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Kristel Van Steen - Publications ORBI
Chaichoompu, K., Yazew, F. A., Tongsima, S., Shaw, P. J., Sakuntabhai, A., Pereira, L., & Van Steen, K. (2017, July 10). Determining fine population structure using iterative pruning. Poster session presented at Drug Discovery & Therapy World Congress 2017, Boston, USA.
SNP-based information is used in several existing clustering methods to detect shared genetic ancestry or to identify population substructure (Price et al. 2006, Raj et al. 2016). Here, we present an ...
Bessonov, K., Gadaleta, F., & Van Steen, K. (2017). Integration of Gene Expression and Methylation to unravel Biological Networks in Glioblastoma Patients. Genetic Epidemiology.
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The vast amount of heterogeneous omics data, encompassing a broad range of biomolecular information, requires novel methods of analysis, including those that integrate the available levels of information. In ...
Bessonov, K., & Van Steen, K. (2016, December). Practical aspects of gene regulatory inference via conditional inference forests from expression data. Genetic Epidemiology.
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Gene regulatory network (GRN) inference is an active area of research that facilitates understanding the complex interplays between biological molecules. We propose a novel framework to create such GRNs, based ...
Chaichoompu, K., Tongsima, S., Shaw, P. J., Sakuntabhai, A., & Van Steen, K. (2016, May 21). A novel unsupervised clustering approach with multiple data types to reveal fine-level structure. Poster session presented at the European Human Genetics Conference 2016 (ESHG 2016), Barcelona, Barcelona, Spain.
Introduction: Several methods exist to identify population substructure that is due to shared genetic ancestry or regional proximity. These may be SNP-based or haplotype-based (Price et al. 2006, Lawson et al ...
Chaichoompu, K., Tongsima, S., Shaw, P. J., Sakuntabhai, A., & Van Steen, K. (2016, April 03). Iterative pruning method of unsupervised clustering for categorical data. Poster session presented at the 13th International Congress of Human Genetics (ICHG 2016), Kyoto, Japan.
Single Nucleotide Polymorphisms (SNPs) are commonly used to identify population structures. Iterative pruning Principal Component Analysis (ipPCA) utilizes SNP profiles to assign individuals to subpopulations ...
Gola, D., Mahachie John, J. M., Van Steen, K., & Konig, I. R. (2016). A roadmap to multifactor dimensionality reduction methods. Briefings in Bioinformatics, 17(2), 293-308.
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Complex diseases are defined to be determined by multiple genetic and environmental factors alone as well as in interactions. To analyze interactions in genetic data, many statistical methods have been ...
Van Lishout, F., Gadaleta, F., Moore, J. H., Wehenkel, L., & Van Steen, K. (2015). gammaMAXT: a fast multiple-testing correction algorithm. BioData Mining, 8(36).
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Background: The purpose of the maxT algorithm is to provide a significance test algorithm that controls the family-wise error rate (FWER) during simultaneous hypothesis testing. However, the requirements in ...
Gusareva, E., Wei, Z., Traherne, J. A., Hugot, J.-P., Cleynen, I., Cho, J. H., Hakonarson, H., & Van Steen, K. (2015, October 05). Epistasis associated to inflammatory bowel disease (IBD) in humans. Poster session presented at International Genetic Epidemiology Society (IGES) meeting, Baltimore, USA.
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Gene-gene interactions underlie biochemical pathways and have been well demonstrated in model organisms. Very few examples exist on replicated epistasis in humans. Here, we performed genome-wide scans to ...
Bessonov, K., Gusareva, E., & Van Steen, K. (2015, April 27). 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.
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Genome-wide association interaction (GWAI) studies have increased in popularity. Yet to date, no standard protocol exists. In practice, any GWAI workflow involves making choices about quality control ...
Bollen, L., Vande Casteele, N., Peeters, M., Bessonov, K., Van Steen, K., Rutgeerts, P., Ferrante, M., Hoylaerts, M. F., Vermeire, S., & Gils, A. (2015). Short-term Effect of Infliximab Is Reflected in the Clot Lysis Profile of Patients with Inflammatory Bowel Disease: A Prospective Study. Inflammatory bowel diseases, 21(3), 570-8.
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BACKGROUND: Inflammatory bowel disease (IBD) is recognized as an independent risk factor for thrombosis. First, we investigate whether the concentration of fibrinolysis inhibitors is increased in patients with ...
Grange, L., Bureau, J.-F., Nikolayeva, I., Paul, R., Van Steen, K., Schwikowski, B., & Sakuntabhai, A. (2015). Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis. BMC genetics, 16(1), 11.
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BackgroundDeciphering the genetic architecture of complex traits is still a major challenge for human genetics. In most cases, genome-wide association studies have only partially explained the heritability of ...
Li, Z., Vermeire, S., Bullens, D., Ferrante, M., Van Steen, K., Noman, M., Bossuyt, X., Rutgeerts, P., Ceuppens, J. L., & Van Assche, G. (2015). Anti-Tumor Necrosis Factor Therapy Restores Peripheral Blood B-cell Subsets and CD40 Expression in Inflammatory Bowel Diseases. Inflammatory Bowel Diseases, 21(12), 2787-96.
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BACKGROUND: Anti-tumor necrosis factor (TNF) therapy has become a standard therapy for severe inflammatory bowel diseases (IBD), but its effect on B lymphocytes is largely unexplored. In this study we ...
Li, Z., Vermeire, S., Bullens, D., Ferrante, M., Van Steen, K., Noman, M., Rutgeerts, P., Ceuppens, J. L., & Van Assche, G. (2015). Restoration of Foxp3+ Regulatory T-cell Subsets and Foxp3- Type 1 Regulatory-like T Cells in Inflammatory Bowel Diseases During Anti-tumor Necrosis Factor Therapy. Inflammatory Bowel Diseases, 21(10), 2418-28.
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BACKGROUND: A defect in regulatory T cells (Tregs) may be involved in the pathogenesis of inflammatory bowel diseases (IBD). Several subsets of human Foxp3+ Tregs (activated and resting Tregs) have now been ...
Pineda, S., Gomez-Rubio, P., Picornell, A., Bessonov, K., Marquez, M., Kogevinas, M., Real, F. X., Van Steen, K., & Malats, N. (2015). Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases. Human Heredity, 79(3-4), 124-36.
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OBJECTIVES: Different types of '-omics' data are becoming available in the post-genome era; still a single -omics assessment provides limited insights to understand the biological mechanism of complex diseases ...
Van Steen, K., & Malats, N. (2015). Perspectives on Data Integration in Human Complex Disease Analysis. Big Data Analytics in Bioinformatics and Healthcare (pp. 39). IGI-global.
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The identification of causal or predictive variants/genes/mechanisms for disease-associated traits is characterized by “complex” networks of molecular phenotypes. Present technology and computer power allow ...
Vande Casteele, N., Ferrante, M., Van Assche, G., Ballet, V., Compernolle, G., Van Steen, K., Simoens, S., Rutgeerts, P., Gils, A., & Vermeire, S. (2015). Trough concentrations of infliximab guide dosing for patients with inflammatory bowel disease. Gastroenterology, 148(7), 1320-9.e3.
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BACKGROUND & AIMS: Infliximab, a tumor necrosis factor antagonist, is effective for treating patients with Crohn's disease (CD) and ulcerative colitis (UC). We aimed to determine whether dosing based on ...
Van Lishout, F., Gadaleta, F., Moore, J. H., Wehenkel, L., & Van Steen, K. (2014). gammaMAXT: a fast multiple-testing correction algorithm. ERCIM 2014 Abstract Book (pp. 47).
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The purpose of the maxT algorithm (1993) is to control the family-wise error rate (FWER) when assessing significance of multiple tests jointly. However, the requirements in terms of computing time and memory ...
Gusareva, E., & Van Steen, K. (2014). Practical aspects of genome-wide association interaction analysis. Human Genetics, 133(11), 1343-58.
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Large-scale epistasis studies can give new clues to system-level genetic mechanisms and a better understanding of the underlying biology of human complex disease traits. Though many novel methods have been ...
Beigel, F., Steinborn, A., Schnitzler, F., Tillack, C., Breiteneicher, S., John, J. M., Van Steen, K., Laubender, R. P., Goke, B., Seiderer, J., Brand, S., & Ochsenkuhn, T. (2014). Risk of malignancies in patients with inflammatory bowel disease treated with thiopurines or anti-TNF alpha antibodies. Pharmacoepidemiology and drug safety, 23(7), 735-44.
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PURPOSE: We aimed to analyse malignancy rates and predictors for the development of malignancies in a large German inflammatory bowel disease (IBD) cohort treated with thiopurines and/or anti-tumour necrosis ...
Bollen, L., Peetermans, M., Peeters, M., Van Steen, K., Hoylaerts, M. F., Declerck, P. J., Verhamme, P., & Gils, A. (2014). Active PAI-1 as marker for venous thromboembolism: case-control study using a comprehensive panel of PAI-1 and TAFI assays. Thrombosis research, 134(5), 1097-102.
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BACKGROUND: Both activated Thrombin Activatable Fibrinolysis Inhibitor (TAFI) and active Plasminogen Activator Inhibitor-1 (PAI-1) attenuate fibrinolysis and may therefore contribute to the pathophysiology of ...
Boulesteix, A.-L., Janitza, S., Hapfelmeier, A., Van Steen, K., & Strobl, C. (2014). Letter to the Editor: On the term 'interaction' and related phrases in the literature on Random Forests. Briefings in bioinformatics.
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In an interesting and quite exhaustive review on Random Forests (RF) methodology in bioinformatics Touw et al. address-among other topics-the problem of the detection of interactions between variables based on ...
de Bruyn, M., Arijs, I., Wollants, W.-J., Machiels, K., Van Steen, K., Van Assche, G., Ferrante, M., Rutgeerts, P., Vermeire, S., & Opdenakker, G. (2014). Neutrophil gelatinase B-associated lipocalin and matrix metalloproteinase-9 complex as a surrogate serum marker of mucosal healing in ulcerative colitis. Inflammatory bowel diseases, 20(7), 1198-207.
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BACKGROUND: The current standard for the assessment of mucosal healing after therapy in inflammatory bowel diseases is endoscopy. However, a high need exists for noninvasive, accurate surrogate markers ...
Gadaleta, F., & Van Steen, K. (2014). Discovering main genetic interactions with LABNet LAsso-based network inference. PloS one, 9(11), 110451.
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Genome-wide association studies can potentially unravel the mechanisms behind complex traits and common genetic diseases. Despite the valuable results produced thus far, many questions remain unanswered. For ...
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.
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Joint association analysis of multiple traits in a genome-wide association study (GWAS), i.e. a multivariate GWAS, offers several advantages over analyzing each trait in a separate GWAS. In this study we ...
Savenije, O. E., Mahachie John, J., Granell, R., Kerkhof, M., Dijk, F. N., de Jongste, J. C., Smit, H. A., Brunekreef, B., Postma, D. S., Van Steen, K., Henderson, J., & Koppelman, G. H. (2014). Association of IL33-IL-1 receptor-like 1 (IL1RL1) pathway polymorphisms with wheezing phenotypes and asthma in childhood. The Journal of allergy and clinical immunology.
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BACKGROUND: Genome-wide association studies identified IL33 and IL-1 receptor-like 1 (IL1RL1)/IL18R1 as asthma susceptibility loci. IL33 and IL1RL1 constitute a single ligand-receptor pathway. OBJECTIVE: In 2 ...
Bessonov, K., & Van Steen, K. (2013, September 17). Replication of large-scale epistasis studies: an example on ankylosing spondylitis. Poster session presented at International Genetic Epidemiology Society (IGES) 2013, Chicago, USA.
Ankylosing spondylitis (AS) is a common form of inflammatory arthritis occurring in approximately 5 out of 1,000 adults of European descent. Recently, the Australo-Anglo-American Spondyloarthritis Consortium ...
Van Lishout, F., Mahachie John, J., Gusareva, E., Urrea, V., Cleynen, I., Theatre, E., Charloteaux, B., Calle, M. L., Wehenkel, L., & Van Steen, K. (2013). An efficient algorithm to perform multiple testing in epistasis screening. BMC Bioinformatics, 14, 138.
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Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved ...
Gusareva, E., Bellenguez, C., Sleegers, K., Ertekin-Taner, N., Harold, D., Lambert, J.-C., & Van Steen, K. (2013, March). Genome-wide Epistasis Screening for Alzheimer‘s Disease. Poster session presented at The ACMG Annual Clinical Genetics Meeting, Phoenix, Arizona, USA.
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Objectives: Alzheimer disease (AlzD) is a complex, progressive neurodegenerative disease where dementia symptoms (memory and other intellectual abilities loss) gradually worsen over a number of years. The ...
Haerynck, F., Mahachie John, J., Van Steen, K., Schelstraete, P., Van daele, S., Loeys, B., Van Thielen, M., De Canck, I., Nuytinck, L., & De Baets, F. (2013). Genetic variations in toll-like receptor pathway and lung function decline in Cystic fibrosis patients. Human immunology, 74(12), 1649-55.
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The toll-like receptor (TLR) family maintains pulmonary homeostasis by pathogen recognition, clearance and regulation of inflammation. Genes affecting inflammation response play a key role in modifying Cystic ...
Hoefkens, E., Nys, K., John, J. M., Van Steen, K., Arijs, I., Van der Goten, J., Van Assche, G., Agostinis, P., Rutgeerts, P., Vermeire, S., & Cleynen, I. (2013). Genetic association and functional role of Crohn disease risk alleles involved in microbial sensing, autophagy, and endoplasmic reticulum (ER) stress. Autophagy, 9(12), 2046-55.
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Genome-wide association studies have identified several genes implicated in autophagy (ATG16L1, IRGM, ULK1, LRRK2, and MTMR3), intracellular bacterial sensing (NOD2), and endoplasmic reticulum (ER) stress ...
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.
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Complex human diseases commonly differ in their phenotypic characteristics, e.g., Crohn's disease (CD) patients are heterogeneous with regard to disease location and disease extent. The genetic susceptibility ...
Salvatore, S., Salvatoni, A., Van Steen, K., Ummarino, D., Hauser, B., & Vandenplas, Y. (2013). Behind the (impedance) baseline in children. Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus / I.S.D.E.
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Impedance baseline is a new parameter recently related to esophageal integrity. The aim of this study was to assess the effect of different factors on impedance baseline in pediatric patients. We analyzed the ...
Salvatore, S., Salvatoni, A., Van Berkel, M., Van Steen, K., Unmarino, D., Ghanma, A., Hauser, B., & Vandenplas, Y. (2013). Esophageal impedance baseline is age dependent. Journal of pediatric gastroenterology and nutrition, 57(4), 506-13.
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OBJECTIVE: Esophageal impedance (multichannel intraluminal impedance [MII]) baseline (impedance baseline [IB]) has been recently considered to be related to esophageal integrity. The aim of this study was to ...
Wei, Z., Wang, W., Bradfield, J., Li, J., Cardinale, C., Frackelton, E., Kim, C., Mentch, F., Van Steen, K., Visscher, P. M., Baldassano, R. N., & Hakonarson, H. (2013). Large Sample Size, Wide Variant Spectrum, and Advanced Machine-Learning Technique Boost Risk Prediction for Inflammatory Bowel Disease. American Journal of Human Genetics.
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We performed risk assessment for Crohn's disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), by using data from the International IBD Genetics Consortium's ...
Van Lishout, F., Vens, C., Urrea, V., Calle, M. L., Wehenkel, L., & Van Steen, K. (2012, December 03). Survival analysis: finding relevant epistatic SNP pairs using Model- Based Multifactor Dimensionality Reduction. Paper presented at 5th International Conference of the ERCIM WG on COMPUTING & STATISTICS, Oviedo, Spain.
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Analyzing the combined effects of genes (and/or environmental factors) on the development of complex diseases is quite challenging, both from the statistical and computational perspective, even using a ...
Gusareva, E., & Van Steen, K. (2012). Integrating biological information in genome-wide association interaction (GWAI) studies. Paper presented at Capita Selecta in Complex Disease Analysis, Liege, Belgium.
Genome-wide association (GWA) studies of Crohn's disease have identified numerous genes. However, a substantial portion of the heritability of this disease remains unexplained. Some gene variants, not ...
Gusareva, E., Mahachie John, J., Isaacs, A., & Van Steen, K. (2012, March 12). Application of mixed polygenic model to control for cryptic/genuine relatedness and population stratification. Poster session presented at HGM 2012, Sydney, Australia.
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In genome-wide association studies (GWAs), population stratification may cause inflated type I errors and overly-optimistic test results, when not properly corrected for. During the past decade, several ...
Mahachie John, J., Cattaert, T., Van Lishout, F., Gusareva, E., & Van Steen, K. (2012, January 05). Lower-Order Effects Adjustment in Quantitative Traits Model-Based Multifactor Dimensionality Reduction. PLoS ONE.
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Identifying gene-gene interactions or gene-environment interactions in studies of human complex diseases remains a big challenge in genetic epidemiology. An additional challenge, often forgotten, is to ...
Aschard, H., Lutz, S., Maus, B., Duell, E. J., Fingerlin, T. E., Chatterjee, N., Kraft, P., & Van Steen, K. (2012). Challenges and opportunities in genome-wide environmental interaction (GWEI) studies. Human Genetics, 131, 1591-1613.
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The interest in performing gene-environment interaction studies has seen a significant increase with the increase of advanced molecular genetics techniques. Practically, it became possible to investigate the ...
Bachert, C., Van Steen, K., Zhang, N., Holtappels, G., Cattaert, T., Maus, B., Buhl, R., Taube, C., Korn, S., Kowalski, M., Bousquet, J., & Howarth, P. (2012). Specific IgE against Staphylococcus aureus enterotoxins: An independent risk factor for asthma. Journal of Allergy and Clinical Immunology (The), 130(2), 376-381.e8.
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Background: The role of IgE in patients with severe asthma is not fully understood. Objective: We sought to investigate whether IgE to Staphylococcus aureus enterotoxins might be relevant to disease severity ...
Op De Beeck, K., Maes, L., Van den Bergh, K., Derua, R., Waelkens, E., Van Steen, K., Vermeersch, P., Westhovens, R., De Vlam, K., Verschueren, P., Hooijkaas, H., Blockmans, D., & Bossuyt, X. (2012). Heterogeneous nuclear ribonucleoproteins as targets of autoantibodies in systemic rheumatic diseases. Arthritis and Rheumatism, 64(1), 213-221.
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BACKGROUND: Heterogeneous nuclear ribonucleoproteins (hnRNP) are abundant nucleoplasmic pre-mRNA-binding proteins. The aim of this study was to unravel the mosaic of autoantibodies to hnRNP's in systemic ...
Cattaert, T., Rial Garcia, J. A., Gusareva, E., & Van Steen, K. (2011, September 19). Comparison Of Different Methods For Detecting Gene-Gene Interactions In Case-Control Data. Poster session presented at 20th Annual IGES Conference, Heidelberg, Germany.
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It is generally believed that epistasis makes an important contribution to the genetic architecture of complex disease, and numerous statistical and bioinformatics methods have been developed to detect it. We ...
Gusareva, E., & Van Steen, K. (2011, September 19). Genome-wide epistasis screening for Crohns’ disease. Poster session presented at 20th Annual IGES Conference, Heidelberg, Germany.
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Genome-wide association (GWA) studies of Crohn's disease have identified numerous genes. However, a substantial portion of the heritability of this disease remains unexplained. Some gene variants, not ...
Mahachie John, J., Gusareva, E., Van Lishout, F., & Van Steen, K. (2011, September 19). A robustness study to investigate the performance of parametric and non-parametric tests used in Model-Based Multifactor Dimensionality Reduction Epistasis Detection. Poster session presented at 20th Annual IGES Conference, Heidelberg, Germany.
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Model-Based Multifactor Dimensionality Reduction (MB-MDR) is data mining technique to identify gene-gene interactions among 1000nds of SNPs in a fast way, without making assumptions about the mode of genetic ...
Gusareva, E., Huyghe, J., & Van Steen, K. (2011, August 01). Genome-wide epistasis screening for asthma associated traits. Poster session presented at Joint statistical Meetings, Miami Beach, Florida, USA.
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Genome-wide association (GWA) studies of asthma and associated traits have identified numerous genes. A substantial portion of the heritability of these traits remains unexplained. Some variants, not ...
Breynaert, C., Ferrante, M., Fidder, H., Van Steen, K., Noman, M., Ballet, V., Vermeire, S., Rutgeerts, P., & Van Assche, G. (2011). Tolerability of shortened infliximab infusion times in patients with inflammatory bowel diseases: a single-center cohort study. American Journal of Gastroenterology, 106(4), 778-85.
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OBJECTIVES: Scheduled maintenance therapy with infliximab decreases the risk of infusion reactions. Many centers have accelerated infusion times to 1 h in selected patients who tolerate 5 mg/kg infliximab ...
Gevaert, P., Van Bruaene, N., Cattaert, T., Van Steen, K., Van Zele, T., Acke, F., De Ruyck, N., Blomme, K., Sousa, A. R., Marshall, R. P., & Bachert, C. (2011). Mepolizumab, a humanized anti-IL-5 mAb, as a treatment option for severe nasal polyposis. Journal of Allergy and Clinical Immunology (The), 128(5), 989-995.e8.
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BACKGROUND: Approximately 85% of nasal polyps (NPs) in white subjects are characterized by prominent eosinophilia. IL-5 is the key driver of eosinophilic differentiation and survival. OBJECTIVE: We sought to ...
Mahachie John, J., Van Lishout, F., & Van Steen, K. (2011). Model-Based Multifactor Dimensionality Reduction to detect epistasis for quantitative traits in the presence of error-free and noisy data. European Journal of Human Genetics, 19, 696-703.
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Detecting gene-gene interactions or epistasis in studies of human complex diseases is a big challenge in the area of epidemiology. To address this problem, several methods have been developed, mainly in the ...
Schnitzler, F., Fidder, H., Boukerroucha, M., Ballet, V., Noman, M., Van Assche, G., Spitz, B., Hoffman, I., Van Steen, K., Vermeire, S., & Rutgeerts, P. (2011). Outcome of pregnancy in women with inflammatory bowel disease treated with antitumor necrosis factor therapy. Inflammatory Bowel Diseases, 17(9), 1846-1854.
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BACKGROUND:: Infliximab (IFX) and adalimumab (ADA) are attractive treatment options in patients with inflammatory bowel disease (IBD) also during pregnancy but there is still limited data on the benefit/risk ...
Van Steen, K. (2011). Perspectives on genome-wide multi-stage family-based association studies. Statistics in Medicine, 30(18), 2201-2221.
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With the establishment of large consortiums of researchers, genome-wide association (GWA) studies have become increasingly popular and feasible. Although most of these association studies focus on unrelated ...
Van Steen, K. (2011). Travelling the world of gene-gene interactions. Briefings in Bioinformatics, 13(1), 1-19.
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Over the last few years, main effect genetic association analysis has proven to be a successful tool to unravel genetic risk components to a variety of complex diseases. In the quest for disease susceptibility ...
Van Steen, K., & Sleegers, K. (2011). A report of the first biennial meeting on Capita Selecta in Complex Disease Analysis (CSCDA2010), Leuven, Belgium, August 25-27, 2010. Annals of Human Genetics, 75(4), 554-7.
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There is a need for interdisciplinary assessments and interpretations of -omics underpinnings of human complex diseases. However, often investigators from different, yet overlapping, disciplines experience ...
Vermeulen, N., de Beeck, K. O., Vermeire, S., Van Steen, K., Michiels, G., Ballet, V., Rutgeerts, P., & Bossuyt, X. (2011). Identification of a novel autoantigen in inflammatory bowel disease by protein microarray. Inflammatory Bowel Diseases, 17(6), 1291-300.
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BACKGROUND: Patients with inflammatory bowel disease (IBD) display immunoreactivity to self-antigens and microbial antigens. We used a protein microarray approach to identify novel autoantigens in IBD. METHODS ...
Ziegler, A., Van Steen, K., & Wellek, S. (2011). Investigating Hardy-Weinberg equilibrium in case-control or cohort studies or meta-analysis. Breast Cancer Research and Treatment, 128(1), 197-201.
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Yu et al. (Breast Cancer Res Treat 117:675-677, 2009) recently stated that testing for deviation from Hardy-Weinberg equilibrium (HWE) is necessary to identify systematic genotyping errors in case-control ...
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).
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We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR. It combines features of the Genome-wide Rapid Association using Mixed Model And ...
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.
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<sec> <title>Background</title> <p>Crohn's Disease (CD) has a heterogeneous presentation, and is typically classified according to extent and location of disease. The genetic susceptibility to CD is well known ...
De Lobel, L., Geurts, P., Baele, G., Castro-Giner, F., Kogevinas, M., & Van Steen, K. (2010). A screening methodology based on Random Forests to improve the detection of gene-gene interactions. European Journal of Human Genetics, 18(1127), 1132.
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The search for susceptibility loci in gene-gene interactions imposes a methodological and computational challenge for statisticians because of the large dimensionality inherent to the modelling of gene-gene ...
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.
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BACKGROUND:: An increased risk of Crohn's disease (CD) has been reported consistently in first-degree relatives of patients. Our aim was to test whether a combination of CD-associated genes involved in innate ...
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.
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Background: Antimicrobial peptides (AMPs) protect the host intestinal mucosa against microorganisms. Abnormal expression of defensins was shown in inflammatory bowel disease (IBD), but it is not clear whether ...
Bogaert, V., Vanbillemont, G., Taes, Y., De Bacquer, D., Deschepper, E., Van Steen, K., & Kaufman, J. M. (2009). Small effect of the androgen receptor gene GGN repeat polymorphism on serum testosterone levels in healthy men. European Journal of Endocrinology, 161(1), 171-7.
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OBJECTIVE: The human androgen receptor (AR) contains a polyglutamine and a polyglycine stretch which are highly polymorphic and are coded respectively by a CAG and GGN repeat in exon 1 of the AR gene. Although ...
Henckaerts, L., Van Steen, K., Verstreken, I., Cleynen, I., Franke, A., Schreiber, S., Rutgeerts, P., & Vermeire, S. (2009). Genetic risk profiling and prediction of disease course in Crohn's disease patients. Clinical Gastroenterology and Hepatology : the Official Clinical Practice Journal of The American Gastroenterological Association, 7(9), 972-980.e2.
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BACKGROUND & AIMS: Clinical presentation at diagnosis and disease course of Crohn's disease (CD) are heterogeneous and variable over time. Early introduction of immunomodulators and/or biologicals might be ...
Raby, B. A., Van Steen, K., Lasky-Su, J., Tantisira, K., Kaplan, F., & Weiss, S. T. (2009). Importin-13 genetic variation is associated with improved airway responsiveness in childhood asthma. Respiratory Research, 10, 67.
Peer reviewed (verified by ORBi)
BACKGROUND: Glucocorticoid function is dependent on efficient translocation of the glucocorticoid receptor (GR) from the cytoplasm to the nucleus of cells. Importin-13 (IPO13) is a nuclear transport receptor ...
Ripatti, S., Becker, T., Bickeboller, H., Dominicus, A., Fischer, C., Humphreys, K., Jonasdottir, G., Moreau, Y., Olsson, M., Ploner, A., Sheehan, N., Van Steen, K., Baur, M., van Duijn, C., & Palmgren, J. (2009). GENESTAT: an information portal for design and analysis of genetic association studies. European Journal of Human Genetics, 17(4), 533-6.
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We present the rationale, the background and the structure for version 2.0 of the GENESTAT information portal (www.genestat.org) for statistical genetics. The fast methodological advances, coupled with a range ...
Schnitzler, F., Fidder, H., Ferrante, M., Noman, M., Arijs, I., Van Assche, G., Hoffman, I., Van Steen, K., Vermeire, S., & Rutgeerts, P. (2009). Long-term outcome of treatment with infliximab in 614 patients with Crohn's disease: results from a single-centre cohort. Gut, 58(4), 492-500.
Peer reviewed
BACKGROUND AND AIMS: This observational study assessed the long-term clinical benefit of infliximab (IFX) in 614 consecutive patients with Crohn's disease (CD) from a single centre during a median follow-up of ...
Schnitzler, F., Fidder, H., Ferrante, M., Noman, M., Arijs, I., Van Assche, G., Hoffman, I., Van Steen, K., Vermeire, S., & Rutgeerts, P. (2009). Mucosal Healing Predicts Long-term Outcome of Maintenance Therapy with Infliximab in Crohn's Disease. Inflammatory Bowel Diseases, 15(9), 1295-1301.
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Background: Infliximab (IFX) treatment induces mucosal healing (MH) in patients with Crohn's disease (CD) but the impact of MH oil the long-term outcome of IFX treatment in CID is still debated. Methods: We ...
Vanbillemont, G., Bogaert, V., De Bacquer, D., Lapauw, B., Goemaere, S., Toye, K., Van Steen, K., Taes, Y., & Kaufman, J. M. (2009). Polymorphisms of the SHBG gene contribute to the interindividual variation of sex steroid hormone blood levels in young, middle-aged and elderly men. Clinical Endocrinology, 70(2), 303-310.
Peer reviewed (verified by ORBi)
In men there is a large interindividual variation of SHBG levels and consequently of testosterone (T) and E-2 levels. Family and twin studies suggested a strong genetic contribution, besides metabolic and ...
Bogaert, V., Taes, Y., Konings, P., Van Steen, K., De Bacquer, D., Goemaere, S., Zmierczak, H., Crabbe, P., & Kaufman, J.-M. (2008). Heritability of blood concentrations of sex-steroids in relation to body composition in young adult male siblings. Clinical Endocrinology, 69(1), 129-35.
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OBJECTIVE: Sex steroid concentrations in men are related to body composition and both are determined by genetic and environmental factors. This study investigates heritability estimates of sex steroid serum ...
Ferrante, M., Vermeire, S., Fidder, H., Schnitzler, F., Noman, M., Van Assche, G., De Hertogh, G., Hoffman, I., D'Hoore, A., Van Steen, K., Geboes, K., Penninckx, F., & Rutgeerts, P. (2008). Long-term outcome after infliximab for refractory ulcerative colitis. Journal of Crohn’s and Colitis [=JCC], 2(3), 219-225.
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Background and aims: Infliximab (IFX) has been shown efficacious for moderate-to-severe ulcerative colitis (UC), but data on long-term efficacy are tacking. We investigated long-term outcome including ...
Ferrante, M., Henckaerts, L., Joossens, M., Pierik, M., Joossens, S., Dotan, N., Norman, G., Altstock, R., Van Steen, K., Rutgeerts, P., Van Assche, G., & Vermeire, S. (2007). New serological markers in inflammatory bowel disease are associated with complicated disease behavior. Gut, 56(10), 1394-1403.
Peer reviewed (verified by ORBi)
OBJECTIVE: The human androgen receptor (AR) contains a polyglutamine and a polyglycine stretch which are highly polymorphic and are coded respectively by a CAG and GGN repeat in exon 1 of the AR gene. Although ...
Van Steen, K., Laird, N. M., Markel, P., & Molenberghs, G. (2007). Approaches to handling incomplete data in family-based association testing. Annals of Human Genetics, 71(Pt 2), 141-51.
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The high throughput of data arising from the complete sequence of the human genome has left statistical geneticists with a rich and extensive information source. The wide availability of software and the ...
Efficace, F., Bottomley, A., Coens, C., Van Steen, K., Conroy, T., Schoffski, P., Schmoll, H., Van Cutsem, E., & Kohne, C. H. (2006). Does a patient's self-reported health-related quality of life predict survival beyond key biomedical data in advanced colorectal cancer? European Journal of Cancer, 42(1), 42-9.
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The purpose of this study was to determine whether baseline patients' self reported health-related quality of life (HRQOL) parameters could predict survival beyond key biomedical prognostic factors in patients ...
Pierik, M., Joossens, S., Van Steen, K., Van Schuerbeek, N., Vlietinck, R., Rutgeerts, P., & Vermeire, S. (2006). Toll-like receptor-1,-2, and-6 polymorphisms influence disease extension in inflammatory bowel diseases. Inflammatory Bowel Diseases, 12(1), 1-8.
Peer reviewed (verified by ORBi)
Background: Evidence that a deficient innate immune response toward the bacterial flora of the gut plays a role in the pathogenesis of inflammatory bowel disease (IBD) is growing. This is underscored by the ...
Raby, B. A., Hwang, E. S., Van Steen, K., Tantisira, K., Peng, S., Litonjua, A., Lazarus, R., Giallourakis, C., Rioux, J. D., Sparrow, D., Silverman, E. K., Glimcher, L. H., & Weiss, S. T. (2006). T-bet polymorphisms are associated with asthma and airway hyperresponsiveness. American Journal of Respiratory & Critical Care Medicine, 173(1), 64-70.
Peer reviewed (verified by ORBi)
RATIONALE: T-bet (TBX21 or T-box 21) is a critical regulator of T-helper 1 lineage commitment and IFN-gamma production. Knockout mice lacking T-bet develop airway hyperresponsiveness (AHR) to methacholine ...
Raby, B. A., Van Steen, K., Lazarus, R., Celedon, J. C., Silverman, E. K., & Weiss, S. T. (2006). Eotaxin polymorphisms and serum total IgE levels in children with asthma. Journal of Allergy and Clinical Immunology (The), 117(2), 298-305.
Peer reviewed (verified by ORBi)
BACKGROUND: Eotaxin (chemokine, CC motif, ligand; CCL11) is a potent eosinophil chemoattractant strongly implicated in the pathobiology of asthma. Genetic variation at the CCL11 locus has been correlated with ...
McQueen, M. B., Murphy, A., Kraft, P., Su, J., Lazarus, R., Laird, N. M., Lange, C., & Van Steen, K. (2005). Comparison of linkage and association strategies for quantitative traits using the COGA dataset. Genetic Epidemiology. Supplement, 29(Suppl I), 1-S9.
Peer reviewed (verified by ORBi)
Genome scans using dense single-nucleotide polymorphism ( SNP) data have recently become a reality. It is thought that the increase in information content for linkage analysis as a result of the denser scans ...
McQueen, M. B., Murphy, A., Kraft, P., Su, J., Lazarus, R., Laird, N. M., Lange, C., & Van Steen, K. (2005). Comparison of linkage and association strategies for quantitative traits using the COGA dataset. BMC Genetics, 6 Suppl 1, 96.
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ABSTRACT : Genome scans using dense single-nucleotide polymorphism (SNP) data have recently become a reality. It is thought that the increase in information content for linkage analysis as a result of the ...
Moerkerke, B., Goetghebeur, E., Van Steen, K., Vanbelle, S., & Cocquyt, V. (2005). Permutation based methods for comparing quality of life between observed treatments. Statistics in Medicine, 24(24), 4055-66.
Peer reviewed (verified by ORBi)
Quality of life is becoming an important outcome for the comparison of aggressive therapies. To measure quality of life (QOL), questionnaires have been designed that ask patients about symptoms and ...
Murphy, A., McGueen, M. B., Su, J., Kraft, P., Lazarus, R., Laird, N. M., Lange, C., & Van Steen, K. (2005). Genomic screening in family-based association testing. BMC Genetics, 6.
Peer reviewed (verified by ORBi)
Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of ...
Murphy, A., McGueen, M. B., Su, J., Kraft, P., Lazarus, R., Laird, N. M., Lange, C., & Van Steen, K. (2005). Genomic screening in family-based association testing. Genetic Epidemiology. Supplement, 29.
Peer reviewed (verified by ORBi)
Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of ...
Raby, B. A., Van Steen, K., Celedon, J. C., Litonjua, A. A., Lange, C., & Weiss, S. T. (2005). Paternal history of asthma and airway responsiveness in children with asthma. American Journal of Respiratory & Critical Care Medicine, 172(5), 552-8.
Peer reviewed (verified by ORBi)
RATIONALE: Little is known regarding the relationship between parental history of asthma and subsequent airway hyperresponsiveness (AHR) in children with asthma. OBJECTIVES: We evaluated this relationship in 1 ...
Van Ranst, M., Joossens, M., Joossens, S., Van Steen, K., Pierik, M., Vermeire, S., & Rutgeerts, P. (2005). Crohn's disease and month of birth. Inflammatory Bowel Diseases, 11(6), 597-9.
Peer reviewed (verified by ORBi)
BACKGROUND: Environmental factors trigger the onset of inflammatory bowel disease (IBD) in genetically predisposed individuals. Exposure to seasonal external factors during the maturation of the immune system ...
Van Steen, K., & Lange, C. (2005). PBAT: a comprehensive software package for genome-wide association analysis of complex family-based studies. Human Genomics, 2(1), 67-9.
Peer reviewed (verified by ORBi)
The PBAT software package (v2.5) provides a unique set of tools for complex family-based association analysis at a genome-wide level. PBAT can handle nuclear families with missing parental genotypes, extended ...
Van Steen, K., McQueen, M. B., Herbert, A., Raby, B., Lyon, H., DeMeo, D. L., Murphy, A., Su, J., Datta, S., Rosenow, C., Christman, M., Silverman, E. K., Laird, N. M., Weiss, S. T., & Lange, C. (2005). Genomic screening and replication using the same data set in family-based association testing. Nature Genetics, 37(7), 683-691.
Peer reviewed (verified by ORBi)
The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of analyzing ...
Van Steen, K., McQueen, M. B., Herbert, A., Rosenow, C., Silverman, E. K., Laird, N. M., Weiss, S. T., & Lange, C. (2005). Genomic screening in family-based association testing and the multiple testing problem. Genetic Epidemiology. Supplement, 28, 164.
Peer reviewed (verified by ORBi)
The Human Genome Project and its spin- offs are making it increasingly feasible to determine the genetic basis of complex traits using genome- wide association studies. The statistical challenge of analyzing ...
Esters, N., Pierik, M., Van Steen, K., Vermeire, S., Claessens, G., Joossens, S., Vlietinck, R., & Rutgeerts, P. (2004). Transmission of CARD15 (NOD2) variants within families of patients with inflammatory bowel disease. American Journal of Gastroenterology, 99(2), 299-305.
Peer reviewed (verified by ORBi)
OBJECTIVES: Three single nucleotide polymorphisms (SNPs) in CARD15 have been independently associated with Crohn's disease (CD). Since nothing is known about the transmission of these variants within families ...
Joossens, S., Vermeire, S., Van Steen, K., Godefridis, G., Claessens, G., Pierik, M., Hietinck, R., Aerts, R., Rutgeerts, P., & Bossuyt, X. (2004). Pancreatic autoantibodies in inflammatory bowel disease. Inflammatory Bowel Diseases, 10(6), 771-777.
Peer reviewed (verified by ORBi)
Background: Autoantibodies against exocrine pancreas (PABs) have been reported to be specific for Crohn's disease (CD), albeit at a low prevalence (30%). We studied PABs in patients with inflammatory bowel ...
Van Steen, K., Tahri, N., & Molenberghs, G. (2004). Introducing the multivariate dale model in population-based genetic association studies. Biometrical Journal = Biometrische Zeitschrift, 46(2), 187-202.
Peer reviewed (verified by ORBi)
Until recently, the most common parametric approaches to study the combined effects of several genetic polymorphisms located within a gene or in a small genomic region are, at the genotype level, logistic ...
Vermeire, S., Rutgeerts, P., Van Steen, K., Joossens, S., Claessens, G., Pierik, M., Peeters, M., & Vlietinck, R. (2004). Genome wide scan in a Flemish inflammatory bowel disease population: support for the IBD4 locus, population heterogeneity, and epistasis. Gut, 53(7), 980-986.
Peer reviewed (verified by ORBi)
Background and aims: Genome wide scans in inflammatory bowel disease (IBD) have indicated various susceptibility regions with replication of 16cen (IBD1), 12q (IBD2), 6p (IBD3), 14q11 (IBD4), and 3p21. As no ...
Jansen, I., Molenberghs, G., Aerts, M., Thijs, H., & Van Steen, K. (2003). A local influence approach applied to binary data from a psychiatric study. Biometrics, 59(2), 410-9.
Peer reviewed (verified by ORBi)
Recently, a lot of concern has been raised about assumptions needed in order to fit statistical models to incomplete multivariate and longitudinal data. In response, research efforts are being devoted to the ...
Vermeire, S., Noman, M., Van Assche, G., Baert, F., Van Steen, K., Esters, N., Joossens, S., Bossuyt, X., & Rutgeerts, P. (2003). Autoimmunity associated with anti-tumor necrosis factor alpha treatment in Crohn's disease: A prospective cohort study. Gastroenterology, 125(1), 32-39.
Peer reviewed (verified by ORBi)
Background & Aims: Infliximab therapy is an effective approach to treating Crohn's disease. Development of antinuclear antibodies has been described in patients treated, but the size of the problem and the ...
Bottomley, A., Thomas, R., Van Steen, K., Flechtner, H., & Djulbegovic, B. (2002). Human recombinant erythropoietin and quality of life: a wonder drug or something to wonder about? Lancet Oncology, 3(3), 145-53.
Peer reviewed (verified by ORBi)
Over the past decade an increasing number of studies have supported the use of recombinant human erythropoietin (epoetin) in cancer patients, suggesting that it improves haemoglobin concentrations for some ...
Van Steen, K., Curran, D., Kramer, J., Molenberghs, G., Van Vreckem, A., Bottomley, A., & Sylvester, R. (2002). Multicollinearity in prognostic factor analyses using the EORTC QLQ-C30: identification and impact on model selection. Statistics in Medicine, 21(24), 3865-3884.
Peer reviewed (verified by ORBi)
Clinical and quality of life (QL) variables from an EORTC clinical trial of first line chemotherapy in advanced breast cancer were used in a prognostic factor analysis of survival and response to chemotherapy ...
Van Steen, K., Curran, D., & Molenberghs, G. (2001). Sensitivity analysis of longitudinal binary quality of life data with drop-out: an example using the EORTC QLQ-C30. Statistics in Medicine, 20(24), 3901-20.
Peer reviewed (verified by ORBi)
Analysing quality of life data (QOL) may be complicated for several reasons. Quality of life data not only involves repeated measures but is also usually collected on ordered categorical responses. In addition ...
Van Maldeghem, H., & Van Steen, K. (1999). Characterizations by automorphism groups of some rank 3 buildings - II: A half strongly-transitive locally finite triangle building is a Bruhat-Tits building. Geometriae Dedicata, 74(2), 113-133.
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We complete the proof of the fact that every locally finite triangle building Delta with a half strongly-transitive automorphism group G (e.g., this happens when Delta is defined via a (B, N)-pair in G) is a ...
Van Maldeghem, H., & Van Steen, K. (1999). Characterizations by automorphism groups of some rank 3 buildings - IV: Hyperbolic p-adic Moufang buildings of rank 3. Geometriae Dedicata, 75(2), 115-122.
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In this paper, we introduce the p-adic Moufang condition for hyperbolic buildings of rank 3. It is the most obvious and simplest generalization of the p-adic Moufang condition for affine buildings, introduced ...
Van Steen, K. (1999). Characterizations by automorphism groups of some rank 3 buildings, III. Moufang-like conditions. Geometriae Dedicata, 74(3), 225-240.
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In this paper, we introduce the root-Moufang condition and the p-adic Moufang condition. We show that affine buildings of type (A) over tilde(2) satisfying the root-Moufang condition are Bruhat-Tits buildings ...
Van Maldeghem, H., & Van Steen, K. (1998). Characterizations by automorphism groups of some rank 3 buildings - I. Some properties of half strongly-transitive triangle buildings. Geometriae Dedicata, 73(2), 119-142.
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In a sequence of papers, we will show that the existence of a (half) strongly-transitive automorphism group acting on a locally finite triangle building Delta forces Delta to be one of the examples arising ...
Van Maldeghem, H., & Van Steen, K. (1997). Moufang affine buildings have Moufang spherical buildings at infinity. Glasgow Mathematical Journal, 39(Part 3), 237-241.
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We show in a direct and elementary way that the spherical building at infinity of every rank 3 affine building which satisfies Tits' Moufang condition, is itself a Moufang building. This result is also true ...