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A high-throughput 3' UTR reporter screening identifies microRNA interactomes of cancer genes.

Van Peer G, Mets E, Claeys S, De Punt I, Lefever S, Ongenaert M, Rondou P, Speleman F, Mestdagh P, Vandesompele J.

PLoS One. 2018 Mar 9;13(3):e0194017. doi: 10.1371/journal.pone.0194017. eCollection 2018.


Localization and Expression of Nuclear Factor of Activated T-Cells 5 in Myoblasts Exposed to Pro-inflammatory Cytokines or Hyperosmolar Stress and in Biopsies from Myositis Patients.

Herbelet S, De Vlieghere E, Gonçalves A, De Paepe B, Schmidt K, Nys E, Weynants L, Weis J, Van Peer G, Vandesompele J, Schmidt J, De Wever O, De Bleecker JL.

Front Physiol. 2018 Feb 21;9:126. doi: 10.3389/fphys.2018.00126. eCollection 2018.


Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma.

Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A.

Cancer Discov. 2018 Mar 6. pii: CD-16-0861. doi: 10.1158/2159-8290.CD-16-0861. [Epub ahead of print]


The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease.

De Wilde B, Beckers A, Lindner S, Kristina A, De Preter K, Depuydt P, Mestdagh P, Sante T, Lefever S, Hertwig F, Peng Z, Shi LM, Lee S, Vandermarliere E, Martens L, Menten B, Schramm A, Fischer M, Schulte J, Vandesompele J, Speleman F.

Oncotarget. 2017 Dec 22;9(9):8334-8349. doi: 10.18632/oncotarget.23614. eCollection 2018 Feb 2.


Prognostic and Therapeutic Implications of Circulating Androgen Receptor Gene Copy Number in Prostate Cancer Patients Using Droplet Digital Polymerase Chain Reaction.

Buelens S, Claeys T, Dhondt B, Poelaert F, Vynck M, Yigit N, Thas O, Ost P, Vandesompele J, Lumen N, Kumps C.

Clin Genitourin Cancer. 2017 Dec 29. pii: S1558-7673(17)30394-4. doi: 10.1016/j.clgc.2017.12.008. [Epub ahead of print]


Computational deconvolution of transcriptomics data from mixed cell populations.

Avila Cobos F, Vandesompele J, Mestdagh P, De Preter K.

Bioinformatics. 2018 Jan 16. doi: 10.1093/bioinformatics/bty019. [Epub ahead of print]


decodeRNA- predicting non-coding RNA functions using guilt-by-association.

Lefever S, Anckaert J, Volders PJ, Luypaert M, Vandesompele J, Mestdagh P.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax042.


Evaluation of relative quantification of alternatively spliced transcripts using droplet digital PCR.

Van Heetvelde M, Van Loocke W, Trypsteen W, Baert A, Vanderheyden K, Crombez B, Vandesompele J, De Leeneer K, Claes KBM.

Biomol Detect Quantif. 2017 Sep 20;13:40-48. doi: 10.1016/j.bdq.2017.09.001. eCollection 2017 Sep.


MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation.

Van Goethem A, Mestdagh P, Van Maerken T, Vandesompele J.

Methods Mol Biol. 2017;1654:197-208. doi: 10.1007/978-1-4939-7231-9_13.


Dual targeting of MDM2 and BCL2 as a therapeutic strategy in neuroblastoma.

Van Goethem A, Yigit N, Moreno-Smith M, Vasudevan SA, Barbieri E, Speleman F, Shohet J, Vandesompele J, Van Maerken T.

Oncotarget. 2017 Jul 4;8(34):57047-57057. doi: 10.18632/oncotarget.18982. eCollection 2017 Aug 22.


High-throughput PCR assay design for targeted resequencing using primerXL.

Lefever S, Pattyn F, De Wilde B, Coppieters F, De Keulenaer S, Hellemans J, Vandesompele J.

BMC Bioinformatics. 2017 Sep 6;18(1):400. doi: 10.1186/s12859-017-1809-3.


A unified censored normal regression model for qPCR differential gene expression analysis.

Pipelers P, Clement L, Vynck M, Hellemans J, Vandesompele J, Thas O.

PLoS One. 2017 Aug 17;12(8):e0182832. doi: 10.1371/journal.pone.0182832. eCollection 2017.


Quality control of digital PCR assays and platforms.

Vynck M, Vandesompele J, Thas O.

Anal Bioanal Chem. 2017 Oct;409(25):5919-5931. doi: 10.1007/s00216-017-0538-9. Epub 2017 Aug 10.


Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.

Willems H, Jacobs A, Hadiwikarta WW, Venken T, Valkenborg D, Van Roy N, Vandesompele J, Hooyberghs J.

PLoS One. 2017 May 25;12(5):e0177384. doi: 10.1371/journal.pone.0177384. eCollection 2017.


Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products.

Verheggen K, Volders PJ, Mestdagh P, Menschaert G, Van Damme P, Gevaert K, Martens L, Vandesompele J.

J Proteome Res. 2017 Jul 7;16(7):2508-2515. doi: 10.1021/acs.jproteome.7b00085. Epub 2017 Jun 5.


Secretome analysis of breast cancer-associated adipose tissue to identify paracrine regulators of breast cancer growth.

Lapeire L, Hendrix A, Lecoutere E, Van Bockstal M, Vandesompele J, Maynard D, Braems G, Van Den Broecke R, Müller C, Bracke M, Cocquyt V, Denys H, De Wever O.

Oncotarget. 2017 Jul 18;8(29):47239-47249. doi: 10.18632/oncotarget.17592.


Zipper plot: visualizing transcriptional activity of genomic regions.

Avila Cobos F, Anckaert J, Volders PJ, Everaert C, Rombaut D, Vandesompele J, De Preter K, Mestdagh P.

BMC Bioinformatics. 2017 May 2;18(1):231. doi: 10.1186/s12859-017-1651-7.


Long non-coding RNAs in cutaneous melanoma: clinical perspectives.

Hulstaert E, Brochez L, Volders PJ, Vandesompele J, Mestdagh P.

Oncotarget. 2017 Jun 27;8(26):43470-43480. doi: 10.18632/oncotarget.16478. Review.


MicroRNA-184 is a downstream effector of albuminuria driving renal fibrosis in rats with diabetic nephropathy.

Zanchi C, Macconi D, Trionfini P, Tomasoni S, Rottoli D, Locatelli M, Rudnicki M, Vandesompele J, Mestdagh P, Remuzzi G, Benigni A, Zoja C.

Diabetologia. 2017 Jun;60(6):1114-1125. doi: 10.1007/s00125-017-4248-9. Epub 2017 Mar 31.


Model-Based Classification for Digital PCR: Your Umbrella for Rain.

Jacobs BKM, Goetghebeur E, Vandesompele J, De Ganck A, Nijs N, Beckers A, Papazova N, Roosens NH, Clement L.

Anal Chem. 2017 Apr 18;89(8):4461-4467. doi: 10.1021/acs.analchem.6b04208. Epub 2017 Apr 7.


Influence of microRNAs and Long Non-Coding RNAs in Cancer Chemoresistance.

Ayers D, Vandesompele J.

Genes (Basel). 2017 Mar 3;8(3). pii: E95. doi: 10.3390/genes8030095. Review.


Reply: Direct Detection of Circulating MicroRNAs Unveiled the Absence of MicroRNA-218-5p in Smoker Subjects.

Conickx G, Mestdagh P, Vandesompele J, Brusselle GG, Bracke KR.

Am J Respir Crit Care Med. 2017 Aug 15;196(4):533. doi: 10.1164/rccm.201701-0224LE. No abstract available.


EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research.

EV-TRACK Consortium, Van Deun J, Mestdagh P, Agostinis P, Akay Ö, Anand S, Anckaert J, Martinez ZA, Baetens T, Beghein E, Bertier L, Berx G, Boere J, Boukouris S, Bremer M, Buschmann D, Byrd JB, Casert C, Cheng L, Cmoch A, Daveloose D, De Smedt E, Demirsoy S, Depoorter V, Dhondt B, Driedonks TA, Dudek A, Elsharawy A, Floris I, Foers AD, Gärtner K, Garg AD, Geeurickx E, Gettemans J, Ghazavi F, Giebel B, Kormelink TG, Hancock G, Helsmoortel H, Hill AF, Hyenne V, Kalra H, Kim D, Kowal J, Kraemer S, Leidinger P, Leonelli C, Liang Y, Lippens L, Liu S, Lo Cicero A, Martin S, Mathivanan S, Mathiyalagan P, Matusek T, Milani G, Monguió-Tortajada M, Mus LM, Muth DC, Németh A, Nolte-'t Hoen EN, O'Driscoll L, Palmulli R, Pfaffl MW, Primdal-Bengtson B, Romano E, Rousseau Q, Sahoo S, Sampaio N, Samuel M, Scicluna B, Soen B, Steels A, Swinnen JV, Takatalo M, Thaminy S, Théry C, Tulkens J, Van Audenhove I, van der Grein S, Van Goethem A, van Herwijnen MJ, Van Niel G, Van Roy N, Van Vliet AR, Vandamme N, Vanhauwaert S, Vergauwen G, Verweij F, Wallaert A, Wauben M, Witwer KW, Zonneveld MI, De Wever O, Vandesompele J, Hendrix A.

Nat Methods. 2017 Feb 28;14(3):228-232. doi: 10.1038/nmeth.4185.


The transcriptome of lung tumor-infiltrating dendritic cells reveals a tumor-supporting phenotype and a microRNA signature with negative impact on clinical outcome.

Pyfferoen L, Brabants E, Everaert C, De Cabooter N, Heyns K, Deswarte K, Vanheerswynghels M, De Prijck S, Waegemans G, Dullaers M, Hammad H, De Wever O, Mestdagh P, Vandesompele J, Lambrecht BN, Vermaelen KY.

Oncoimmunology. 2016 Nov 8;6(1):e1253655. doi: 10.1080/2162402X.2016.1253655. eCollection 2017.


Corrigendum: Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W.

Sci Rep. 2017 Jan 24;7:41112. doi: 10.1038/srep41112. No abstract available.


miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure.

Van Peer G, De Paepe A, Stock M, Anckaert J, Volders PJ, Vandesompele J, De Baets B, Waegeman W.

Nucleic Acids Res. 2017 Apr 20;45(7):e51. doi: 10.1093/nar/gkw1260.


Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples.

Van Goethem A, Yigit N, Everaert C, Moreno-Smith M, Mus LM, Barbieri E, Speleman F, Mestdagh P, Shohet J, Van Maerken T, Vandesompele J.

Sci Rep. 2016 Nov 30;6:37876. doi: 10.1038/srep37876.


Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay.

Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W.

Sci Rep. 2016 Oct 26;6:36111. doi: 10.1038/srep36111.


Stage 4S neuroblastoma tumors show a characteristic DNA methylation portrait.

Decock A, Ongenaert M, De Wilde B, Brichard B, Noguera R, Speleman F, Vandesompele J.

Epigenetics. 2016 Sep 6:0. [Epub ahead of print]


Flexible analysis of digital PCR experiments using generalized linear mixed models.

Vynck M, Vandesompele J, Nijs N, Menten B, De Ganck A, Thas O.

Biomol Detect Quantif. 2016 Jun 24;9:1-13. doi: 10.1016/j.bdq.2016.06.001. eCollection 2016 Sep.


RT-qPCR gene expression analysis in zebrafish: Preanalytical precautions and use of expressed repetitive elements for normalization.

Vanhauwaert S, Lefever S, Coucke P, Speleman F, De Paepe A, Vandesompele J, Willaert A.

Methods Cell Biol. 2016;135:329-42. doi: 10.1016/bs.mcb.2016.02.002. Epub 2016 Mar 4.


MicroRNA Profiling Reveals a Role for MicroRNA-218-5p in the Pathogenesis of Chronic Obstructive Pulmonary Disease.

Conickx G, Mestdagh P, Avila Cobos F, Verhamme FM, Maes T, Vanaudenaerde BM, Seys LJ, Lahousse L, Kim RY, Hsu AC, Wark PA, Hansbro PM, Joos GF, Vandesompele J, Bracke KR, Brusselle GG.

Am J Respir Crit Care Med. 2017 Jan 1;195(1):43-56. doi: 10.1164/rccm.201506-1182OC.


Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR.

Mestdagh P, Lefever S, Volders PJ, Derveaux S, Hellemans J, Vandesompele J.

Sci Data. 2016 Jul 5;3:160052. doi: 10.1038/sdata.2016.52.


Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia.

Wallaert A, Durinck K, Van Loocke W, Van de Walle I, Matthijssens F, Volders PJ, Avila Cobos F, Rombaut D, Rondou P, Mestdagh P, Vandesompele J, Poppe B, Taghon T, Soulier J, Van Vlierberghe P, Speleman F.

Leukemia. 2016 Sep;30(9):1927-30. doi: 10.1038/leu.2016.82. Epub 2016 Apr 22. No abstract available.


Asthma inflammatory phenotypes show differential microRNA expression in sputum.

Maes T, Cobos FA, Schleich F, Sorbello V, Henket M, De Preter K, Bracke KR, Conickx G, Mesnil C, Vandesompele J, Lahousse L, Bureau F, Mestdagh P, Joos GF, Ricciardolo FL, Brusselle GG, Louis R.

J Allergy Clin Immunol. 2016 May;137(5):1433-46. doi: 10.1016/j.jaci.2016.02.018.


Targeted resequencing and variant validation using pxlence PCR assays.

Coppieters F, Verniers K, De Leeneer K, Vandesompele J, Lefever S.

Biomol Detect Quantif. 2015 Oct 9;6:22-6. doi: 10.1016/j.bdq.2015.09.001. eCollection 2016 Jan.


Melanoma addiction to the long non-coding RNA SAMMSON.

Leucci E, Vendramin R, Spinazzi M, Laurette P, Fiers M, Wouters J, Radaelli E, Eyckerman S, Leonelli C, Vanderheyden K, Rogiers A, Hermans E, Baatsen P, Aerts S, Amant F, Van Aelst S, van den Oord J, de Strooper B, Davidson I, Lafontaine DL, Gevaert K, Vandesompele J, Mestdagh P, Marine JC.

Nature. 2016 Mar 24;531(7595):518-22. doi: 10.1038/nature17161.


Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples.

Zeka F, Vanderheyden K, De Smet E, Cuvelier CA, Mestdagh P, Vandesompele J.

Sci Rep. 2016 Feb 22;6:21418. doi: 10.1038/srep21418.


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.


Quantitative and Functional Requirements for Bioluminescent Cancer Models.

Feys L, Descamps B, Vanhove C, Vermeulen S, Vandesompele JO, Vanderheyden K, Messens K, Bracke M, De Wever O.

In Vivo. 2016 Jan-Feb;30(1):1-11.


Renal microRNA- and RNA-profiles in progressive chronic kidney disease.

Rudnicki M, Perco P, D Haene B, Leierer J, Heinzel A, Mühlberger I, Schweibert N, Sunzenauer J, Regele H, Kronbichler A, Mestdagh P, Vandesompele J, Mayer B, Mayer G.

Eur J Clin Invest. 2016 Mar;46(3):213-26. doi: 10.1111/eci.12585. Epub 2016 Jan 21.


Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma.

Decock A, Ongenaert M, Cannoodt R, Verniers K, De Wilde B, Laureys G, Van Roy N, Berbegall AP, Bienertova-Vasku J, Bown N, Clément N, Combaret V, Haber M, Hoyoux C, Murray J, Noguera R, Pierron G, Schleiermacher G, Schulte JH, Stallings RL, Tweddle DA; Children’s Cancer and Leukaemia Group (CCLG), De Preter K, Speleman F, Vandesompele J.

Oncotarget. 2016 Jan 12;7(2):1960-72. doi: 10.18632/oncotarget.6477.


Inhibition of CDK4/6 as a novel therapeutic option for neuroblastoma.

Rihani A, Vandesompele J, Speleman F, Van Maerken T.

Cancer Cell Int. 2015 Jul 30;15:76. doi: 10.1186/s12935-015-0224-y. eCollection 2015.


RNA expression signatures and posttranscriptional regulation in diabetic nephropathy.

Rudnicki M, Beckers A, Neuwirt H, Vandesompele J.

Nephrol Dial Transplant. 2015 Aug;30 Suppl 4:iv35-42. doi: 10.1093/ndt/gfv079. Review.


MYCN-driven regulatory mechanisms controlling LIN28B in neuroblastoma.

Beckers A, Van Peer G, Carter DR, Gartlgruber M, Herrmann C, Agarwal S, Helsmoortel HH, Althoff K, Molenaar JJ, Cheung BB, Schulte JH, Benoit Y, Shohet JM, Westermann F, Marshall GM, Vandesompele J, De Preter K, Speleman F.

Cancer Lett. 2015 Sep 28;366(1):123-32. doi: 10.1016/j.canlet.2015.06.015. Epub 2015 Jun 26.


Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M.

Genome Biol. 2015 Jun 25;16:133. doi: 10.1186/s13059-015-0694-1.


Alternative Routes to Induce Naïve Pluripotency in Human Embryonic Stem Cells.

Duggal G, Warrier S, Ghimire S, Broekaert D, Van der Jeught M, Lierman S, Deroo T, Peelman L, Van Soom A, Cornelissen R, Menten B, Mestdagh P, Vandesompele J, Roost M, Slieker RC, Heijmans BT, Deforce D, De Sutter P, De Sousa Lopes SC, Heindryckx B.

Stem Cells. 2015 Sep;33(9):2686-98. doi: 10.1002/stem.2071. Epub 2015 Jun 24.


RDML-Ninja and RDMLdb for standardized exchange of qPCR data.

Ruijter JM, Lefever S, Anckaert J, Hellemans J, Pfaffl MW, Benes V, Bustin SA, Vandesompele J, Untergasser A; RDML consortium.

BMC Bioinformatics. 2015 Jun 20;16:197. doi: 10.1186/s12859-015-0637-6.


Non-coding RNAs in the pathogenesis of COPD.

De Smet EG, Mestdagh P, Vandesompele J, Brusselle GG, Bracke KR.

Thorax. 2015 Aug;70(8):782-91. doi: 10.1136/thoraxjnl-2014-206560. Epub 2015 May 20. Review.


Identification of miRNAs contributing to neuroblastoma chemoresistance.

Ayers D, Mestdagh P, Van Maerken T, Vandesompele J.

Comput Struct Biotechnol J. 2015 Apr 29;13:307-19. doi: 10.1016/j.csbj.2015.04.003. eCollection 2015.

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