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Items: 10

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

PMID:
28245209
8.

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.

9.

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.

10.

miRBase Tracker: keeping track of microRNA annotation changes.

Van Peer G, Lefever S, Anckaert J, Beckers A, Rihani A, Van Goethem A, Volders PJ, Zeka F, Ongenaert M, Mestdagh P, Vandesompele J.

Database (Oxford). 2014 Aug 25;2014. pii: bau080. doi: 10.1093/database/bau080. Print 2014.

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