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Items: 13


dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data.

Huynh-Thu VA, Geurts P.

Sci Rep. 2018 Feb 21;8(1):3384. doi: 10.1038/s41598-018-21715-0.


SCENIC: single-cell regulatory network inference and clustering.

Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S.

Nat Methods. 2017 Nov;14(11):1083-1086. doi: 10.1038/nmeth.4463. Epub 2017 Oct 9.


Strand-specific, high-resolution mapping of modified RNA polymerase II.

Milligan L, Huynh-Thu VA, Delan-Forino C, Tuck A, Petfalski E, Lombraña R, Sanguinetti G, Kudla G, Tollervey D.

Mol Syst Biol. 2016 Jun 10;12(6):874. doi: 10.15252/msb.20166869.


Combining tree-based and dynamical systems for the inference of gene regulatory networks.

Huynh-Thu VA, Sanguinetti G.

Bioinformatics. 2015 May 15;31(10):1614-22. doi: 10.1093/bioinformatics/btu863. Epub 2015 Jan 7.


Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.

Potier D, Davie K, Hulselmans G, Naval Sanchez M, Haagen L, Huynh-Thu VA, Koldere D, Celik A, Geurts P, Christiaens V, Aerts S.

Cell Rep. 2014 Dec 24;9(6):2290-303. doi: 10.1016/j.celrep.2014.11.038. Epub 2014 Dec 18.


Bridging physiological and evolutionary time-scales in a gene regulatory network.

Marchand G, Huynh-Thu VA, Kane NC, Arribat S, Varès D, Rengel D, Balzergue S, Rieseberg LH, Vincourt P, Geurts P, Vignes M, Langlade NB.

New Phytol. 2014 Jul;203(2):685-96. doi: 10.1111/nph.12818. Epub 2014 May 2.


NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms.

Ruyssinck J, Huynh-Thu VA, Geurts P, Dhaene T, Demeester P, Saeys Y.

PLoS One. 2014 Mar 25;9(3):e92709. doi: 10.1371/journal.pone.0092709. eCollection 2014.


Identification of a microRNA landscape targeting the PI3K/Akt signaling pathway in inflammation-induced colorectal carcinogenesis.

Josse C, Bouznad N, Geurts P, Irrthum A, Huynh-Thu VA, Servais L, Hego A, Delvenne P, Bours V, Oury C.

Am J Physiol Gastrointest Liver Physiol. 2014 Feb;306(3):G229-43. doi: 10.1152/ajpgi.00484.2012. Epub 2013 Dec 12.


Myelin-derived lipids modulate macrophage activity by liver X receptor activation.

Bogie JF, Timmermans S, Huynh-Thu VA, Irrthum A, Smeets HJ, Gustafsson JÅ, Steffensen KR, Mulder M, Stinissen P, Hellings N, Hendriks JJ.

PLoS One. 2012;7(9):e44998. doi: 10.1371/journal.pone.0044998. Epub 2012 Sep 12.


Wisdom of crowds for robust gene network inference.

Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G.

Nat Methods. 2012 Jul 15;9(8):796-804. doi: 10.1038/nmeth.2016.


Statistical interpretation of machine learning-based feature importance scores for biomarker discovery.

Huynh-Thu VA, Saeys Y, Wehenkel L, Geurts P.

Bioinformatics. 2012 Jul 1;28(13):1766-74. doi: 10.1093/bioinformatics/bts238. Epub 2012 Apr 25.


MicroRNAs profiling in murine models of acute and chronic asthma: a relationship with mRNAs targets.

Garbacki N, Di Valentin E, Huynh-Thu VA, Geurts P, Irrthum A, Crahay C, Arnould T, Deroanne C, Piette J, Cataldo D, Colige A.

PLoS One. 2011 Jan 28;6(1):e16509. doi: 10.1371/journal.pone.0016509.


Inferring regulatory networks from expression data using tree-based methods.

Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P.

PLoS One. 2010 Sep 28;5(9). pii: e12776. doi: 10.1371/journal.pone.0012776.

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