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The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation.

Polycarpou-Schwarz M, Groß M, Mestdagh P, Schott J, Grund SE, Hildenbrand C, Rom J, Aulmann S, Sinn HP, Vandesompele J, Diederichs S.

Oncogene. 2018 May 16. doi: 10.1038/s41388-018-0281-5. [Epub ahead of print]


Expression Profiling Identifies the Noncoding Processed Transcript of HNRNPU with Proliferative Properties in Pancreatic Ductal Adenocarcinoma.

Sutaria DS, Jiang J, Azevedo-Pouly ACP, Lee EJ, Lerner MR, Brackett DJ, Vandesompele J, Mestdagh P, Schmittgen TD.

Noncoding RNA. 2017 Aug 25;3(3). pii: E24. doi: 10.3390/ncrna3030024.


Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic background.

Ghimire S, Van der Jeught M, Neupane J, Roost MS, Anckaert J, Popovic M, Van Nieuwerburgh F, Mestdagh P, Vandesompele J, Deforce D, Menten B, Chuva de Sousa Lopes S, De Sutter P, Heindryckx B.

Sci Rep. 2018 Apr 12;8(1):5884. doi: 10.1038/s41598-018-24051-5.


A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.

Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N; Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R.

Cancer Cell. 2018 Apr 9;33(4):690-705.e9. doi: 10.1016/j.ccell.2018.03.014. Epub 2018 Apr 2.


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.


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 May;8(5):582-599. doi: 10.1158/2159-8290.CD-16-0861. Epub 2018 Mar 6.


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.


Computational deconvolution of transcriptomics data from mixed cell populations.

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

Bioinformatics. 2018 Jun 1;34(11):1969-1979. doi: 10.1093/bioinformatics/bty019.


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.


Discovering cancer vulnerabilities using high-throughput micro-RNA screening.

Nikolic I, Elsworth B, Dodson E, Wu SZ, Gould CM, Mestdagh P, Marshall GM, Horvath LG, Simpson KJ, Swarbrick A.

Nucleic Acids Res. 2017 Dec 15;45(22):12657-12670. doi: 10.1093/nar/gkx1072.


microRNA profiling in lung tissue and bronchoalveolar lavage of cigarette smoke-exposed mice and in COPD patients: a translational approach.

Conickx G, Avila Cobos F, van den Berge M, Faiz A, Timens W, Hiemstra PS, Joos GF, Brusselle GG, Mestdagh P, Bracke KR.

Sci Rep. 2017 Oct 9;7(1):12871. doi: 10.1038/s41598-017-13265-8.


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.


How long noncoding RNAs enforce their will on mitochondrial activity: regulation of mitochondrial respiration, reactive oxygen species production, apoptosis, and metabolic reprogramming in cancer.

De Paepe B, Lefever S, Mestdagh P.

Curr Genet. 2018 Feb;64(1):163-172. doi: 10.1007/s00294-017-0744-1. Epub 2017 Sep 6. Review.


MicroRNAs as future therapeutic targets in COPD?

Bracke KR, Mestdagh P.

Eur Respir J. 2017 May 25;49(5). pii: 1700431. doi: 10.1183/13993003.00431-2017. Print 2017 May. No abstract available.


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.


Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data.

Everaert C, Luypaert M, Maag JLV, Cheng QX, Dinger ME, Hellemans J, Mestdagh P.

Sci Rep. 2017 May 8;7(1):1559. doi: 10.1038/s41598-017-01617-3.


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.


Direct comparison of distinct naive pluripotent states in human embryonic stem cells.

Warrier S, Van der Jeught M, Duggal G, Tilleman L, Sutherland E, Taelman J, Popovic M, Lierman S, Chuva De Sousa Lopes S, Van Soom A, Peelman L, Van Nieuwerburgh F, De Coninck DIM, Menten B, Mestdagh P, Van de Sompele J, Deforce D, De Sutter P, Heindryckx B.

Nat Commun. 2017 Apr 21;8:15055. doi: 10.1038/ncomms15055.


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.


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.


The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states.

Barry G, Briggs JA, Hwang DW, Nayler SP, Fortuna PR, Jonkhout N, Dachet F, Maag JL, Mestdagh P, Singh EM, Avesson L, Kaczorowski DC, Ozturk E, Jones NC, Vetter I, Arriola-Martinez L, Hu J, Franco GR, Warn VM, Gong A, Dinger ME, Rigo F, Lipovich L, Morris MJ, O'Brien TJ, Lee DS, Loeb JA, Blackshaw S, Mattick JS, Wolvetang EJ.

Sci Rep. 2017 Jan 5;7:40127. doi: 10.1038/srep40127.


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. Erratum in: Sci Rep. 2017 Jan 24;7:41112.


Long Noncoding RNA Expression Profiling in Normal B-Cell Subsets and Hodgkin Lymphoma Reveals Hodgkin and Reed-Sternberg Cell-Specific Long Noncoding RNAs.

Tayari MM, Winkle M, Kortman G, Sietzema J, de Jong D, Terpstra M, Mestdagh P, Kroese FG, Visser L, Diepstra A, Kok K, van den Berg A, Kluiver J.

Am J Pathol. 2016 Sep;186(9):2462-72. doi: 10.1016/j.ajpath.2016.05.011. Epub 2016 Jul 14.


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.


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.


Next generation sequencing of microRNAs from isogenic neuroblastoma cell lines isolated before and after treatment.

Roth SA, Knutsen E, Fiskaa T, Utnes P, Bhavsar S, Hald ØH, Løkke C, Mestdagh P, Johansen SD, Flægstad T, Einvik C.

Cancer Lett. 2016 Mar 1;372(1):128-36. doi: 10.1016/j.canlet.2015.11.026. Epub 2015 Dec 17.


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.


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.


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.


An update on LNCipedia: a database for annotated human lncRNA sequences.

Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P.

Nucleic Acids Res. 2015 Apr 30;43(8):4363-4. doi: 10.1093/nar/gkv295. Epub 2015 Mar 31. No abstract available.


RT-qPCR-based quantification of small non-coding RNAs.

Zeka F, Mestdagh P, Vandesompele J.

Methods Mol Biol. 2015;1296:85-102. doi: 10.1007/978-1-4939-2547-6_9.


Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma.

Rihani A, Van Goethem A, Ongenaert M, De Brouwer S, Volders PJ, Agarwal S, De Preter K, Mestdagh P, Shohet J, Speleman F, Vandesompele J, Van Maerken T.

Sci Rep. 2015 Mar 12;5:9027. doi: 10.1038/srep09027.


miR-135a Inhibits Cancer Stem Cell-Driven Medulloblastoma Development by Directly Repressing Arhgef6 Expression.

Hemmesi K, Squadrito ML, Mestdagh P, Conti V, Cominelli M, Piras IS, Sergi LS, Piccinin S, Maestro R, Poliani PL, Speleman F, De Palma M, Galli R.

Stem Cells. 2015 May;33(5):1377-89. doi: 10.1002/stem.1958.


Determining differentially expressed miRNAs and validating miRNA--target relationships using the SPRET/Ei mouse strain.

Timmermans S, Van Hauwermeiren F, Puimège L, Dejager L, Van Wonterghem E, Vanhooren V, Mestdagh P, Libert C, Vandenbroucke RE.

Mamm Genome. 2015 Feb;26(1-2):94-107. doi: 10.1007/s00335-014-9550-y. Epub 2014 Dec 10.


Ectopic microRNA-150-5p transcription sensitizes glucocorticoid therapy response in MM1S multiple myeloma cells but fails to overcome hormone therapy resistance in MM1R cells.

Palagani A, Op de Beeck K, Naulaerts S, Diddens J, Sekhar Chirumamilla C, Van Camp G, Laukens K, Heyninck K, Gerlo S, Mestdagh P, Vandesompele J, Berghe WV.

PLoS One. 2014 Dec 4;9(12):e113842. doi: 10.1371/journal.pone.0113842. eCollection 2014.


Non-coding RNAs and respiratory disease.

Mestdagh P, Vandesompele J, Brusselle G, Vermaelen K.

Thorax. 2015 Apr;70(4):388-90. doi: 10.1136/thoraxjnl-2014-206404. Epub 2014 Nov 5. Review.


An update on LNCipedia: a database for annotated human lncRNA sequences.

Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P.

Nucleic Acids Res. 2015 Jan;43(Database issue):D174-80. doi: 10.1093/nar/gku1060. Epub 2014 Nov 5. Erratum in: Nucleic Acids Res. 2015 Apr 30;43(8):4363-4.


MiR-34a deficiency accelerates medulloblastoma formation in vivo.

Thor T, Künkele A, Pajtler KW, Wefers AK, Stephan H, Mestdagh P, Heukamp L, Hartmann W, Vandesompele J, Sadowski N, Becker L, Garrett L, Hölter SM, Horsch M, Calzada-Wack J, Klein-Rodewald T, Racz I, Zimmer A, Beckers J, Neff F, Klopstock T, De Antonellis P, Zollo M, Wurst W, Fuchs H, Gailus-Durner V, Schüller U, de Angelis MH, Eggert A, Schramm A, Schulte JH.

Int J Cancer. 2015 May 15;136(10):2293-303. doi: 10.1002/ijc.29294. Epub 2014 Nov 25.


The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia.

Durinck K, Wallaert A, Van de Walle I, Van Loocke W, Volders PJ, Vanhauwaert S, Geerdens E, Benoit Y, Van Roy N, Poppe B, Soulier J, Cools J, Mestdagh P, Vandesompele J, Rondou P, Van Vlierberghe P, Taghon T, Speleman F.

Haematologica. 2014 Dec;99(12):1808-16. doi: 10.3324/haematol.2014.115683. Epub 2014 Oct 24.


The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling.

Van Deun J, Mestdagh P, Sormunen R, Cocquyt V, Vermaelen K, Vandesompele J, Bracke M, De Wever O, Hendrix A.

J Extracell Vesicles. 2014 Sep 18;3. doi: 10.3402/jev.v3.24858. eCollection 2014.

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