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Items: 1 to 50 of 275

1.

SPsimSeq: semi-parametric simulation of bulk and single cell RNA sequencing data.

Assefa AT, Vandesompele J, Thas O.

Bioinformatics. 2020 Feb 17. pii: btaa105. doi: 10.1093/bioinformatics/btaa105. [Epub ahead of print]

PMID:
32065619
2.

Closing the circle: current state and perspectives of circular RNA databases.

Vromman M, Vandesompele J, Volders PJ.

Brief Bioinform. 2020 Jan 30. pii: bbz175. doi: 10.1093/bib/bbz175. [Epub ahead of print]

PMID:
31998941
3.

Vapor nanobubble is the more reliable photothermal mechanism for inducing endosomal escape of siRNA without disturbing cell homeostasis.

Fraire JC, Houthaeve G, Liu J, Raes L, Vermeulen L, Stremersch S, Brans T, García-Díaz Barriga G, De Keulenaer S, Van Nieuwerburgh F, De Rycke R, Vandesompele J, Mestdagh P, Raemdonck K, De Vos WH, De Smedt S, Braeckmans K.

J Control Release. 2020 Jan 2;319:262-275. doi: 10.1016/j.jconrel.2019.12.050. [Epub ahead of print]

PMID:
31904400
4.

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles.

Everaert C, Helsmoortel H, Decock A, Hulstaert E, Van Paemel R, Verniers K, Nuytens J, Anckaert J, Nijs N, Tulkens J, Dhondt B, Hendrix A, Mestdagh P, Vandesompele J.

Sci Rep. 2019 Nov 26;9(1):17574. doi: 10.1038/s41598-019-53892-x.

5.

The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35.

Liu PY, Tee AE, Milazzo G, Hannan KM, Maag J, Mondal S, Atmadibrata B, Bartonicek N, Peng H, Ho N, Mayoh C, Ciaccio R, Sun Y, Henderson MJ, Gao J, Everaert C, Hulme AJ, Wong M, Lan Q, Cheung BB, Shi L, Wang JY, Simon T, Fischer M, Zhang XD, Marshall GM, Norris MD, Haber M, Vandesompele J, Li J, Mestdagh P, Hannan RD, Dinger ME, Perini G, Liu T.

Nat Commun. 2019 Nov 5;10(1):5026. doi: 10.1038/s41467-019-12971-3.

6.

The generation and use of recombinant extracellular vesicles as biological reference material.

Geeurickx E, Tulkens J, Dhondt B, Van Deun J, Lippens L, Vergauwen G, Heyrman E, De Sutter D, Gevaert K, Impens F, Miinalainen I, Van Bockstal PJ, De Beer T, Wauben MHM, Nolte-'t-Hoen ENM, Bloch K, Swinnen JV, van der Pol E, Nieuwland R, Braems G, Callewaert N, Mestdagh P, Vandesompele J, Denys H, Eyckerman S, De Wever O, Hendrix A.

Nat Commun. 2019 Jul 23;10(1):3288. doi: 10.1038/s41467-019-11182-0.

7.

Author Correction: Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes.

Rombaut D, Chiu HS, Decaesteker B, Everaert C, Yigit N, Peltier A, Janoueix-Lerosey I, Bartenhagen C, Fischer M, Roberts S, D'Haene N, De Preter K, Speleman F, Denecker G, Sumazin P, Vandesompele J, Lefever S, Mestdagh P.

Sci Rep. 2019 Jul 17;9(1):10536. doi: 10.1038/s41598-019-46785-6.

8.

SMARTer single cell total RNA sequencing.

Verboom K, Everaert C, Bolduc N, Livak KJ, Yigit N, Rombaut D, Anckaert J, Lee S, Venø MT, Kjems J, Speleman F, Mestdagh P, Vandesompele J.

Nucleic Acids Res. 2019 Sep 19;47(16):e93. doi: 10.1093/nar/gkz535.

9.

Publisher Correction: In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors.

Vanhauwaert S, Decaesteker B, De Brouwer S, Leonelli C, Durinck K, Mestdagh P, Vandesompele J, Sermon K, Denecker G, Van Neste C, Speleman F, De Preter K.

Sci Rep. 2019 Jun 4;9(1):8360. doi: 10.1038/s41598-019-44435-5.

10.

Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes.

Rombaut D, Chiu HS, Decaesteker B, Everaert C, Yigit N, Peltier A, Janoueix-Lerosey I, Bartenhagen C, Fischer M, Roberts S, D'Haene N, De Preter K, Speleman F, Denecker G, Sumazin P, Vandesompele J, Lefever S, Mestdagh P.

Sci Rep. 2019 Apr 5;9(1):5685. doi: 10.1038/s41598-019-42107-y. Erratum in: Sci Rep. 2019 Jul 17;9(1):10536.

11.

Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes.

Loontiens S, Depestel L, Vanhauwaert S, Dewyn G, Gistelinck C, Verboom K, Van Loocke W, Matthijssens F, Willaert A, Vandesompele J, Speleman F, Durinck K.

BMC Genomics. 2019 Mar 20;20(1):228. doi: 10.1186/s12864-019-5608-2.

12.

Evaluating the applicability of mouse SINEs as an alternative normalization approach for RT-qPCR in brain tissue of the APP23 model for Alzheimer's disease.

Janssens J, Crans RAJ, Van Craenenbroeck K, Vandesompele J, Stove CP, Van Dam D, De Deyn PP.

J Neurosci Methods. 2019 May 15;320:128-137. doi: 10.1016/j.jneumeth.2019.03.005. Epub 2019 Mar 5.

13.

Cost-effective and robust genotyping using double-mismatch allele-specific quantitative PCR.

Lefever S, Rihani A, Van der Meulen J, Pattyn F, Van Maerken T, Van Dorpe J, Hellemans J, Vandesompele J.

Sci Rep. 2019 Feb 15;9(1):2150. doi: 10.1038/s41598-019-38581-z.

14.

Discovery and validation of a serum microRNA signature to characterize oligo- and polymetastatic prostate cancer: not ready for prime time.

Dhondt B, De Bleser E, Claeys T, Buelens S, Lumen N, Vandesompele J, Beckers A, Fonteyne V, Van der Eecken K, De Bruycker A, Paul J, Gramme P, Ost P.

World J Urol. 2019 Dec;37(12):2557-2564. doi: 10.1007/s00345-018-2609-8. Epub 2018 Dec 21.

PMID:
30578441
15.

A mechanistic classification of clinical phenotypes in neuroblastoma.

Ackermann S, Cartolano M, Hero B, Welte A, Kahlert Y, Roderwieser A, Bartenhagen C, Walter E, Gecht J, Kerschke L, Volland R, Menon R, Heuckmann JM, Gartlgruber M, Hartlieb S, Henrich KO, Okonechnikov K, Altmüller J, Nürnberg P, Lefever S, de Wilde B, Sand F, Ikram F, Rosswog C, Fischer J, Theissen J, Hertwig F, Singhi AD, Simon T, Vogel W, Perner S, Krug B, Schmidt M, Rahmann S, Achter V, Lang U, Vokuhl C, Ortmann M, Büttner R, Eggert A, Speleman F, O'Sullivan RJ, Thomas RK, Berthold F, Vandesompele J, Schramm A, Westermann F, Schulte JH, Peifer M, Fischer M.

Science. 2018 Dec 7;362(6419):1165-1170. doi: 10.1126/science.aat6768.

PMID:
30523111
16.

Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients.

Zeka F, Decock A, Van Goethem A, Vanderheyden K, Demuynck F, Lammens T, Helsmoortel HH, Vermeulen J, Noguera R, Berbegall AP, Combaret V, Schleiermacher G, Laureys G, Schramm A, Schulte JH, Rahmann S, Bienertová-Vašků J, Mazánek P, Jeison M, Ash S, Hogarty MD, Moreno-Smith M, Barbieri E, Shohet J, Berthold F, Van Maerken T, Speleman F, Fischer M, De Preter K, Mestdagh P, Vandesompele J.

JCI Insight. 2018 Dec 6;3(23). pii: 97021. doi: 10.1172/jci.insight.97021.

17.

Increased levels of systemic LPS-positive bacterial extracellular vesicles in patients with intestinal barrier dysfunction.

Tulkens J, Vergauwen G, Van Deun J, Geeurickx E, Dhondt B, Lippens L, De Scheerder MA, Miinalainen I, Rappu P, De Geest BG, Vandecasteele K, Laukens D, Vandekerckhove L, Denys H, Vandesompele J, De Wever O, Hendrix A.

Gut. 2020 Jan;69(1):191-193. doi: 10.1136/gutjnl-2018-317726. Epub 2018 Dec 5. No abstract available.

18.

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors.

Vanhauwaert S, Decaesteker B, De Brouwer S, Leonelli C, Durinck K, Mestdagh P, Vandesompele J, Sermon K, Denecker G, Van Neste C, Speleman F, De Preter K.

Sci Rep. 2018 Nov 30;8(1):17468. doi: 10.1038/s41598-018-35868-5. Erratum in: Sci Rep. 2019 Jun 4;9(1):8360.

19.

Long noncoding RNA expression profiling in cancer: Challenges and opportunities.

Lorenzi L, Avila Cobos F, Decock A, Everaert C, Helsmoortel H, Lefever S, Verboom K, Volders PJ, Speleman F, Vandesompele J, Mestdagh P.

Genes Chromosomes Cancer. 2019 Apr;58(4):191-199. doi: 10.1002/gcc.22709. Epub 2019 Jan 20. Review.

PMID:
30461116
20.

LNCipedia 5: towards a reference set of human long non-coding RNAs.

Volders PJ, Anckaert J, Verheggen K, Nuytens J, Martens L, Mestdagh P, Vandesompele J.

Nucleic Acids Res. 2019 Jan 8;47(D1):D135-D139. doi: 10.1093/nar/gky1031.

21.

Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines.

Volders PJ, Lefever S, Baute S, Nuytens J, Vanderheyden K, Menten B, Mestdagh P, Vandesompele J.

Noncoding RNA. 2018 Sep 13;4(3). pii: E21. doi: 10.3390/ncrna4030021.

22.

Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope?

Helsmoortel H, Everaert C, Lumen N, Ost P, Vandesompele J.

Noncoding RNA Res. 2018 May 23;3(2):64-74. doi: 10.1016/j.ncrna.2018.05.001. eCollection 2018 Jun. Review.

23.

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data.

Assefa AT, De Paepe K, Everaert C, Mestdagh P, Thas O, Vandesompele J.

Genome Biol. 2018 Jul 24;19(1):96. doi: 10.1186/s13059-018-1466-5.

24.

On determining the power of digital PCR experiments.

Vynck M, Vandesompele J, Thas O.

Anal Bioanal Chem. 2018 Sep;410(23):5731-5739. doi: 10.1007/s00216-018-1212-6. Epub 2018 Jun 30.

PMID:
29961092
25.

A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing.

Verboom K, Van Loocke W, Volders PJ, Decaesteker B, Cobos FA, Bornschein S, de Bock CE, Atak ZK, Clappier E, Aerts S, Cools J, Soulier J, Taghon T, Van Vlierberghe P, Vandesompele J, Speleman F, Durinck K.

Haematologica. 2018 Dec;103(12):e585-e589. doi: 10.3324/haematol.2018.190587. Epub 2018 Jun 28. No abstract available.

26.

Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice.

Renard M, Vanhauwaert S, Vanhomwegen M, Rihani A, Vandamme N, Goossens S, Berx G, Van Vlierberghe P, Haigh JJ, Decaesteker B, Van Laere J, Lambertz I, Speleman F, Vandesompele J, Willaert A.

Sci Rep. 2018 May 16;8(1):7642. doi: 10.1038/s41598-018-25389-6.

27.

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 Aug;37(34):4750-4768. doi: 10.1038/s41388-018-0281-5. Epub 2018 May 16.

PMID:
29765154
28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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. 2018 Jun;16(3):197-205.e5. doi: 10.1016/j.clgc.2017.12.008. Epub 2017 Dec 29.

PMID:
29366632
35.

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. Review.

PMID:
29351586
36.

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.

37.

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.

38.

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.

PMID:
28986791
39.

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.

40.

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.

41.

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.

42.

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.

PMID:
28799053
43.

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.

44.

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.

PMID:
28534634
45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

PMID:
28350455
50.

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.

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