposure.

Coussement L, Bolca S, Van Criekinge W, Trooskens G, Mensaert K, Poels K, Roche N, Blondeel P, Godderis L, Depypere H, De Meyer T.

Sci Rep. 2018 Sep 11;8(1):13617. doi: 10.1038/s41598-018-31767-x.

7.

Cost-effectiveness of SelectMDx for prostate cancer in four European countries: a comparative modeling study.

Govers TM, Hessels D, Vlaeminck-Guillem V, Schmitz-Dräger BJ, Stief CG, Martinez-Ballesteros C, Ferro M, Borque-Fernando A, Rubio-Briones J, Sedelaar JPM, van Criekinge W, Schalken JA.

Prostate Cancer Prostatic Dis. 2019 Mar;22(1):101-109. doi: 10.1038/s41391-018-0076-3. Epub 2018 Aug 20.

PMID:
30127462
8.

Integrated transcriptomic and epigenomic analysis of ovarian cancer reveals epigenetically silenced GULP1.

Maldonado L, Brait M, Izumchenko E, Begum S, Chatterjee A, Sen T, Loyo M, Barbosa A, Poeta ML, Makarev E, Zhavoronkov A, Fazio VM, Angioli R, Rabitti C, Ongenaert M, Van Criekinge W, Noordhuis MG, de Graeff P, Wisman GBA, van der Zee AGJ, Hoque MO.

Cancer Lett. 2018 Oct 1;433:242-251. doi: 10.1016/j.canlet.2018.06.030. Epub 2018 Jun 28.

PMID:
29964205
9.

Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR.

Kint S, De Spiegelaere W, De Kesel J, Vandekerckhove L, Van Criekinge W.

PLoS One. 2018 Jun 14;13(6):e0199091. doi: 10.1371/journal.pone.0199091. eCollection 2018.

10.

Author Correction: Analysis of DNA methylation in cancer: location revisited.

Koch A, Joosten SC, Feng Z, de Ruijter TC, Draht MX, Melotte V, Smits KM, Veeck J, Herman JG, Van Neste L, Van Criekinge W, de Meyer T, van Engeland M.

Nat Rev Clin Oncol. 2018 Jul;15(7):467. doi: 10.1038/s41571-018-0028-9.

PMID:
29713045
11.

Analysis of DNA methylation in cancer: location revisited.

Koch A, Joosten SC, Feng Z, de Ruijter TC, Draht MX, Melotte V, Smits KM, Veeck J, Herman JG, Van Neste L, Van Criekinge W, De Meyer T, van Engeland M.

Nat Rev Clin Oncol. 2018 Jul;15(7):459-466. doi: 10.1038/s41571-018-0004-4. Review. Erratum in: Nat Rev Clin Oncol. 2018 Apr 30;:.

PMID:
29666440
12.

Evaluation of an Epigenetic Assay for Predicting Repeat Prostate Biopsy Outcome in African American Men.

Waterhouse RL Jr, Van Neste L, Moses KA, Barnswell C, Silberstein JL, Jalkut M, Tutrone R, Sylora J, Anglade R, Murdock M, Shiffman Z, Vandenberg T, Shah N, Carter M, Krispin M, Groskopf J, Van Criekinge W.

Urology. 2019 Jun;128:62-65. doi: 10.1016/j.urology.2018.04.001. Epub 2018 Apr 13.

13.

Epigenetic markers in circulating cell-free DNA as prognostic markers for survival of castration-resistant prostate cancer patients.

Hendriks RJ, Dijkstra S, Smit FP, Vandersmissen J, Van de Voorde H, Mulders PFA, van Oort IM, Van Criekinge W, Schalken JA.

Prostate. 2018 Apr;78(5):336-342. doi: 10.1002/pros.23477. Epub 2018 Jan 12.

14.

Novel Stool-Based Protein Biomarkers for Improved Colorectal Cancer Screening: A Case-Control Study.

Bosch LJW, de Wit M, Pham TV, Coupé VMH, Hiemstra AC, Piersma SR, Oudgenoeg G, Scheffer GL, Mongera S, Sive Droste JT, Oort FA, van Turenhout ST, Larbi IB, Louwagie J, van Criekinge W, van der Hulst RWM, Mulder CJJ, Carvalho B, Fijneman RJA, Jimenez CR, Meijer GA.

Ann Intern Med. 2017 Dec 19;167(12):855-866. doi: 10.7326/M17-1068. Epub 2017 Nov 21.

PMID:
29159365
15.

Stable Oxidative Cytosine Modifications Accumulate in Cardiac Mesenchymal Cells From Type2 Diabetes Patients: Rescue by α-Ketoglutarate and TET-TDG Functional Reactivation.

Spallotta F, Cencioni C, Atlante S, Garella D, Cocco M, Mori M, Mastrocola R, Kuenne C, Guenther S, Nanni S, Azzimato V, Zukunft S, Kornberger A, Sürün D, Schnütgen F, von Melchner H, Di Stilo A, Aragno M, Braspenning M, van Criekinge W, De Blasio MJ, Ritchie RH, Zaccagnini G, Martelli F, Farsetti A, Fleming I, Braun T, Beiras-Fernandez A, Botta B, Collino M, Bertinaria M, Zeiher AM, Gaetano C.

Circ Res. 2018 Jan 5;122(1):31-46. doi: 10.1161/CIRCRESAHA.117.311300. Epub 2017 Nov 20.

PMID:
29158345
16.

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.

Olexiouk V, Van Criekinge W, Menschaert G.

Nucleic Acids Res. 2018 Jan 4;46(D1):D497-D502. doi: 10.1093/nar/gkx1130.

17.

Decoy receptor 1 (DCR1) promoter hypermethylation and response to irinotecan in metastatic colorectal cancer.

Bosch LJW, Trooskens G, Snaebjornsson P, Coupé VMH, Mongera S, Haan JC, Richman SD, Koopman M, Tol J, de Meyer T, Louwagie J, Dehaspe L, van Grieken NCT, Ylstra B, Verheul HMW, van Engeland M, Nagtegaal ID, Herman JG, Quirke P, Seymour MT, Punt CJA, van Criekinge W, Carvalho B, Meijer GA.

Oncotarget. 2017 Jun 27;8(38):63140-63154. doi: 10.18632/oncotarget.18702. eCollection 2017 Sep 8.

18.

A urinary biomarker-based risk score correlates with multiparametric MRI for prostate cancer detection.

Hendriks RJ, van der Leest MMG, Dijkstra S, Barentsz JO, Van Criekinge W, Hulsbergen-van de Kaa CA, Schalken JA, Mulders PFA, van Oort IM.

Prostate. 2017 Oct;77(14):1401-1407. doi: 10.1002/pros.23401. Epub 2017 Aug 29.

PMID:
28853167
19.

Epigenetic risk score improves prostate cancer risk assessment.

Van Neste L, Groskopf J, Grizzle WE, Adams GW, DeGuenther MS, Kolettis PN, Bryant JE, Kearney GP, Kearney MC, Van Criekinge W, Gaston SM.

Prostate. 2017 Sep;77(12):1259-1264. doi: 10.1002/pros.23385. Epub 2017 Aug 1.

PMID:
28762545
20.

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study.

Hemmings SMJ, Malan-Müller S, van den Heuvel LL, Demmitt BA, Stanislawski MA, Smith DG, Bohr AD, Stamper CE, Hyde ER, Morton JT, Marotz CA, Siebler PH, Braspenning M, Van Criekinge W, Hoisington AJ, Brenner LA, Postolache TT, McQueen MB, Krauter KS, Knight R, Seedat S, Lowry CA.

Psychosom Med. 2017 Oct;79(8):936-946. doi: 10.1097/PSY.0000000000000512.

21.

Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer.

Tomar T, Alkema NG, Schreuder L, Meersma GJ, de Meyer T, van Criekinge W, Klip HG, Fiegl H, van Nieuwenhuysen E, Vergote I, Widschwendter M, Schuuring E, van der Zee AGJ, de Jong S, Wisman GBA.

BMC Med. 2017 Jun 23;15(1):116. doi: 10.1186/s12916-017-0870-0.

22.

Cost-effectiveness of a new urinary biomarker-based risk score compared to standard of care in prostate cancer diagnostics - a decision analytical model.

Dijkstra S, Govers TM, Hendriks RJ, Schalken JA, Van Criekinge W, Van Neste L, Grutters JPC, Sedelaar JPM, van Oort IM.

BJU Int. 2017 Nov;120(5):659-665. doi: 10.1111/bju.13861. Epub 2017 Apr 29.

23.

Genome-wide DNA Methylation Profiling Reveals Methylation Markers Associated with 3q Gain for Detection of Cervical Precancer and Cancer.

Verlaat W, Snijders PJF, Novianti PW, Wilting SM, De Strooper LMA, Trooskens G, Vandersmissen J, Van Criekinge W, Wisman GBA, Meijer CJLM, Heideman DAM, Steenbergen RDM.

Clin Cancer Res. 2017 Jul 15;23(14):3813-3822. doi: 10.1158/1078-0432.CCR-16-2641. Epub 2017 Jan 24.

24.

Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome.

Van Neste C, Laird A, O'Mahony F, Van Criekinge W, Deforce D, Van Nieuwerburgh F, Powles T, Harrison DJ, Stewart GD, De Meyer T.

Cell Oncol (Dordr). 2017 Jun;40(3):293-297. doi: 10.1007/s13402-016-0313-5. Epub 2017 Jan 10.

PMID:
28074387
25.

CLINICAL EVALUATION OF AN EPIGENETIC ASSAY TO PREDICT MISSED CANCER IN PROSTATE BIOPSY SPECIMENS.

Partin AW, VAN Criekinge W, Trock BJ, Epstein JI, VAN Neste L.

Trans Am Clin Climatol Assoc. 2016;127:313-327.

26.

A Four-Gene Promoter Methylation Marker Panel Consisting of GREM1, NEURL, LAD1, and NEFH Predicts Survival of Clear Cell Renal Cell Cancer Patients.

van Vlodrop IJH, Joosten SC, De Meyer T, Smits KM, Van Neste L, Melotte V, Baldewijns MMLL, Schouten LJ, van den Brandt PA, Jeschke J, Yi JM, Schuebel KE, Ahuja N, Herman JG, Aarts MJ, Bosman FT, Van Criekinge W, van Engeland M.

Clin Cancer Res. 2017 Apr 15;23(8):2006-2018. doi: 10.1158/1078-0432.CCR-16-1236. Epub 2016 Oct 18.

27.

Validation of a DNA Methylation-Mutation Urine Assay to Select Patients with Hematuria for Cystoscopy.

van Kessel KE, Beukers W, Lurkin I, Ziel-van der Made A, van der Keur KA, Boormans JL, Dyrskjøt L, Márquez M, Ørntoft TF, Real FX, Segersten U, Malats N, Malmström PU, Van Criekinge W, Zwarthoff EC.

J Urol. 2017 Mar;197(3 Pt 1):590-595. doi: 10.1016/j.juro.2016.09.118. Epub 2016 Oct 13.

PMID:
27746284
28.

Genome-wide methylome analysis using MethylCap-seq uncovers 4 hypermethylated markers with high sensitivity for both adeno- and squamous-cell cervical carcinoma.

Wang R, van Leeuwen RW, Boers A, Klip HG, de Meyer T, Steenbergen RD, van Criekinge W, van der Zee AG, Schuuring E, Wisman GB.

Oncotarget. 2016 Dec 6;7(49):80735-80750. doi: 10.18632/oncotarget.12598.

29.

Molecular and epigenetic features of melanomas and tumor immune microenvironment linked to durable remission to ipilimumab-based immunotherapy in metastatic patients.

Seremet T, Koch A, Jansen Y, Schreuer M, Wilgenhof S, Del Marmol V, Liènard D, Thielemans K, Schats K, Kockx M, Van Criekinge W, Coulie PG, De Meyer T, van Baren N, Neyns B.

J Transl Med. 2016 Aug 2;14(1):232. doi: 10.1186/s12967-016-0990-x.

30.

RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis.

Clausen MJ, Melchers LJ, Mastik MF, Slagter-Menkema L, Groen HJ, Laan BF, van Criekinge W, de Meyer T, Denil S, van der Vegt B, Wisman GB, Roodenburg JL, Schuuring E.

Epigenetics. 2016 Sep;11(9):653-663. Epub 2016 Jul 5.

31.

Risk score predicts high-grade prostate cancer in DNA-methylation positive, histopathologically negative biopsies.

Van Neste L, Partin AW, Stewart GD, Epstein JI, Harrison DJ, Van Criekinge W.

Prostate. 2016 Sep;76(12):1078-87. doi: 10.1002/pros.23191. Epub 2016 Apr 28.

32.

WRN Promoter CpG Island Hypermethylation Does Not Predict More Favorable Outcomes for Patients with Metastatic Colorectal Cancer Treated with Irinotecan-Based Therapy.

Bosch LJ, Luo Y, Lao VV, Snaebjornsson P, Trooskens G, Vlassenbroeck I, Mongera S, Tang W, Welcsh P, Herman JG, Koopman M, Nagtegaal ID, Punt CJ, van Criekinge W, Meijer GA, Monnat RJ Jr, Carvalho B, Grady WM.

Clin Cancer Res. 2016 Sep 15;22(18):4612-22. doi: 10.1158/1078-0432.CCR-15-2703. Epub 2016 Apr 27.

33.

Detection of High-grade Prostate Cancer Using a Urinary Molecular Biomarker-Based Risk Score.

Van Neste L, Hendriks RJ, Dijkstra S, Trooskens G, Cornel EB, Jannink SA, de Jong H, Hessels D, Smit FP, Melchers WJ, Leyten GH, de Reijke TM, Vergunst H, Kil P, Knipscheer BC, Hulsbergen-van de Kaa CA, Mulders PF, van Oort IM, Van Criekinge W, Schalken JA.

Eur Urol. 2016 Nov;70(5):740-748. doi: 10.1016/j.eururo.2016.04.012. Epub 2016 Apr 20.

PMID:
27108162
34.

Dynamic epigenetic changes to VHL occur with sunitinib in metastatic clear cell renal cancer.

Stewart GD, Powles T, Van Neste C, Meynert A, O'Mahony F, Laird A, Deforce D, Van Nieuwerburgh F, Trooskens G, Van Criekinge W, De Meyer T, Harrison DJ.

Oncotarget. 2016 May 3;7(18):25241-50. doi: 10.18632/oncotarget.8308.

35.

Corrigendum: A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq.

Steyaert S, Diddens J, Galle J, De Meester E, De Keulenaer S, Bakker A, Sohnius-Wilhelmi N, Frankl-Vilches C, Van der Linden A, Van Criekinge W, Berghe WV, De Meyer T.

Sci Rep. 2016 Mar 17;6:22472. doi: 10.1038/srep22472. No abstract available.

36.

Discovery of new methylation markers to improve screening for cervical intraepithelial neoplasia grade 2/3.

Boers A, Wang R, van Leeuwen RW, Klip HG, de Bock GH, Hollema H, van Criekinge W, de Meyer T, Denil S, van der Zee AGJ, Schuuring E, Wisman GBA.

Clin Epigenetics. 2016 Mar 9;8:29. doi: 10.1186/s13148-016-0196-3. eCollection 2016.

37.

A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq.

Steyaert S, Diddens J, Galle J, De Meester E, De Keulenaer S, Bakker A, Sohnius-Wilhelmi N, Frankl-Vilches C, Van der Linden A, Van Criekinge W, Vanden Berghe W, De Meyer T.

Sci Rep. 2016 Feb 11;6:20957. doi: 10.1038/srep20957. Erratum in: Sci Rep. 2016;6:22472.

38.

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing.

Decock A, Ongenaert M, Van Criekinge W, Speleman F, Vandesompele J.

Sci Data. 2016 Feb 2;3:160004. doi: 10.1038/sdata.2016.4.

39.

BMP-SMAD Signaling Regulates Lineage Priming, but Is Dispensable for Self-Renewal in Mouse Embryonic Stem Cells.

Gomes Fernandes M, Dries R, Roost MS, Semrau S, de Melo Bernardo A, Davis RP, Ramakrishnan R, Szuhai K, Maas E, Umans L, Abon Escalona V, Salvatori D, Deforce D, Van Criekinge W, Huylebroeck D, Mummery C, Zwijsen A, de Sousa Lopes SM.

Stem Cell Reports. 2016 Jan 12;6(1):85-94. doi: 10.1016/j.stemcr.2015.11.012. Epub 2015 Dec 17.

40.

Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison.

De Meyer T, Bady P, Trooskens G, Kurscheid S, Bloch J, Kros JM, Hainfellner JA, Stupp R, Delorenzi M, Hegi ME, Van Criekinge W.

Sci Rep. 2015 Oct 20;5:15375. doi: 10.1038/srep15375.

41.

Forensic Loci Allele Database (FLAD): Automatically generated, permanent identifiers for sequenced forensic alleles.

Van Neste C, Van Criekinge W, Deforce D, Van Nieuwerburgh F.

Forensic Sci Int Genet. 2016 Jan;20:e1-e3. doi: 10.1016/j.fsigen.2015.09.006. Epub 2015 Sep 21.

PMID:
26456067
42.

Identification and validation of WISP1 as an epigenetic regulator of metastasis in oral squamous cell carcinoma.

Clausen MJ, Melchers LJ, Mastik MF, Slagter-Menkema L, Groen HJ, van der Laan BF, van Criekinge W, de Meyer T, Denil S, Wisman GB, Roodenburg JL, Schuuring E.

Genes Chromosomes Cancer. 2016 Jan;55(1):45-59. doi: 10.1002/gcc.22310. Epub 2015 Sep 22.

PMID:
26391330
43.

Evaluation of an Epigenetic Profile for the Detection of Bladder Cancer in Patients with Hematuria.

van Kessel KE, Van Neste L, Lurkin I, Zwarthoff EC, Van Criekinge W.

J Urol. 2016 Mar;195(3):601-7. doi: 10.1016/j.juro.2015.08.085. Epub 2015 Aug 29.

PMID:
26327355
44.

MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data.

Koch A, De Meyer T, Jeschke J, Van Criekinge W.

BMC Genomics. 2015 Aug 26;16:636. doi: 10.1186/s12864-015-1847-z.

45.

Mining for viral fragments in methylation enriched sequencing data.

Mensaert K, Van Criekinge W, Thas O, Schuuring E, Steenbergen RD, Wisman GB, De Meyer T.

Front Genet. 2015 Feb 4;6:16. doi: 10.3389/fgene.2015.00016. eCollection 2015.

46.

Spectrin repeat containing nuclear envelope 1 and forkhead box protein E1 are promising markers for the detection of colorectal cancer in blood.

Melotte V, Yi JM, Lentjes MH, Smits KM, Van Neste L, Niessen HE, Wouters KA, Louwagie J, Schuebel KE, Herman JG, Baylin SB, van Criekinge W, Meijer GA, Ahuja N, van Engeland M.

Cancer Prev Res (Phila). 2015 Feb;8(2):157-64. doi: 10.1158/1940-6207.CAPR-14-0198. Epub 2014 Dec 23.

47.

Strategies for validation and testing of DNA methylation biomarkers.

Noehammer C, Pulverer W, Hassler MR, Hofner M, Wielscher M, Vierlinger K, Liloglou T, McCarthy D, Jensen TJ, Nygren A, Gohlke H, Trooskens G, Braspenning M, Van Criekinge W, Egger G, Weinhaeusel A.

Epigenomics. 2014;6(6):603-22. doi: 10.2217/epi.14.43. Review.

PMID:
25531255
48.

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration.

Crappé J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G.

Nucleic Acids Res. 2015 Mar 11;43(5):e29. doi: 10.1093/nar/gku1283. Epub 2014 Dec 15.

49.

On cross-sectional associations of leukocyte telomere length with cardiac systolic, diastolic and vascular function: the Asklepios study.

Denil SL, Rietzschel ER, De Buyzere ML, Van Daele CM, Segers P, De Bacquer D, Van Criekinge W, Bekaert S, Gillebert TC, De Meyer T; Asklepios Investigators.

PLoS One. 2014 Dec 15;9(12):e115071. doi: 10.1371/journal.pone.0115071. eCollection 2014.

50.

Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace(®)-application.

Van Neste C, Gansemans Y, De Coninck D, Van Hoofstat D, Van Criekinge W, Deforce D, Van Nieuwerburgh F.

Forensic Sci Int Genet. 2015 Mar;15:2-7. doi: 10.1016/j.fsigen.2014.10.006. Epub 2014 Oct 14.

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