ORCID Profile
0000-0002-9050-4370
Current Organisations
KU Leuven
,
Ghent University
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Publisher: Public Library of Science (PLoS)
Date: 17-08-2017
Publisher: Springer Science and Business Media LLC
Date: 22-02-2015
Publisher: Springer Science and Business Media LLC
Date: 07-08-2017
Publisher: American Geophysical Union (AGU)
Date: 08-2007
DOI: 10.1029/2006WR005187
Publisher: Oxford University Press (OUP)
Date: 26-07-2012
DOI: 10.1111/J.1467-9868.2011.01020.X
Abstract: We present a semiparametric statistical model for the probabilistic index which can be defined as P(Y⩽Y*), where Y and Y* are independent random response variables associated with covariate patterns X and X* respectively. A link function defines the relationship between the probabilistic index and a linear predictor. Asymptotic normality of the estimators and consistency of the covariance matrix estimator are established through semiparametric theory. The model is illustrated with several ex les, and the estimation theory is validated in a simulation study.
Publisher: Wiley
Date: 02-2020
DOI: 10.1002/ENV.911
Publisher: Elsevier BV
Date: 03-2012
DOI: 10.1016/J.WATRES.2011.11.076
Abstract: Characterizing the microbial community of water is important in different domains, ranging from food and beverage production to wastewater treatment. Conventional methods, such as heterotrophic plate count, selective plating and molecular techniques, are time consuming and labor intensive. A flow cytometry based approach was developed for a fast and objective comparison of microbial communities based on the distribution of cellular features from single cells within these communities. The method consists of two main parts, firstly the generation of fingerprint data by flow cytometry and secondly a novel statistical pipeline for the analysis of flow cytometric data. The combined method was shown to be useful for the discrimination and classification of different brands of drinking water. It was also successfully applied to detect changes in microbial community composition of drinking water caused by changing environmental factors. Generally, the method can be used as a fast fingerprinting method of microbial communities in aquatic s les and as a tool to detect shifts within these communities.
Publisher: Springer Science and Business Media LLC
Date: 15-11-2012
Publisher: Springer Science and Business Media LLC
Date: 06-2007
Publisher: Walter de Gruyter GmbH
Date: 2013
Publisher: Wiley
Date: 05-2009
DOI: 10.1002/ENV.929
Publisher: Springer Science and Business Media LLC
Date: 14-09-2012
Publisher: Wiley
Date: 16-04-2012
DOI: 10.1111/J.1541-0420.2012.01750.X
Abstract: We present an adaptive percentile modified Wilcoxon rank sum test for the two-s le problem. The test is basically a Wilcoxon rank sum test applied on a fraction of the s le observations, and the fraction is adaptively determined by the s le observations. Most of the theory is developed under a location-shift model, but we demonstrate that the test is also meaningful for testing against more general alternatives. The test may be particularly useful for the analysis of massive datasets in which quasi-automatic hypothesis testing is required. We investigate the power characteristics of the new test in a simulation study, and we apply the test to a microarray experiment on colorectal cancer. These empirical studies demonstrate that the new test has good overall power and that it succeeds better in finding differentially expressed genes as compared to other popular tests. We conclude that the new nonparametric test is widely applicable and that its power is comparable to the power of the Baumgartner-Weiß-Schindler test.
Publisher: Springer Science and Business Media LLC
Date: 26-02-2018
Publisher: IWA Publishing
Date: 2006
DOI: 10.2166/WST.2006.002
Abstract: When introducing new wastewater treatment plants (WWTP), investors and policy makers often want to know if there indeed is a beneficial effect of the installation of a WWTP on the river water quality. Such an effect can be established in time as well as in space. Since both temporal and spatial components affect the output of a monitoring network, their dependence structure has to be modelled. River water quality data typically come from a river monitoring network for which the spatial dependence structure is unidirectional. Thus the traditional spatio-temporal models are not appropriate, as they cannot take advantage of this directional information. In this paper, a state-space model is presented in which the spatial dependence of the state variable is represented by a directed acyclic graph, and the temporal dependence by a first-order autoregressive process. The state-space model is extended with a linear model for the mean to estimate the effect of the activation of a WWTP on the dissolved oxygen concentration downstream.
Publisher: Oxford University Press (OUP)
Date: 31-08-2014
DOI: 10.1093/BIOINFORMATICS/BTU587
Abstract: Motivation : In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations. Results : A variant calling tool, Q-cpileup, is proposed, which exploits the Qs of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open-source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical s les, we show that Q-cpileup is able to reduce the number of false-positive findings. The filtering strategy is adaptive and provides an optimized threshold for in idual s les in each sequencing run. Additionally, linkage information is kept between single-nucleotide polymorphisms as variants are called at the codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their antiviral drug responses. A comparison with existing SNP caller tools reveals that calling variants at the codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%. Availability : The VirVarSeq is available, together with a user’s guide and test data, at sourceforge: rojects/virtools/?source=directory Contact : bie.verbist@ugent.be Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Oxford University Press (OUP)
Date: 02-05-2014
DOI: 10.1093/BIOINFORMATICS/BTU313
Abstract: Motivation: Recently, De Neve et al. proposed a modification of the Wilcoxon–Mann–Whitney (WMW) test for assessing differential expression based on RT-qPCR data. Their test, referred to as the unified WMW (uWMW) test, incorporates a robust and intuitive normalization and quantifies the probability that the expression from one treatment group exceeds the expression from another treatment group. However, no software package for this test was available yet. Results: We have developed a Bioconductor package for analyzing RT-qPCR data with the uWMW test. The package also provides graphical tools for visualizing the effect sizes. Availability and implementation: The unifiedWMWqPCR package and its user documentation can be obtained through Bioconductor. Contact: JanR.DeNeve@UGent.be
No related grants have been discovered for lieven clement.