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Vân Anh Huynh-Thu - Publications ORBI
Milligan, L., Huynh-Thu, V. A., Delan-Forino, C., Tuck, A., Petfalski, E., Lombraña, R., Sanguinetti, Kudla, G., & Tollervey, D. (2016). Strand-specific, high-resolution mapping of modified RNA polymerase II. Molecular Systems Biology, 12(6), 874.
Peer reviewed
Reversible modification of the RNAPII C-terminal domain links transcription with RNA processing and surveillance activities. To better understand this, we mapped the location of RNAPII carrying the five types ...
Huynh-Thu, V. A., & Sanguinetti, G. (2015). Combining tree-based and dynamical systems for the inference of gene regulatory networks. Bioinformatics, 31(10), 1614-1622.
Peer reviewed (verified by ORBi)
Motivation: Reconstructing the topology of gene regulatory networks (GRNs) from time series of gene expression data remains an important open problem in computational systems biology. Existing GRN inference ...
Potier, D., Davie, K., Hulselmans, G., Naval Sanchez, M., Haagen, L., Huynh-Thu, V. A., Koldere, D., Celik, A., Geurts, P., Christiaens, V., & Aerts, S. (2014). Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference. Cell Reports, 9(6), 2290-2303.
Peer reviewed (verified by ORBi)
Genome control is operated by transcription factors (TFs) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their ...
Ruyssinck, J., Huynh-Thu, V. A., Geurts, P., Dhaene, T., Demeester, P., & Saeys, Y. (2014). NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms. PLoS ONE, 9(3), 92709.
Peer reviewed (verified by ORBi)
One of the long-standing open challenges in computational systems biology is the topology inference of gene regulatory networks from high-throughput omics data. Recently, two community-wide efforts, DREAM4 and ...
JOSSE, C., Bouznad, N., Geurts, P., Irrthum, A., Huynh-Thu, V. A., Servais, L., Hego, A., Delvenne, P., Bours, V., & Oury, C. (2014). Identification of a microRNA landscape targeting the PI3K/Akt signaling pathway in inflammation-induced colorectal carcinogenesis. American Journal of Physiology - Gastrointestinal and Liver Physiology, 306, 229-43.
Peer reviewed (verified by ORBi)
Inflammation can contribute to tumor formation; however, markers that predict progression are still lacking. In the present study, the well-established azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced ...
Marchand, G., Huynh-Thu, V. A., Kane, N. C., Arribat, S., Vares, D., Rengel, D., Balzergue, S., Rieseberg, L. H., Vincourt, P., Geurts, P., Vignes, M., & Langlade, N. B. (2014). Bridging physiological and evolutionary time-scales in a gene regulatory network. The New phytologist, 203(2), 685-696.
Peer reviewed (verified by ORBi)
Gene regulatory networks (GRNs) govern phenotypic adaptations and reflect the trade-offs between physiological responses and evolutionary adaptation that act at different time-scales. To identify patterns of ...
Huynh-Thu, V. A., Wehenkel, L., & Geurts, P. (2013). Gene regulatory network inference from systems genetics data using tree-based methods. In A., de la Fuente (Ed.), Gene Network Inference - Verification of Methods for Systems Genetics Data (pp. 63-85). Springer.
Peer reviewed
One of the pressing open problems of computational systems biology is the elucidation of the topology of gene regulatory networks (GRNs). In an attempt to solve this problem, the idea of systems genetics is to ...
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. (2012). Myelin-Derived Lipids Modulate Macrophage Activity by Liver X Receptor Activation. PLoS ONE, 7(9), 44998.
Peer reviewed (verified by ORBi)
Multiple sclerosis is a chronic, inflammatory, demyelinating disease of the central nervous system in which macrophages and microglia play a central role. Foamy macrophages and microglia, containing ...
Huynh-Thu, V. A., Saeys, Y., Wehenkel, L., & Geurts, P. (2012). Statistical interpretation of machine learning-based feature importance scores for biomarker discovery. Bioinformatics, 28(13), 1766-1774.
Peer reviewed (verified by ORBi)
Motivation: Univariate statistical tests are widely used for biomarker discovery in bioinformatics. These procedures are simple, fast and their output is easily interpretable by biologists but they can only ...
Huynh-Thu, V. A. (2012). Machine learning-based feature ranking: Statistical interpretation and gene network inference. Unpublished doctoral thesis, Université de Liège, ​Liège, ​​Belgium.
Machine learning techniques, and in particular supervised learning methods, are nowadays widely used in bioinformatics. Two prominent applications that we target specifically in this thesis are biomarker ...
Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., & Geurts, P. (2010). Inferring Regulatory Networks from Expression Data Using Tree-Based Methods. PLoS ONE, 5(9), 12776.
Peer reviewed (verified by ORBi)
One of the pressing open problems of computational systems biology is the elucidation of the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in particular microarray gene ...
Huynh-Thu, V. A., Hiard, S., Geurts, P., Muller, M., Struman, I., Martial, J., & Wehenkel, L. (2007, September). Detection of micro-RNA/gene interactions involved in angiogenesis using machine learning techniques. Poster session presented at Workshop on Machine Learning in Systems Biology (MLSB07), Evry, France.
Motivation: Angiogenesis is the process responsible for the growth of new blood vessels from existing ones. It is also associated with the development of cancer, as tumors need to be irrigated by blood vessels ...