Melograna, F., Li, Z., Galazzo, G., van Best, N., Mommers, M., Penders, J., Stella, F., & Van Steen, K. (15 May 2023). Edge and modular significance assessment in individual-specific networks. Scientific Reports, 13 (1), 7868. doi:10.1038/s41598-023-34759-8 |
Li, Z., Melograna, F., Hoskens, H., Duroux, D., Marazita, M. L., Walsh, S., Weinberg, S. M., Shriver, M. D., Müller-Myhsok, B., Claes, P., & Van Steen, K. (2023). netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/304725. doi:10.1101/2023.05.04.539350 |
Singhal, P., Veturi, Y., Dudek, S. M., Lucas, A., Frase, A., Van Steen, K., Schrodi, S. J., Fasel, D., Weng, C., Pendergrass, R., Schaid, D. J., Kullo, I. J., Dikilitas, O., Sleiman, P. M. A., Hakonarson, H., Moore, J. H., Williams, S. M., Ritchie, M. D., & Verma, S. S. (06 April 2023). Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. American Journal of Human Genetics, 110 (4), 575 - 591. doi:10.1016/j.ajhg.2023.03.007 |
Poulet, C.* , Debit, A.* , Josse, C., Jerusalem, G., Azencott, C.-A., Bours, V., & Van Steen, K. (2023). Assessing Random Forest self-reproducibility for optimal short biomarker signature discovery. ORBi-University of Liège. https://orbi.uliege.be/handle/2268/303314. doi:10.1101/2023.03.29.534695 * These authors have contributed equally to this work. |
Duroux, D., & Van Steen, K. (19 March 2023). netANOVA: novel graph clustering technique with significance assessment via hierarchical ANOVA. Briefings in Bioinformatics, 24 (2). doi:10.1093/bib/bbad029 |
Yousefi, B., Melograna, F., Galazzo, G., van Best, N., Mommers, M., Penders, J., Schwikowski, B., & Van Steen, K. (22 January 2023). Capturing the dynamics of microbiomes using individual-specific networks. Frontiers in Microbiology, 14. doi:10.1101/2023.01.22.525058 |
Chaichoompu, K., Wilantho, A., Wangkumhang, P., Tongsima, S., Cavadas, B., Pereira, L., & Van Steen, K. (2023). Fine-scale subpopulation detection via an SNP-based unsupervised method: A case study on the 1000 Genomes Project resources. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 28 (2023), 245 - 256. doi:10.1142/9789811270611_0023 |
Riemens, R. J. M., Kenis, G., Nolz, J., Susano Chaves, S. C., Duroux, D., Pishva, E., Mastroeni, D., Van Steen, K., Haaf, T., & van den Hove, D. L. A. (08 December 2022). Targeted Methylation Profiling of Single Laser-Capture Microdissected Post-Mortem Brain Cells by Adapted Limiting Dilution Bisulfite Pyrosequencing (LDBSP). International Journal of Molecular Sciences, 23 (24), 15571. doi:10.3390/ijms232415571 |
Bhardwaj, A., Josse, C., VAN DAELE, D., Poulet, C., Chavez, M., Struman, I., & Van Steen, K. (2022). Deeper insights into long-term survival heterogeneity of Pancreatic Ductal Adenocarcinoma (PDAC) patients using integrative individual-and group-level transcriptome network analyses. Scientific Reports, 12 (11027). doi:10.1038/s41598-022-14592-1 |
Duroux, D., Climente-González, H., Azencott, C.-A., & Van Steen, K. (2022). Interpretable network-guided epistasis detection. GigaScience, 11. doi:10.1093/gigascience/giab093 |
Gregorich, M., Melograna, F., Sunqvist, M., Michiels, S., Van Steen, K., & Heinze, G. (2022). Individual-specific networks for prediction modelling–A scoping review of methods. BMC Medical Research Methodology, 22 (1), 1-17. doi:10.1186/s12874-022-01544-6 |
Joiret, M., Mahachie John, J., Gusareva, E., & Van Steen, K. (2022). Correction: Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies. BioData Mining, 15 (1), 1-1. doi:10.1186/s13040-022-00296-9 |
Kumari, P., Bikram Pradhan, Maria Koromina, George P. Patrinos, & Van Steen, K. (2022). Discovery of new drug indications for COVID- 19: A drug repurposing approach. PLoS ONE, 17 (5), 0267095. doi:10.1371/journal.pone.0267095 |
Simons, C. C., Schouten, L. J., Godschalk, R. W., van Schooten, F.-J., Stoll, M., Van Steen, K., van den Brandt, P. A., & Weijenberg, M. P. (2022). Polymorphisms in the mTOR-PI3K-Akt pathway, energy balance-related exposures and colorectal cancer risk in the Netherlands Cohort Study. BioData Mining, 15 (1), 1-20. doi:10.1186/s13040-021-00286-3 |
Walakira, A., Ocira, J., Duroux, D., Fouladi, R., Moškon, M., Rozman, D., & Van Steen, K. (2022). Detecting gene–gene interactions from GWAS using diffusion kernel principal components. BMC Bioinformatics, 23 (1), 1-18. doi:10.1186/s12859-022-04580-7 |
Duroux, D., Van Steen, K., & Federico Melograna. (22 July 2021). Patient heterogeneity assessments via network-based ANOVA [Poster presentation]. 42nd Conference of the International Society for Clinical Biostatistics (ISCB). |
Abegaz, F., Van Lishout, F., John, J. M. M., Chiachoompu, K., Bhardwaj, A., Duroux, D., Gusareva, E. S., Wei, Z., Hakonarson, H., & Van Steen, K. (2021). Performance of model-based multifactor dimensionality reduction methods for epistasis detection by controlling population structure. BioData Mining, 14 (1), 1-20. doi:10.1186/s13040-021-00247-w |
Graff, S., Zanella, D., Stefanuto, P.-H., HENKET, M., PAULUS, V., GUISSARD, F., MOERMANS, C., Van Steen, K., Louis, R., & Schleich, F. (2021). Are Volatile Organic Compounds Able to Identify Airflow Decline in Asthma? Journal of Asthma and Allergy, 14, 67-70. doi:10.2147/JAA.S289278 |
Hall, M., Wallace, J., Lucas, A., Van Steen, K., Moore, J., & Ritchie, M. (2021). Novel EDGE encoding method enhances ability to identify genetic interactions. PLoS Genetics, 17 (6), 1009534. doi:10.1371/journal.pgen.1009534 |
Matschinske, J., Alcaraz, N., Benis, A., Golebiewski, M., Grimm, D. G., Heumos, L., Kacprowski, T., Lazareva, O., List, M., Louadi, Z., Josch K Pauling, Nico Pfeifer, Richard Röttger, Veit Schwämmle, Gregor Sturm, Alberto Traverso, Van Steen, K., Martiela Vaz de Freitas, Gerda Cristal Villalba Silva, ... David B Blumenthal. (2021). The AIMe registry for artificial intelligence in biomedical research. Nature Methods, 18 (10), 1128-1131. doi:10.1038/s41592-021-01241-0 |
Riemens, R. J., Kenis, G., Nolz, J., Chaves, S. C. S., Duroux, D., Pishva, E., Mastroeni, D., Van Steen, K., Haaf, T., & van den Hove, D. L. (2021). Targeted methylation profiling of single laser-capture microdissected post-mortem brain cells by adapted limiting dilution bisulfite pyrosequencing (LDBSP). ORBi-University of Liège. https://orbi.uliege.be/handle/2268/292194. |
Comte, B., Baumbach, J., Benis, A., Basílio, J., Debeljak, N., Flobak, Å., Franken, C., Harel, N., He, F., Kuiper, M., Juan Albino Méndez Pérez, Estelle Pujos-Guillot, Tadeja Režen, Damjana Rozman, Johannes A Schmid, Jeanesse Scerri, Paolo Tieri, Van Steen, K., Sona Vasudevan, ... Harald HHW Schmidt. (2020). Network and systems medicine: position paper of the european collaboration on science and technology action on open multiscale systems medicine. Network and Systems Medicine, 3 (1), 67-90. doi:10.1089/nsm.2020.0004 |
Duroux, D.* , Héctor Climente-González* , Camargo Fernandez Baca, A., Lars Wienbrandt, David Ellinghaus, Chloe-Agathe Azencott, & Van Steen, K. (14 October 2019). Improving efficiency in epistasis detection with a gene-based analysis using functional filters [Poster presentation]. IGES. * These authors have contributed equally to this work. |
Joiret, M., Mahachie John, J., Gusareva, E., & Van Steen, K. (10 June 2019). Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies. BioData Mining, 12 (11), 1-23. doi:10.1186/s13040-019-0199-7 |
Debit, A., Poulet, C., JOSSE, C., Azencott, C.-A., Jerusalem, G., Van Steen, K., & BOURS, V. (15 March 2019). TOWARDS AN ACCURATE CANCER DIAGNOSIS MODELIZATION:COMPARISON OF RANDOM FOREST STRATEGIES [Poster presentation]. 19th BeSHG meeting 15th March 2019 Liege, Belgium, Liege, Belgium. |
Gusareva, E. S., Twizere, J.-C., Sleegers, K., Dourlen, P., Abisambra, J. F., Meier, S., Cloyd, R., Weiss, B., Dermaut, B., Bessonov, K., van der Lee, S. J., Carrasquillo, M. M., Katsumata, Y., Cherkaoui, M., Asselbergh, B., Ikram, M. A., Mayeux, R., Farrer, L. A., Haines, J. L., ... Van Steen, K. (2018). Male-specific epistasis between WWC1 and TLN2 genes is associated with Alzheimer's disease. Neurobiology of Aging, 72, 188.e3-188.e12. doi:10.1016/j.neurobiolaging.2018.08.001 |
Noël, G., Chaichoompu, K., Leclercq, G., Fabre, E., Gengler, N., Van Steen, K., & Francis, F. (15 November 2017). Human based genetic tools to refine genetic populations structure of honey bees (Apis mellifera ssp L.) (Hymenoptera: Apoidea: Apidae) colonies at regional scale [Paper presentation]. EUROPEAN PhD NETWORK "INSECT SCIENCE" VIII Annual Meeting. |
Debit, A., Wenric, S., JOSSE, C., Van Steen, K., & Bours, V. (May 2017). Normalization and correction for batch effects via RUV for RNA-seq data: practical implications for Breast Cancer Research [Poster presentation]. European Human Genetics Conference ESHG 2017, Copenhagen, Denmark. |
Bessonov, K., Gadaleta, F., & Van Steen, K. (2017). Integration of Gene Expression and Methylation to unravel Biological Networks in Glioblastoma Patients. Genetic Epidemiology. doi:10.1002/gepi.22028 |
Bessonov, K., & Van Steen, K. (2016). Practical aspects of gene regulatory inference via conditional inference forests from expression data. Genetic Epidemiology. doi:10.1002/gepi.22017 |
Pineda San Juan, S., Real, F. X., Kogevinas, M., Carrato, A., Chanock, S. J., Malats, N., & Van Steen, K. (2015). Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer. PLoS Genetics. doi:10.1371/journal.pgen.1005689 |
Van Lishout, F., Gadaleta, F., Moore, J. H., Wehenkel, L., & Van Steen, K. (20 November 2015). gammaMAXT: a fast multiple-testing correction algorithm. BioData Mining, 8 (36). doi:10.1186/s13040-015-0069-x |
Bessonov, K., Gusareva, E., & Van Steen, K. (2015). A cautionary note on the impact of protocol changes for Genome-Wide Association SNP x SNP Interaction studies: an example on ankylosing spondylitis. Human Genetics. doi:10.1007/s00439-015-1560-7 |
Pineda San Juan, S., Gómez-Rubio, P., Antoni, P., Bessonov, K., Márquez, M., Kogevinas, M., Real, F., Van Steen, K., & Malats, N. (2015). Framework for the integration of genomics, epigenomics, and transcriptomics in complex diseases. Human Heredity. |
Pineda San Juan, S., Malats, N., & Van Steen, K. (24 November 2014). Integration analysis of ‘OMICS’ data using penalized regression methods: An application to bladder cancer [Paper presentation]. CSCDA meeting 2014. |
Van Lishout, F., Gadaleta, F., Moore, J. H., Wehenkel, L., & Van Steen, K. (2014). gammaMAXT: a fast multiple-testing correction algorithm. In ERCIM 2014 Abstract Book (pp. 47). |
Pineda San Juan, S., Malats, N., & Van Steen, K. (03 September 2014). Integration analysis of ‘OMICS’ data using penalized regression methods: An application to bladder cancer [Paper presentation]. SEE: XXXII Scientific Meeting of the Spanish Epidemiology Society. |
Pineda San Juan, S., Malats, N., & Van Steen, K. (01 April 2014). Integration analysis of ‘OMICS’ data using penalized regression methods: An application to bladder cancer [Paper presentation]. EMGM: European Mathematical Genetics Meeting Köln, Germany. |
Gadaleta, F., & Van Steen, K. (2014). Discovering main genetic interactions with LABNet LAsso-based network inference. PLoS ONE, 9 (11), 110451. doi:10.1371/journal.pone.0110451 |
Galesloot, T. E., Van Steen, K., Kiemeney, L. A. L. M., Janss, L. L., & Vermeulen, S. H. (2014). A comparison of multivariate genome-wide association methods. PLoS ONE, 9 (4), 95923. doi:10.1371/journal.pone.0095923 |
Van Lishout, F., Bessonov, K., Duan, Q., Gusareva, E., Mahachie John, J., Tantishira, K., & Van Steen, K. (25 October 2013). Genome-wide environmental interaction analysis using multidimensional data reduction principles to identify asthma pharmacogenetic loci in relation to corticosteroid therapy [Poster presentation]. Annual Society of Human Genetics Annual Meeting 2013, Boston, United States. |
Pineda San Juan, S., Milne, R., Van Steen, K., & Malats, N. (22 May 2013). Statistical approaches for the integration of 'omics' and epidemiological data: an application to bladder cancer [Paper presentation]. XIV Scientific Meeting of the Spanish Biometrics Society. |
Pineda San Juan, S., Milne, R., Van Steen, K., & Malats, N. (May 2013). Statistical approaches for the integration of 'omics' and epidemiological data: an application to bladder cancer [Paper presentation]. XIV Scientific Meeting of the Spanish Biometrics Society. |
Van Lishout, F., Mahachie John, J., Gusareva, E., Urrea, V., Cleynen, I., Theatre, E., CHARLOTEAUX, B., Calle, M. L., Wehenkel, L., & Van Steen, K. (24 April 2013). An efficient algorithm to perform multiple testing in epistasis screening. BMC Bioinformatics, 14, 138. doi:10.1186/1471-2105-14-138 |
Breynaert, C., Dresselaers, T., Perrier, C., Arijs, I., Cremer, J., Van Lommel, L., Van Steen, K., Ferrante, M., Schuit, F., Vermeire, S., Rutgeerts, P., Himmelreich, U., Ceuppens, J. L., Geboes, K., & Van Assche, G. (2013). Unique gene expression and MR T2 relaxometry patterns define chronic murine dextran sodium sulphate colitis as a model for connective tissue changes in human Crohn's disease. PLoS ONE, 8 (7), 68876. doi:10.1371/journal.pone.0068876 |
De Greef, E., Mahachie John, J., Hoffman, I., Smets, F., Van Biervliet, S., Scaillon, M., Hauser, B., Paquot, I., Alliet, P., Arts, W., Dewit, O., Peeters, H., Baert, F., D'Haens, G., Rahier, J.-F., Etienne, I., Bauraind, O., Van Gossum, A., Vermeire, S., ... Veereman, G. (2013). Profile of pediatric Crohn's disease in Belgium. Journal of Crohn's and Colitis, 7 (11), 588-98. doi:10.1016/j.crohns.2013.04.016 |
Maus, B., Jung, C., Mahachie John, J., Hugot, J.-P., Genin, E., & Van Steen, K. (2013). Molecular reclassification of Crohn's disease: a cautionary note on population stratification. PLoS ONE, 8 (10), 77720. doi:10.1371/journal.pone.0077720 |
Van Lishout, F., Vens, C., Urrea, V., Calle, M. L., Wehenkel, L., & Van Steen, K. (03 December 2012). Survival analysis: finding relevant epistatic SNP pairs using Model- Based Multifactor Dimensionality Reduction [Paper presentation]. 5th International Conference of the ERCIM WG on COMPUTING & STATISTICS, Oviedo, Spain. |
Mahachie John, J., Cattaert, T., Van Lishout, F., Gusareva, E., & Van Steen, K. (2012). Lower-Order Effects Adjustment in Quantitative Traits Model-Based Multifactor Dimensionality Reduction. PLoS ONE. doi:10.1371/journal.pone.0029594 |
Lødrup Carlsen, K., Roll, S., Carlsen, K.-H., Mowinckel, P., Wijga, A., Brunekreef, B., Torrent, M., Roberts, G., Arshad, H., Kull, I., Krämer, U., von Berg, A., Eller, E., Høst, A., Kuehni, C., Spycher, B., Sunyer, J., Chen, C.-M., Reich, A., ... Keil, T. (2012). Does pet ownership in infancy lead to asthma or allergy at school age? Pooled analysis of individual participant data from 11 European birth cohorts. PLoS ONE. doi:10.1371/journal.pone.0043214 |
Van Lishout, F., Cattaert, T., Mahachie John, J., Gusareva, E., Urrea, V., Cleynen, I., Theatre, E., Charloteaux, B., Kvasz, A., Calle, M. L., Wehenkel, L., & Van Steen, K. (13 December 2011). An Efficient Algorithm to Perform Multiple Testing in Epistasis Screening [Paper presentation]. Benelux Bioinformatics Conference 2011, Luxembourg, Luxembourg. |
Mahachie John, J., Cattaert, T., De Lobel, L., Van Lishout, F., Empain, A., & Van Steen, K. (2011). Comparison of genetic association strategies in the presence of rare alleles. BMC Proceedings. doi:10.1186/1753-6561-5-S9-S32 |
Moens, L. N., De Rijk, P., Reumers, J., Van den Bossche, M. J. A., Glassee, W., De Zutter, S., Lenaerts, A.-S., Nordin, A., Nilsson, L.-G., Medina Castello, I., Norrback, K.-F., Goossens, D., Van Steen, K., Adolfsson, R., & Del-Favero, J. (2011). Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population. PLoS ONE, 6 (8), 23450. doi:10.1371/journal.pone.0023450 |
Cattaert, T., Urrea, V., Naj, A. C., De Lobel, L., De Wit, V., Fu, M., Mahachie John, J., Shen, H. Q., Calle, M. L., Ritchie, M. D., Edwards, T. L., & Van Steen, K. (2010). FAM-MDR: A Flexible Family-Based Multifactor Dimensionality Reduction Technique to Detect Epistasis Using Related Individuals. PLoS ONE, 5 (4). doi:10.1371/journal.pone.0010304 |
Cleynen, I., Mahachie John, J., Henckaerts, L., Van Moerkercke, W., Rutgeerts, P., Van Steen, K., & Vermeire, S. (2010). Molecular Reclassification of Crohn's Disease by Cluster Analysis of Genetic Variants. PLoS ONE, 5 (9), 12952. doi:10.1371/journal.pone.0012952 |
Joossens, M., Van Steen, K., Branche, J., Sendid, B., Rutgeerts, P., Vasseur, F., Poulain, D., Broly, F., Colombel, J.-F., Vermeire, S., & Chamaillard, M. (2010). Familial aggregation and antimicrobial response dose-dependently affect the risk for Crohn's disease. Inflammatory Bowel Diseases, 16 (1), 58-67. doi:10.1002/ibd.20985 |
Arijs, I., De Hertogh, G., Lemaire, K., Quintens, R., Van Lommel, L., Van Steen, K., Leemans, P., Cleynen, I., Van Assche, G., Vermeire, S., Geboes, K., Schuit, F., & Rutgeerts, P. (2009). Mucosal Gene Expression of Antimicrobial Peptides in Inflammatory Bowel Disease Before and After First Infliximab Treatment. PLoS ONE, 4 (11), 7984. doi:10.1371/journal.pone.0007984 |