Research Explorer

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Researcher

Jan Fostier

Publications & Research Data

Awards & Distinctions

140 Results

2025

Advancing practical pan-genomics with compressed indexing

Lore DepuydtJan FostierTravis Gagie

Approximate sequence alignment using search schemes

Luca RendersJan FostierKathleen Marchal

b-move : faster lossless approximate pattern matching in a run-length compressed index

Lore DepuydtLuca RendersSimon Van de VyverLennart VeysTravis GagieJan Fostier

A1 Journal Article in ALGORITHMS FOR MOLECULAR BIOLOGY

ELLIPSIS : robust quantification of splicing in scRNA-seq

Marie Van HeckeNiko BeerenwinkelThibault LootensJan FostierRobrecht RaedtKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Methods for single-biomolecule translocation event detection from nanopore current signal : a review

Pratima UpreteeWouter BotermansKoen MartensSanjin MarionJan FostierNilesh Madhu

A1 Journal Article in IEEE SENSORS JOURNAL

Search schemes for approximate pattern matching : an overview

Lore DepuydtJan FostierSimon GottliebGregory KucherovKnut ReinertLuca Renders

Bookchapter in The Expanding World of Compressed Data : A Festschrift for Giovanni Manzini's 60th Birthday

Uncovering splicing diversity : graph-based methods for splicing quantiﬁcation and mRNA transcript reconstruction at single cell resolution

Marie Van HeckeKathleen MarchalJan Fostier

2024

Automated design of efficient search schemes for lossless approximate pattern matching

Luca RendersLore DepuydtSven RahmannJan Fostier

B-move : faster bidirectional character extensions in a run-length compressed index

Lore DepuydtLuca RendersSimon Van de VyverLennart VeysT. GagieJan Fostier

Faster maximal exact matches with lazy LCP evaluation

Adrián GogaLore DepuydtNathaniel K. BrownJan FostierTravis GagieGonzalo Navarro

Lossless approximate pattern matching : automated design of efficient search schemes

Luca RendersLore DepuydtSven RahmannJan Fostier

A1 Journal Article in JOURNAL OF COMPUTATIONAL BIOLOGY

2023

Detecting translocation of DNA nanostructures through nanopores : first steps towards structural barcode readout

Pratima UpreteeSybren SantermansKoen MartensJuliette GeversSanjin MarionWouter Van Den BoschJan FostierNilesh Madhu

Improved node and arc multiplicity estimation in de Bruijn graphs using approximate inference in conditional random fields

Aranka SteyaertP. AudenaertJan Fostier

A1 Journal Article in IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Modelling de Bruijn graphs using conditional random fields

Aranka SteyaertJan FostierP. Audenaert

Oracle selection provides insight into how far off practice is from Utopia in plant breeding

David VanavermaeteSteven MaenhoutJan FostierBernard De Baets

A1 Journal Article in FRONTIERS IN PLANT SCIENCE

Pan-genome de Bruijn graph using the bidirectional FM-index

Lore DepuydtLuca RendersThomas AbeelJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

2022

Adaptive scoping : balancing short- and long-term genetic gain in plant breeding

David VanavermaeteJan FostierSteven MaenhoutBernard De Baets

A1 Journal Article in EUPHYTICA

Approximate pattern matching using search schemes and in-text verification

Luca RendersLore DepuydtJan Fostier

Approximate pattern matching using search schemes and in-text verification

Luca RendersLore DepuydtJan Fostier

BLSSpeller to discover novel regulatory motifs in maize

Razgar Seyed RahmaniDries DecapJan FostierKathleen Marchal

A1 Journal Article in DNA RESEARCH

Halvade somatic : somatic variant calling with Apache Spark

Dries DecapLouise de Schaetzen van BrienenMaarten LarmuseauPascal CostanzaCharlotte HerzeelRoel WuytsKathleen MarchalJan Fostier

A1 Journal Article in GIGASCIENCE

2021

Deep scoping : a breeding strategy to preserve, reintroduce and exploit genetic variation

David VanavermaeteJan FostierSteven MaenhoutBernard De Baets

A1 Journal Article in THEORETICAL AND APPLIED GENETICS

Dynamic partitioning of search patterns for approximate pattern matching using search schemes

Luca RendersKathleen MarchalJan Fostier

A1 Journal Article in ISCIENCE

Exploring and exploiting genetic variation for balancing short- and long-term genetic gains in plant breeding

David VanavermaeteBernard De BaetsJan FostierSteven Maenhout

Multithreaded variant calling in elPrep 5

Charlotte HerzeelPascal CostanzaDries DecapJan FostierRoel WuytsWilfried Verachtert

A1 Journal Article in PLOS ONE

2020

Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields

Aranka SteyaertP. AudenaertJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

BLAMM : BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs

A1 Journal Article in BMC BIOINFORMATICS

Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples

Louise de Schaetzen van BrienenMaarten LarmuseauKim Van der EeckenFrederic De RyckPauline Robbe VandewalleAnna SchuhJan FostierPiet OstKathleen Marchal

A1 Journal Article in BMC MEDICAL GENOMICS

Computational assessment of the feasibility of protonation-based protein sequencing

Giles MiclotteKoen MartensJan Fostier

A1 Journal Article in PLOS ONE

GABAC : an arithmetic coding solution for genomic data

Jan VogesTom ParidaensFabian MuenteferingLiudmila S. MainzerBrian BlissMingyu YangIdoia OchoaJan FostierJoern OstermannMikel Hernaez

A1 Journal Article in BIOINFORMATICS

Preservation of genetic variation in a breeding population for long-term genetic gain

David VanavermaeteJan FostierSteven MaenhoutBernard De Baets

A1 Journal Article in G3-GENES GENOMES GENETICS

2019

Accurate determination of node and arc multiplicities in de Bruijn graphs using conditional random fields

Aranka SteyaertP. AudenaertJan Fostier

Correction of third generation sequencing reads through read-to-graph alignment

Giles MiclotteJan FostierP. Audenaert

elPrep 4 : a multithreaded framework for sequence analysis

Charlotte HerzeelPascal CostanzaDries DecapJan FostierWilfried Verachtert

A1 Journal Article in PLOS ONE

Error correction of Illumina sequencing data

Mahdi HeydariJan FostierYves Van de Peer

GABAC : an arithmetic coding solution for genomic data

Tom ParidaensJ. VogesM. HernaezJan FostierJ. Ostermann

Illumina error correction near highly repetitive DNA regions improves de novo genome assembly

Mahdi HeydariGiles MiclotteYves Van de PeerJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

Iterative seeding for sequence to graph alignment

Giles MiclotteP. AudenaertJan Fostier

2018

A BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs

BrownieAligner : accurate alignment of Illumina sequencing data to de Bruijn graphs

Mahdi HeydariGiles MiclotteYves Van de PeerJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

Distributed pattern mining and data publication in life sciences using big data technologies

Dieter De WitteErik MannensJan Fostier

Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern

Nele VandersickelMasaya WatanabeQian TaoJan FostierKatja ZeppenfeldAlexander Panfilov

A1 Journal Article in PLOS COMPUTATIONAL BIOLOGY

Hybrid long read error correction using inexact seeds and flow graphs

Giles MiclotteP. AudenaertJan Fostier

Iterative seeding for sequence to graph alignment

Giles MiclotteP. AudenaertJan Fostier

2017

Evaluation of the impact of Illumina error correction tools on de novo genome assembly

Mahdi HeydariGiles MiclottePiet DemeesterYves Van de PeerJan Fostier

A1 Journal Article in BMC BIOINFORMATICS

Hadoop-based solutions for variant calling and variant analysis

Dries DecapJan Fostier

Halvade-RNA : parallel variant calling from transcriptomic data using MapReduce

Dries DecapJoke ReumersCharlotte HerzeelPascal CostanzaJan Fostier

A1 Journal Article in PLOS ONE

OMSim : a simulator for optical map data

Giles MiclotteStéphane PlaisanceStephane RombautsYves Van de PeerP. AudenaertJan Fostier

A1 Journal Article in BIOINFORMATICS

Studying the regulatory landscape of flowering plants

Jan Van de VeldeKlaas VandepoeleJan Fostier

2016

Exploiting natural selection to study adaptive behavior

Sergio Pulido TamayoKathleen MarchalJan FostierJos Vanderleyden

High performance computing for large-scale genomic prediction

Arne De ConinckBernard De BaetsJan Fostier

Jabba: hybrid error correction for long sequencing reads

Giles MiclotteMahdi HeydariPiet DemeesterStephane RombautsYves Van de PeerP. AudenaertJan Fostier

A1 Journal Article in ALGORITHMS FOR MOLECULAR BIOLOGY

Needles: toward large-scale genomic prediction with marker-by-environment interaction

Arne De ConinckBernard De BaetsDrosos KourounisFabio VerbosioOlaf SchenkSteven MaenhoutJan Fostier

A1 Journal Article in GENETICS

Network-guided data integration and gene prioritization

Lieven VerbekeJan FostierKathleen Marchal

OMSim: simulating optical mapping data

Giles MiclotteP. AudenaertJan Fostier

Performance analysis of a parallel, multi-node pipeline for DNA sequencing

Dries DecapJoke ReumersCharlotte HerzeelPascal CostanzaJan Fostier

2015

BLSSpeller : exhaustive comparative discovery of conserved cis-regulatory elements

Dieter De WitteJan Van de VeldeDries DecapMichiel Van BelP. AudenaertPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

A1 Journal Article in BIOINFORMATICS

Efficient uncertainty quantification of large two-dimensional optical systems with a parallelized stochastic Galerkin method

Zdravko ZubacJan FostierDaniël De ZutterDries Vande Ginste

A1 Journal Article in OPTICS EXPRESS

elPrep: high-performance preparation of sequence alignment/map files for variant calling

Charlotte HerzeelPascal CostanzaDries DecapJan FostierJoke Reumers

A1 Journal Article in PLOS ONE

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

Sergio Pulido TamayoAminael Sanchez RodriguezToon SwingsBram Van den BergheAkanksha DubeyHans SteenackersJan MichielsJan FostierKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Full-wave simulations of electromagnetic scattering problems with billions of unknowns

Bart MichielsJan FostierIgnace BogaertDaniël De Zutter

A1 Journal Article in IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION

Halvade: scalable sequence analysis with MapReduce

Dries DecapJoke ReumersCharlotte HerzeelPascal CostanzaJan Fostier

A1 Journal Article in BIOINFORMATICS

Including explicit marker-by-environment interaction for large-scale genomic prediction

Arne De ConinckDrosos KourounisFabio VerbosioOlaf SchenkBernard De BaetsSteven MaenhoutJan Fostier

Jabba: hybrid error correction for long sequencing reads using maximal exact matches

Giles MiclotteMahdi HeydariPiet DemeesterP. AudenaertJan Fostier

Jabba: Hybrid error correction of long sequencing reads (outstanding presentation award)

Giles MiclotteMahdi HeydariPiet DemeesterP. AudenaertJan Fostier

Pathway relevance ranking for tumor samples through network-based data integration

Lieven VerbekeJimmy Van den EyndenAna Carolina Elisa Fierro GutierrezPiet DemeesterJan FostierKathleen Marchal

A1 Journal Article in PLOS ONE

Pathway relevance ranking for tumor samples through network-based data integration (award for Outstanding Oral Poster Presentation )

Lieven VerbekeJimmy Van den EyndenPiet DemeesterKathleen MarchalJan Fostier

Preconditioner for a scattering solver based on the intrusive stochastic Galerkin method accelerated with MLFMM

Zdravko ZubacJan FostierDaniël De ZutterDries Vande Ginste

Solving billions of unknowns using the parallel MLFMA and a Tier 1 supercomputer

Jan FostierBart MichielsIgnace BogaertDaniël De Zutter

Towards parallel large-scale genomic prediction by coupling sparse and dense matrix algebra

Arne De ConinckDrosos KourounisFabio VerbosioOlaf SchenkBernard De BaetsSteven MaenhoutJan Fostier

2014

A high performance computing approach for genomic prediction

Arne De ConinckJan FostierSteven MaenhoutBernard De Baets

A parallel, distributed-memory framework for comparative motif discovery

Dieter De WitteMichiel Van BelP. AudenaertPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

A well-scaling parallel algorithm for the computation of the translation operator in the MLFMA

Bart MichielsIgnace BogaertJan FostierDaniël De Zutter

A1 Journal Article in IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION

DAIRRy-BLUP: a high-performance computing approach to genomic prediction

Arne De ConinckJan FostierSteven MaenhoutBernard De Baets

A1 Journal Article in GENETICS

Halvade: whole genome analysis with MapReduce

Dries DecapJ ReumersC HerzeelP CostanzaJan Fostier

In-memory, distributed content-based recommender system

Simon DoomsP. AudenaertJan FostierToon De PessemierLuc Martens

A1 Journal Article in JOURNAL OF INTELLIGENT INFORMATION SYSTEMS

Parallel, distributed-memory computation of the translation operator in three dimensions

Bart MichielsIgnace BogaertJan FostierDaniël De Zutter

Parallel, distributed-memory MLFMA for large-scale electromagnetic simulations

Jan FostierIgnace BogaertDaniël De Zutter

Weak scaling analysis for the parallel MLFMA: the quest for ever larger simulations

Bart MichielsJan FostierIgnace BogaertDaniël De Zutter

2013

A generic framework for the parallel MLFMA

Bart MichielsJan FostierIgnace BogaertDaniël De Zutter

A weak scalability study of the parallel computation of the translation operator in the MLFMA

Bart MichielsIgnace BogaertJan FostierDaniël De Zutter

Comparative motif discovery in the cloud

Dieter De WitteJan Van de VeldeMichiel Van BelP. AudenaertPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks

Lieven VerbekePiet DemeesterJan FostierKathleen Marchal

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks

Lieven VerbekeLore ClootsPiet DemeesterJan FostierKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Identifying relevant pathways for different breast cancer subtypes using network based data integration

Lieven VerbekeAC FierroJimmy Van den EyndenPiet DemeesterJan FostierKathleen Marchal

Parallel fast multipole methods for the simulation of extremely large electromagnetic scattering problems

Bart MichielsDaniël De ZutterIgnace BogaertJan Fostier

Performing large full-wave simulations by means of a parallel MLFMA implementation

Bart MichielsJan FostierIgnace BogaertDaniël De Zutter

Scalable parallel computation of the translation operator in three dimensions

Bart MichielsIgnace BogaertJan FostierDaniël De Zutter

The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees

Sofie DemeyerTom MichoelJan FostierP. AudenaertMario PickavetPiet Demeester

A1 Journal Article in PLOS ONE

Weak scalability analysis of the distributed-memory parallel MLFMA

Bart MichielsJan FostierIgnace BogaertDaniël De Zutter

A1 Journal Article in IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION

2012

A high performance computing approach to the dicovery of conserved motifs

Dieter De WitteMichiel Van BelPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

Alignment-free genome-wide comparative motif discovery in 4 Monocot species

Dieter De WitteMichiel Van BelPiet DemeesterBart DhoedtKlaas VandepoeleJan Fostier

Exploring the complementarity of eQTL mapping methods (poster)

Lieven VerbekeKathleen MarchalJan Fostier

Flexible motif discovery using feature selection trees: a high performance computing approach

Dries DecapBart DhoedtJan FostierYvan Saeys

Flexible motif discovery using feature selection trees: a high performance computing approach (poster)

Dries DecapBart DhoedtJan FostierYvan Saeys

i-ADHoRe 3.0 : fast and sensitive detection of genomic homology in extremely large data sets

Sebastian ProostJan FostierDieter De WitteBart DhoedtPiet DemeesterYves Van de PeerKlaas Vandepoele

A1 Journal Article in NUCLEIC ACIDS RESEARCH

O(1) Computation of Legendre polynomials and Gauss-Legendre nodes and weights for parallel computing

Ignace BogaertBart MichielsJan Fostier

A1 Journal Article in SIAM JOURNAL ON SCIENTIFIC COMPUTING

Online execution time prediction for computationally intensive applications with periodic progress updates

Maria ChtepenFHA ClaeysBart DhoedtFilip De TurckJan FostierPiet DemeesterPA Vanrolleghem

A1 Journal Article in JOURNAL OF SUPERCOMPUTING

2011

A fast 2-D parallel multilevel fast multipole algorithm solver for oblique plane wave incidence

Jan FostierBart MichielsIgnace BogaertDaniël De Zutter

A1 Journal Article in RADIO SCIENCE

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

Jan FostierSebastian ProostBart DhoedtYvan SaeysPiet DemeesterYves Van de PeerKlaas Vandepoele

A1 Journal Article in BIOINFORMATICS

Accurate and efficient algorithms for boundary element methods in electromagnetic scattering: a tribute to the work of F. Olyslager

Kristof CoolsIgnace BogaertJan FostierJoris PeetersDries Vande GinsteHendrik RogierDaniël De Zutter

A1 Journal Article in RADIO SCIENCE

Homogenization of an ensemble of Swiss Rolls by means of the MLFMA

Bart MichielsIgnace BogaertJan FostierDaniël De Zutter

Simulation of a Luneburg lens using a broadband multilevel fast multipole algorithm

Bart MichielsIgnace BogaertJan FostierJoris PeetersDaniël De Zutter

A1 Journal Article in RADIO SCIENCE

Swiss roll ensemble homogenization by full-wave simulations

Bart MichielsIgnace BogaertJan FostierDaniël De Zutter

A1 Journal Article in MICROWAVE AND OPTICAL TECHNOLOGY LETTERS

Towards a scalable parallel MLFMA in three dimensions

Bart MichielsJan FostierIgnace BogaertPiet DemeesterDaniël De Zutter

Towards an asynchronous, scalable MLFMA for three-dimensional electromagnetic problems

Bart MichielsJan FostierJoris PeetersIgnace BogaertDaniël De Zutter

2010

A broadband stable and efficient addition theorem for the two-dimensional Helmholtz equation

Ignace BogaertDaniël De ZutterKristof CoolsJan FostierBart MichielsJoris Peeters

Acceleration of the Calderón preconditioned PMCHWT solver by the asynchronously parallelized NSPWMLFMA

Kristof CoolsJoris PeetersIgnace BogaertJan FostierBart MichielsFP AndriulliDaniël De Zutter

An open-source implementation for full-wave 2D scattering by million-wavelength-size objects

Jan FostierFemke Olyslager

A1 Journal Article in IEEE ANTENNAS AND PROPAGATION MAGAZINE

Analysis of a scalable, parallel, 2D MLFMA solver

Jan FostierDaniël De Zutter

Combining Calderon preconditioning with fast multipole methods

Joris PeetersIgnace BogaertKristof CoolsJan FostierDaniël De Zutter

Design of asynchronous and scalable MLFMA implementations

Jan FostierBart MichielsJoris PeetersIgnace BogaertKristof CoolsDaniël De Zutter

Determination of the macroscopic permeability of swiss rolls

Bart MichielsIgnace BogaertJan FostierKristof CoolsDaniël De Zutter

Recent advances in boundary element methods applied to conducting and dielectric electromagnetic scattering problems

Kristof CoolsIgnace BogaertJan FostierJoris PeetersDries Vande GinsteHendrik RogierDaniël De Zutter

Well-conditioned conforming boundary integral based solvers for the modeling of scattering by penetrable objects

Kristof CoolsFP AndriulliP Ylä-OijalaJoris PeetersIgnace BogaertJan FostierDaniël De Zutter

2009

Design of accurate and efficient boundary-integral-based solvers for the study of electromagnetic scattering

Kristof CoolsIgnace BogaertJan FostierJoris PeetersDaniël De Zutter

Fast full-wave scattering at extremely large and complex multiscale objects

Bart MichielsJan FostierJoris PeetersIgnace BogaertS TurczynskiDA PawlakFemke Olyslager

Full-wave electromagnetic scattering at extremely large 2-D objects

Jan FostierFemke Olyslager

A1 Journal Article in ELECTRONICS LETTERS

Scalability of the parallel MLFMA

Jan FostierFemke Olyslager

Two-dimensional full-wave scattering at one million wavelength objects

Jan FostierFemke Olyslager

2008

A fast 2.5-D parallel multilevel fast multipole algorithm solver

Jan FostierFemke Olyslager

A fully scalable, asynchronous parallel MLFMA

Jan FostierFemke Olyslager

Accurate wideband evaluation of the shielding effectiveness of complex enclosures using an asynchronous parallel NSPWMLFMA

Joris PeetersIgnace BogaertJan FostierFemke Olyslager

Advances in broadband and time-domain fast multipole research

Femke OlyslagerIgnace BogaertKristof CoolsJan FostierJoris PeetersDaniël De Zutter

An asynchronous parallel MLFMA for scattering at multiple dielectric objects

Jan FostierFemke Olyslager

A1 Journal Article in IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION

An open-source, kernel-independent, asynchronous, parallel MLFMA framework

Jan FostierJoris PeetersIgnace BogaertFemke Olyslager

An open-source, kernel-independent, asynchronous, parallel MLFMA framework

Full-wave 3D simulations using the broadband NSPWMLFMA

Joris PeetersIgnace BogaertJan FostierFemke Olyslager

NSPWMLFMA: A low frequency stable formulation of the MLFMA in three dimensions

Ignace BogaertJoris PeetersJan FostierFemke Olyslager

Provably scalable parallel multilevel fast multipole algorithm

Jan FostierFemke Olyslager

A1 Journal Article in ELECTRONICS LETTERS

Recent advances in fast multipole methods to simulate ever larger and more complex structures

Femke OlyslagerKristof CoolsIgnace BogaertJan FostierJoris PeetersFP AndriulliE Michielssen

2007

A GRID computer implementation of the multilevel fast multipole algorithm for full-wave analysis of optical devices

Jan FostierFemke Olyslager

A1 Journal Article in IEICE TRANSACTIONS ON COMMUNICATIONS

An asynchronous parallel multilevel fast multipole algorithm

Jan FostierFemke Olyslager

Fast and accurate evaluation of enclosures with the method of moments by using splay trees

Femke OlyslagerJan FostierJoris PeetersDaniël De Zutter

New parallel approaches for fast multipole solvers (invited paper)

Joris PeetersJan FostierFemke OlyslagerDaniël De Zutter

2006

A parallel multilevel fast multipole algorithm for GRID computing allowing optical full-wave simulations

Jan FostierFemke Olyslager

Characterization of speckle/despeckling in active millimeter wave imaging systems using a first order 1.5D model - art. no. 619409.

I OCKETB NAUWELAERSJan FostierLieven MeertFemke OlyslagerG KOERSJ STIENSR VOUNCKXI JAGER

Efficient and accurate techniques to simulate electromagnetic crystals

Femke OlyslagerDavy PissoortJan FostierIgnace BogaertJürgen De ZaeytijdEric Michielssen

Fast and accurate evaluation of the shielding effectiveness of complex enclosures

Femke OlyslagerJan Fostier

Parallel multilevel fast multipole algorithm for GRID computing allowing full-wave electromagnetic simulations (abstract)

Jan FostierFemke Olyslager