Publications and communications of Vân Anh Huynh-Thu

Pierre, N., Huynh-Thu, V. A., Baiwir, D., Mazzucchelli, G., Fleron, M., Trzpiot, L., Eppe, G., De Pauw, E., Laharie, D., Satsangi, J., Bossuyt, P., Vuitton, L., Vieujean, S., Colombel, J.-F., Meuwis, M.-A., Louis, E., & GETAID and the SPARE-Biocycle research group. (2024). External validation of serum biomarkers predicting short-term and mid/long-term relapse in patients with Crohn's disease stopping infliximab. Gut, 2024-332648. doi:10.1136/gutjnl-2024-332648

Pierre, N., Huynh-Thu, V. A., Baiwir, D., VIEUJEAN, S., Bequet, E., Reenaers, C., Van Kemseke, C., Salée, C., Massot, C., Fleron, M., Mazzucchelli, G., Trzpiot, L., Eppe, G., De Pauw, E., Louis, E., & Meuwis, M.-A. (2024). Serum proteome signatures associated with ileal and colonic ulcers in Crohn's disease. Journal of Proteomics, 105199. doi:10.1016/j.jprot.2024.105199

Pierre, N., Huynh-Thu, V. A., Baiwir, D., VIEUJEAN, S., Bequet, E., Reenaers, C., Van Kemseke, C., Salée, C., Massot, C., Fleron, M., Mazzucchelli, G., Trzpiot, L., Eppe, G., De Pauw, E., Louis, E., & Meuwis, M.-A. (02 February 2024). Distinct blood protein profiles associated with ileal and colonic ulcers in Crohn’s disease [Poster presentation]. Belgian Week of Gastroenterology 2024, Antwerp, Belgium.

Pierre, N., Huynh-Thu, V. A., Baiwir, D., VIEUJEAN, S., Bequet, E., Reenaers, C., Van Kemseke, C., Salée, C., Massot, C., Fleron, M., Mazzucchelli, G., Trzpiot, L., Eppe, G., De Pauw, E., Louis, E., & Meuwis, M.-A. (2024). Distinct blood protein profiles associated with ileal and colonic ulcers in Crohn’s disease [Poster presentation]. European Crohn's and Colitis Organisation 2024, Stockholm, Sweden.

Pierre, N., Huynh-Thu, V. A., Baiwir, D., VIEUJEAN, S., Bequet, E., Reenaers, C., Van Kemseke, C., Salée, C., Massot, C., Fleron, M., Mazzucchelli, G., Trzpiot, L., Eppe, G., De Pauw, E., Louis, E., & Meuwis, M.-A. (2024). Distinct blood protein profiles associated with ileal and colonic ulcers in Crohn’s disease [Paper presentation]. Belgian Week of Gastroenterology 2024.

Claes, Y., Huynh-Thu, V. A., & Geurts, P. (2023). Knowledge-Guided Additive Modeling for Supervised Regression. Lecture Notes in Computer Science. doi:10.1007/978-3-031-45275-8_5

Pierre, N., Huynh-Thu, V. A., Baiwir, D., Mazzucchelli, G., Fleron, M., Trzpiot, L., Eppe, G., Laharie, D., Satsangi, J., Colombel, J. F., Hertervig, E., Meuwis, M.-A., & Louis, E. (30 January 2023). Distinct biological profiles associated with the risk of short-term relapse and mid/long-term relapse in Crohn’s disease patients stopping infliximab. Journal of Crohn's and Colitis, 17 (Supplement_1), 3-i6. doi:10.1093/ecco-jcc/jjac190.0002

Huynh-Thu, V. A., & Geurts, P. (2023). Optimizing model-agnostic random subspace ensembles. Machine Learning. doi:10.1007/s10994-023-06427-5

Pierre, N., Huynh-Thu, V. A., Baiwir, D., Mazzucchelli, G., Fleron, M., Trzpiot, L., Eppe, G., David, L., Jack, S., Jean-Frédéric, C., Erik, H., Meuwis, M.-A., & Louis, E. (2023). Distinct biological profiles associated with the risk of short-term relapse and mid/long-term relapse in Crohn’s disease patients stopping infliximab [Paper presentation]. Belgian Week of Gastroenterology 2023.

Pierre, N., Huynh-Thu, V. A., Baiwir, D., Mazzucchelli, G., Fleron, M., Trzpiot, L., Eppe, G., David Laharie, Jack Satsangi, Jean-Frédéric Colombel, Erik Hertervig, Meuwis, M.-A., & Louis, E. (2023). Distinct biological profiles associated with the risk of short-term relapse and mid/long-term relapse in Crohn’s disease patients stopping infliximab. Acta Gastro-Enterologica Belgica.

Pierre, N., Huynh-Thu, V. A., Baiwir, D., Mazzucchelli, G., Fleron, M., Trzpiot, L., Eppe, G., David Laharie, Jack Satsangi, Jean-Frédéric Colombel, Erik Hertervig, Meuwis, M.-A., & Louis, E. (2023). Distinct biological profiles associated with the risk of short-term relapse and mid/long-term relapse in Crohn’s disease patients stopping infliximab [Paper presentation]. European Crohn's and Colitis Organisation (ECCO) congress.

Pierre, N., Huynh-Thu, V. A., Marichal, T., Allez, M., Bouhnik, Y., Laharie, D., Bourreille, A., Colombel, J.-F., Meuwis, M.-A., Louis, E., & GETAID (Groupe d’Etude Thérapeutique des Affections Inflammatoires du tube Digestif). (2022). Distinct blood protein profiles associated with the risk of short-term and mid/long-term clinical relapse in patients with Crohn's disease stopping infliximab: when the remission state hides different types of residual disease activity. Gut, 2022-327321. doi:10.1136/gutjnl-2022-327321

Pierre, N., Baiwir, D., Mazzucchelli, G., Fleron, M., PAULISSEN, G., Huynh-Thu, V. A., De Pauw, E., Eppe, G., LOUIS, E., & MEUWIS, M.-A. (04 May 2022). Improving precision of selected reaction monitoring with a two steps internal standard normalisation [Paper presentation]. 5th Symposium of the Belgian Proteomics Association.

Pierre, N., Baiwir, D., Mazzucchelli, G., Fleron, M., Paulissen, G., Huynh-Thu, V. A., De Pauw, E., Eppe, G., Louis, E., & Meuwis, M.-A. (2022). Improving precision of selected reaction monitoring with a two steps internal standard normalisation [Poster presentation]. Next-Generation Protein Analysis and Detection (4th edition), Ghent, Belgium.

Sutera, A., Louppe, G., Huynh-Thu, V. A., Wehenkel, L., & Geurts, P. (2021). From global to local MDI variable importances for random forests and when they are Shapley values. Advances in Neural Information Processing Systems.

Pierre, N., Baiwir, D., Huynh-Thu, V. A., Mazzucchelli, G., Smargiasso, N., De Pauw, E., Bouhnik, Y., Laharie, D., Colombel, J.-F., Meuwis, M.-A., & Louis, E. (2021). Discovery of biomarker candidates associated with the risk of short-term and mid/long-term relapse after infliximab withdrawal in Crohn's patients: a proteomics-based study. Gut. doi:10.1136/gutjnl-2020-322100

Pierre, N., Huynh-Thu, V. A., Allez, M., Bouhnik, Y., Laharie, D., Bourreille, A., Colombel, J. F., Meuwis, M.-A., & Louis, E. (2021). Blood proteins related to immunoregulation or cellular junctions reveal distinct biological profiles associated with the risk of short-term versus mid/long-term relapse in Crohn’s Disease patients stopping infliximab. Journal of Crohn's and Colitis. doi:10.1093/ecco-jcc/jjab075.011

Pierre, N., Huynh-Thu, V. A., Matthieu, A., Yoram, B., David, L., Arnaud, B., Jean-Frédéric, C., Meuwis, M.-A., & Louis, E. (2021). Blood proteins linked to immune tolerance, inflammation and cellular junctions reveal a succession of pathophysiological events preceding the relapse in Crohn’s disease patients stopping infliximab [Paper presentation]. 33rd Belgian Week of Gastroenterology 2021, Belgium.

Pierre, N., Huynh-Thu, V. A., Matthieu Allez, Yoram Bouhnik, David Laharie, Arnaud Bourreille, Jean-Frédéric Colombel, Meuwis, M.-A., & Louis, E. (2021). Blood proteins related to immunoregulation or cellular junctions reveal distinct biological profiles associated with the risk of short-term versus mid/long-term relapse in Crohn’s Disease patients stopping infliximab [Paper presentation]. European Crohn's and Colitis Organisation (ECCO) congress 2021.

Pierre, N., Huynh-Thu, V. A., Matthieu Allez, Yoram Bouhnik, David Laharie, Arnaud Bourreille, Jean-Frédéric Colombel, Meuwis, M.-A., & Louis, E. (2021). Blood proteins linked to immune tolerance, inflammation and cellular junctions reveal a succession of pathophysiological events preceding the relapse in Crohn’s disease patients stopping infliximab. Acta Gastro-Enterologica Belgica.

Vecoven, N., Begon, J.-M., Sutera, A., Geurts, P., & Huynh-Thu, V. A. (2020). Nets versus trees for feature ranking and gene network inference. In Proceeding of the 23rd International Conference on Discovery Science (DS 2020). Springer. doi:10.1007/978-3-030-61527-7_16

Huynh-Thu, V. A., & Geurts, P. (2019). Unsupervised gene network inference with decision trees and Random forests. In G. Sanguinetti & V. A. Huynh-Thu (Eds.), Gene Regulatory Networks. New York, United States - New York: Humana Press. doi:10.1007/978-1-4939-8882-2_8

Huynh-Thu, V. A., & Sanguinetti, G. (2019). Tree-based learning of regulatory network topologies and dynamics with Jump3. In G. Sanguinetti & V. A. Huynh-Thu (Eds.), Gene Regulatory Networks. New York, United States - New York: Humana Press. doi:10.1007/978-1-4939-8882-2_9

Huynh-Thu, V. A., & Sanguinetti, G. (2019). Gene regulatory network inference: An Introductory Survey. In G. Sanguinetti & V. A. Huynh-Thu (Eds.), Gene Regulatory Networks. New York, United States - New York: Humana Press. doi:10.1007/978-1-4939-8882-2_1

Sanguinetti, G., & Huynh-Thu, V. A. (Eds.). (2019). Gene Regulatory Networks. New York, United States - New York: Humana Press.

Huynh-Thu, V. A., & Geurts, P. (21 February 2018). dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data. Scientific Reports, 8, 3384. doi:10.1038/s41598-018-21715-0

Vecoven, N., Begon, J.-M., Huynh-Thu, V. A., & Geurts, P. (2017). Nets versus trees for feature ranking and gene network inference. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/231719.

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., & Aerts, S. (09 October 2017). SCENIC: single-cell regulatory network inference and clustering. Nature Methods, 14, 1083–1086. doi:10.1038/nmeth.4463

Milligan, L., Huynh-Thu, V. A., Delan-Forino, C., Tuck, A., Petfalski, E., Lombraña, R., Sanguinetti, Kudla, G., & Tollervey, D. (June 2016). Strand-specific, high-resolution mapping of modified RNA polymerase II. Molecular Systems Biology, 12 (6), 874. doi:10.15252/msb.20166869

Sutera, A., Louppe, G., Huynh-Thu, V. A., Wehenkel, L., & Geurts, P. (2016). Context-dependent feature analysis with random forests. In Uncertainty In Artificial Intelligence: Proceedings of the Thirty-Two Conference (2016).

Huynh-Thu, V. A., & Sanguinetti, G. (2016). Combining tree-based and dynamical systems for the inference of gene regulatory networks [Paper presentation]. Workshop on Network inference: New methods and new data.

Huynh-Thu, V. A., & Sanguinetti, G. (07 December 2015). Combining tree-based and dynamical systems for the inference of gene regulatory networks [Paper presentation]. Benelux Bioinformatics Conference (BBC15), Antwerp, Belgium.

Huynh-Thu, V. A., & Sanguinetti, G. (April 2015). Combining tree-based and dynamical systems for the inference of gene regulatory networks [Poster presentation]. 19th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Warsaw, Poland.

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. doi:10.1093/bioinformatics/btu863

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. (18 December 2014). Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference. Cell Reports, 9 (6), 2290-2303. doi:10.1016/j.celrep.2014.11.038

Huynh-Thu, V. A., & Sanguinetti, G. (06 September 2014). A hybrid approach for the inference and modelling of gene regulatory networks [Paper presentation]. Workshop on Machine Learning in Systems Biology (MLSB14), Strasbourg, France.

Ruyssinck, J., Huynh-Thu, V. A., Geurts, P., Dhaene, T., Demeester, P., & Saeys, Y. (25 March 2014). NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms. PLoS ONE, 9 (3), 92709. doi:10.1371/journal.pone.0092709

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. doi:10.1152/ajpgi.00484.2012

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. New Phytologist, 203 (2), 685-696. doi:10.1111/nph.12818

Huynh-Thu, V. A. (26 June 2013). Network reconstruction from time series expression data using tree-based methods [Paper presentation]. Dynamics of biological networks: from nodes’ dynamics to network evolution, Edinburgh, United Kingdom.

Huynh-Thu, V. A., & Geurts, P. (2013). Gene regulatory network inference from expression and genetic data using tree-based methods [Paper presentation]. STATSEQ meeting on Gene Network Inference with Systems genetic data and beyond, Paris, France.

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. doi:10.1007/978-3-642-45161-4_5

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. (12 September 2012). Myelin-Derived Lipids Modulate Macrophage Activity by Liver X Receptor Activation. PLoS ONE, 7 (9), 44998. doi:10.1371/journal.pone.0044998

Marbach, D., Costello, J. C., Küffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Aderhold, A., Bonneau, R., Chen, Y., Cordero, F., Crane, M., Dondelinger, F., Drton, M., Esposito, R., Foygel, R., de la Fuente, A., Gertheiss, J., Geurts, P., ... Stolovitzky, G. (15 July 2012). Wisdom of crowds for robust gene network inference. Nature Methods, 9, 796-804. doi:10.1038/nmeth.2016

Huynh-Thu, V. A., Vandel, J., Irrthum, A., Wehenkel, L., & Geurts, P. (01 June 2012). Inferring gene regulatory networks from genetical genomics data [Paper presentation]. Capita Selecta in Complex Disease Analysis, Liege, Belgium.

Huynh-Thu, V. A., Saeys, Y., Wehenkel, L., & Geurts, P. (25 April 2012). Statistical interpretation of machine learning-based feature importance scores for biomarker discovery. Bioinformatics, 28 (13), 1766-1774. doi:10.1093/bioinformatics/bts238

Huynh-Thu, V. A. (2012). Machine learning-based feature ranking: Statistical interpretation and gene network inference [Doctoral thesis, ULiège - Université de Liège]. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/108611

Garbacki, N., Di Valentin, E., Huynh-Thu, V. A., Geurts, P., Irrthum, A., Crahay, C., Arnould, T., Deroanne, C., Piette, J., Cataldo, D., & Colige, A. (2011). MicroRNAs Profiling in Murine Models of Acute and Chronic Asthma: A Relationship with mRNAs Targets. PLoS ONE. doi:10.1371/journal.pone.0016509

Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., Saeys, Y., & Geurts, P. (2011). Inferring gene regulatory networks from expression data using tree-based methods [Paper presentation]. ISMB/ECCB 2011, Vienna, Austria.

Huynh-Thu, V. A., Saeys, Y., Wehenkel, L., & Geurts, P. (2011). Statistical interpretation of machine learning-based feature rankings for biomarker discovery [Paper presentation]. Benelux Bioinformatics Conference (BBC11), Luxembourg, Luxembourg.

Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., Saeys, Y., & Geurts, P. (16 November 2010). Regulatory network inference with GENIE3: application to the DREAM5 challenge [Paper presentation]. 3rd Annual Joint Conference on Systems Biology, Regulatory Genomics, and Reverse Engineering Challenges, New York City, United States - New York.

Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., & Geurts, P. (October 2010). Inferring Regulatory Networks from Expression Data using Tree-based Methods [Paper presentation]. Workshop on Machine Learning in Systems Biology (MLSB10), Edinburgh, United Kingdom.

Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., & Geurts, P. (28 September 2010). Inferring Regulatory Networks from Expression Data Using Tree-Based Methods. PLoS ONE, 5 (9), 12776. doi:10.1371/journal.pone.0012776

Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., & Geurts, P. (September 2010). Inferring regulatory networks from expression data using tree-based methods [Poster presentation]. ECCB 2010, Ghent, Belgium.

Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., & Geurts, P. (September 2009). Inferring regulatory networks from expression data using tree-based methods [Poster presentation]. Benelux Bioinformatics Conference (BBC09), Liège, Belgium.

Huynh-Thu, V. A., Irrthum, A., Wehenkel, L., & Geurts, P. (2009). Inferring regulatory networks from expression data using tree-based methods [Paper presentation]. 2009 joint conference on Systems Biology, Regulatory Genomics, and Reverse Engineering Challenges, Boston, United States - Massachusetts.

Huynh-Thu, V. A., Wehenkel, L., & Geurts, P. (December 2008). Exploiting tree-based variable importances to selectively identify relevant variables [Poster presentation]. Benelux Bioinformatics Conference (BBC08), Maastricht, Netherlands.

Huynh-Thu, V. A., Wehenkel, L., & Geurts, P. (May 2008). Deriving p-values for tree-based variable importance measures [Paper presentation]. Benelearn, Spa, Belgium.

Huynh-Thu, V. A., Wehenkel, L., & Geurts, P. (2008). Exploiting tree-based variable importances to selectively identify relevant variables. Proceedings of Machine Learning Research, 4, 60-73.

Huynh-Thu, V. A., Wehenkel, L., & Geurts, P. (2008). Exploiting tree-based variable importances to selectively identify relevant variables [Paper presentation]. Third Workshop on New Challenges for Feature Selection in Data Mining and Knowledge Discovery (FSDM 2008).

Huynh-Thu, V. A., Hiard, S., Geurts, P., Muller, M., Struman, I., Martial, J., & Wehenkel, L. (September 2007). Detection of micro-RNA/gene interactions involved in angiogenesis using machine learning techniques [Poster presentation]. Workshop on Machine Learning in Systems Biology (MLSB07), Evry, France.