Vân Anh Huynh-Thu

[ULiege ORBi repository] [Google Scholar]

Note that all my papers can be downloaded from ORBi (the University of Liege repository). Downloads of unlocked files are fully anonymous, and for the locked files I only need to perform one mouse click to send you a copy.


Gene regulatory network inference: an introductory survey
Huynh-Thu V. A. and Sanguinetti G.
arXiv preprint, 2018.

dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data
Huynh-Thu V. A. and Geurts P.
Scientific Reports 8:3384, 2018.


SCENIC: single-cell regulatory network inference and clustering
Aibar S., González-Blas C. B., Moerman T., Huynh-Thu V. A., Imrichova H., Hulselmans G., Rambow F., Marine J.-C., Geurts P., Aerts J., van den Oord J., Atak Z. K., Wouters J., and Aerts S.
Nature Methods, 14:1083–1086, 2017.


Context-dependent feature analysis with random forests
Sutera A., Louppe G., Huynh-Thu V. A., Wehenkel L., and Geurts P.
In: Proceedings of the Thirty-Second Conference on Uncertainty in Artificial Intelligence (UAI), 2016.
[ORBi] [Supplementary materials]

Strand-specific, high-resolution mapping of modified RNA polymerase II
Milligan L., Huynh-Thu V. A., Delan-Forino C., Tuck A., Petfalski E., Lombraña R., Sanguinetti G., Kudla G., and Tollervey D.
Molecular Systems Biology, 12(6):874, 2016.


Combining tree-based and dynamical systems for the inference of gene regulatory networks
Huynh-Thu V. A. and Sanguinetti G.
Bioinformatics, 31(10):1614-1622, 2015.


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 V. A., Koldere D., Celik A., Geurts P., Christiaens V., and Aerts S.
Cell Reports, 9(6):2290–2303, 2014.

Bridging physiological and evolutionary time-scales in a gene regulatory network
Marchand G., Huynh-Thu V. A., Kane N., Arribat S., Varès D., Rengel D., Balzergue S., Rieseberg L., Vincourt P., Geurts P., Vignes M., and Langlade N. B.
New Phytologist, 203(2):685-696, 2014.

NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance algorithms
Ruyssinck J., Huynh-Thu V. A., Geurts P., Dhaene T., Demeester P., and Saeys Y.
PLoS ONE, 9(3):e92709, 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 V. A., Servais L., Hego A., Delvenne P., Bours V., and Oury C.
American Journal of Physiology - Gastrointestinal and Liver Physiology, 306(3):G229-G243, 2014.


Gene regulatory network inference from systems genetics data using tree-based methods
Huynh-Thu V. A., Wehenkel L., and Geurts P.
In: A. de la Fuente (Ed.), Gene Network Inference - Verification of Methods for Systems Genetics Data, Springer, pp. 63-85, 2013.


Myelin-derived lipids modulate macrophage activity by liver X receptor activation
Bogie J. F. J., Timmermans S., Huynh-Thu V. A., Irrthum A., Smeets H. J. M., Gustafsson J.-A., Steffensen K. R., Mulder M., Stinissen P., Hellings N., Hendriks J. J. A.
PLoS ONE, 7(9):e44998, 2012.

Wisdom of crowds for robust gene network inference
Marbach D., Costello J. C., Küffner R., Vega N., Prill R. J., Camacho D. M., Allison K. R., the DREAM5 consortium (including Geurts P., Huynh-Thu V. A., Irrthum A., Saeys Y., and Wehenkel L.), Kellis M., Collins J. J., and Stolovitzky G.
Nature Methods, 9:796-804, 2012.

Statistical interpretation of machine learning-based feature importance scores for biomarker discovery
Huynh-Thu V. A., Saeys Y., Wehenkel L., and Geurts P.
Bioinformatics, 28(13):1766-1774, 2012.

Machine learning-based feature ranking: Statistical interpretation and gene network inference
Huynh-Thu V. A., PhD thesis, Jan. 2012.
Slides of the defense here.


MicroRNAs profiling in murine models of acute and chronic asthma: a relationship with mRNAs targets
Garbacki N., Di Valentin E., Huynh-Thu V. A., Geurts P., Irrthum A., Crahay C., Arnould T., Deroanne C., Piette J., Cataldo D., and Colige A.
PLoS ONE, 6(1):e16509, 2011.


Inferring regulatory networks from expression data using tree-based methods
Huynh-Thu V. A., Irrthum A., Wehenkel L., and Geurts P.
PLoS ONE, 5(9):e12776, 2010.


Exploiting tree-based variable importances to selectively identify relevant variables
Huynh-Thu V. A., Wehenkel L., and Geurts P.
JMLR Workshop and Conference Proceedings, 4:60-73, 2008.