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Items: 15

1.

SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups.

Everaert C, Volders PJ, Morlion A, Thas O, Mestdagh P.

BMC Bioinformatics. 2020 Feb 17;21(1):58. doi: 10.1186/s12859-020-3407-z.

2.

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.

3.

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.

4.

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.

5.

TFutils: Data structures for transcription factor bioinformatics.

Stubbs BJ, Gopaulakrishnan S, Glass K, Pochet N, Everaert C, Raby B, Carey V.

Version 2. F1000Res. 2019 Feb 5 [revised 2019 Jan 1];8:152. doi: 10.12688/f1000research.17976.2. eCollection 2019.

6.

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.

7.

Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development.

Lupberger J, Croonenborghs T, Roca Suarez AA, Van Renne N, Jühling F, Oudot MA, Virzì A, Bandiera S, Jamey C, Meszaros G, Brumaru D, Mukherji A, Durand SC, Heydmann L, Verrier ER, El Saghire H, Hamdane N, Bartenschlager R, Fereshetian S, Ramberger E, Sinha R, Nabian M, Everaert C, Jovanovic M, Mertins P, Carr SA, Chayama K, Dali-Youcef N, Ricci R, Bardeesy NM, Fujiwara N, Gevaert O, Zeisel MB, Hoshida Y, Pochet N, Baumert TF.

Gastroenterology. 2019 Aug;157(2):537-551.e9. doi: 10.1053/j.gastro.2019.04.003. Epub 2019 Apr 9.

8.

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.

9.

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
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

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