Research Explorer

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Researcher

Kathleen Marchal

Publications & Research Data

Awards & Distinctions

288 Results

2026

Characterization of antimicrobial resistance in bacteria, including plasmids, through the development of a generic NGS-based workflow

Johannes BerbersKathleen MarchalSigrid De KeersmaeckerNancy Roosens

DNA-SIP metagenome analysis to assess the impact of genetic history on the adaptive potential towards phenylurea herbicides in BPS derived microbial communities

Luis Patricio Puchaicela HuacaKathleen MarchalAminael Sanchez Rodriguez

2025

Application of metagenomics for antimicrobial resistance detection in a One Health context

Bram BloemenKathleen MarchalSigrid De Keersmaecker

Approximate sequence alignment using search schemes

Luca RendersJan FostierKathleen Marchal

Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches

Yari Van LaereMarie-Alice FraitureAndrea GobboSigrid C. J. De KeersmaeckerKathleen MarchalNancy H. C. RoosensKevin Vanneste

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Detection of Bacillus production strains and contaminants in food enzyme products

Alexander Van UffelenAndres Posadas YabarMarie-Alice FraitureNancy H. C. RoosensSigrid C. J. De KeersmaeckerKathleen MarchalKevin Vanneste

A2 Journal Article in FOOD CHEMISTRY: MOLECULAR SCIENCES

ELLIPSIS : robust quantification of splicing in scRNA-seq

Marie Van HeckeNiko BeerenwinkelThibault LootensJan FostierRobrecht RaedtKathleen Marchal

A1 Journal Article in BIOINFORMATICS

EPS inhibitor treatment of Salmonella impacts evolution without selecting for resistance to biofilm inhibition

Mathieu JoosSybren Van GinnekenXabier VillanuevaMarie DijkmansGuglielmo A. CoppolaCamilo Andrés Pérez RomeroThijs VackierErik Van der EyckenKathleen MarchalBram Lories et al.

A1 Journal Article in NPJ BIOFILMS AND MICROBIOMES

Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing : a case study on fluoroquinolone resistance

Bram BloemenMathieu GandMoniek RingenierBert BogaertsKevin VannesteKathleen MarchalNancy H. C. RoosensJeroen DewulfFilip BoyenSigrid C. J. De Keersmaecker

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Prior knowledge injection into deep learning models predicting gene expression from whole slide images

Max HallemeeschMarija PizuricaPaloma RabaeyOlivier GevaertThomas DemeesterKathleen Marchal

smartSim : simulation of splice aware single cell smart-seq3 data

Marie Van HeckeKathleen Marchal

A2 Journal Article in BIOINFORMATICS ADVANCES

Synthetic multimodal data modelling for data imputation

Francisco Carrillo-PerezMarija PizuricaKathleen MarchalOlivier Gevaert

Editorial material

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

Marie Van HeckeKathleen MarchalJan Fostier

2024

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Alexander Van UffelenAndres Posadas YabarNancy H. C. RoosensKathleen MarchalSigrid C. J. De KeersmaeckerKevin Vanneste

A1 Journal Article in SCIENTIFIC DATA

Digital profiling of gene expression from histology images with linearized attention

Marija PizuricaYuanning ZhengFrancisco Carrillo-PerezHumaira NoorWei YaoChristian WohlfartAntoaneta VladimirovaKathleen MarchalOlivier Gevaert

A1 Journal Article in NATURE COMMUNICATIONS

Network-based data analytics for pathway driven target discovery

Pieter-Paul StrybolKathleen MarchalTim Van den Bulcke

Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling

Florence BuytaersBavo VerhaegenTom Van NieuwenhuysenNancy H. C. RoosensKevin VannesteKathleen MarchalSigrid C. J. De Keersmaecker

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

2023

A computational exploration of MHC-based immune selection signals in large cancer genome sequencing datasets

Arne ClaeysJimmy Van den EyndenKathleen Marchal

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Arne ClaeysPeter MerseburgerJasper StautKathleen MarchalJimmy Van den Eynden

A1 Journal Article in BMC GENOMICS

Cohort analysis to identify metastatic prostate cancer drivers

Louise de Schaetzen van BrienenKathleen MarchalPiet Ost

Competitive interactions facilitate resistance development against antimicrobials

Luka SvetIlse ParijsSimon IsphordingBram LoriesKathleen MarchalHans P. Steenackers

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (vol 52, pg 331, 2020)

Isidro Cortes-CirianoRuibin XiDhawal JainYoungsook L. JungDmitry GordeninDavid S. PellmanKathleen Marchal

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

Bram BloemenMathieu GandKevin VannesteKathleen MarchalNancy H. C. RoosensSigrid C. J. De Keersmaecker

A1 Journal Article in SCIENTIFIC REPORTS

Development of strain-level shotgun metagenomics approaches to detect and characterize microbiological contaminants in the context of food safety

Florence BuytaersKathleen MarchalSigrid De Keersmaecker

Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii

Yue ZhangYves Van de PeerBei LuSisi ZhangJingru CheJinming ChenKathleen MarchalXingyu Yang

A1 Journal Article in BMC BIOLOGY

Transforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices

Stéphanie NouwsBavo VerhaegenSarah DenayerFlorence CrombéDenis PiérardBert BogaertsKevin VannesteKathleen MarchalNancy H. C. RoosensSigrid C. J. De Keersmaecker

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium

Johannes BerbersKevin VannesteNancy H. C. J. RoosensKathleen MarchalPieter-Jan CeyssensSigrid C. J. De Keersmaecker

A1 Journal Article in MICROBIAL GENOMICS

Whole slide imaging-based prediction of TP53 mutations identifies an aggressive disease phenotype in prostate cancer

Marija PizuricaMaarten LarmuseauKim Van der EeckenLouise de Schaetzen van BrienenFrancisco Carrillo-PerezSimon IsphordingNicolaas LumenJo Van DorpePiet OstSofie Verbeke et al.

A1 Journal Article in CANCER RESEARCH

WSI based prediction of TP53 mutations identifies aggressive disease phenotype in prostate cancer

Marija PizuricaMaarten LarmuseauKim Van der EeckenLouise de Schaetzen van BrienenFrancisco Carrillo-PerezSimon IsphordingNicolaas LumenJo Van DorpePiet OstSofie Verbeke et al.

2022

Antibiotic cycling affects resistance evolution independently of collateral sensitivity

Pauline BrepoelsKenny AppermansCamilo Andrés Pérez RomeroBram LoriesKathleen MarchalHans P. Steenackers

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Applications of network-based and integrative approaches in plant systems biology

Razgar Seyed RahmaniKathleen MarchalGiles Miclotte

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Arne ClaeysJasper StautPeter MerseburgerKathleen MarchalJimmy Van den Eynden

BLSSpeller to discover novel regulatory motifs in maize

Razgar Seyed RahmaniDries DecapJan FostierKathleen Marchal

A1 Journal Article in DNA RESEARCH

Comparative transcriptome analysis of two maize genotypes with different tolerance to salt stress

Taher MohasseliRazgar Seyed RahmaniReza DarvishzadehSara DezhsetanKathleen Marchal

A1 Journal Article in CEREAL RESEARCH COMMUNICATIONS

Development, evaluation and optimization of next generation sequencing data analysis tools in support of a fast response for public health and food chain safety

Assia SaltykovaKathleen MarchalDieter DeforceSigrid De KeersmaeckerNancy Roosens

Evolution of isoform‐level gene expression patterns across tissues during lotus species divergence

Yue ZhangXingyu YangYves Van de PeerJinming ChenKathleen MarchalTao Shi

A1 Journal Article in PLANT JOURNAL

Extracting functional insights from loss-of-function screens using deep link prediction

Pieter-Paul StrybolMaarten LarmuseauLouise de Schaetzen van BrienenTim Van den BulckeKathleen Marchal

A2 Journal Article in CELL REPORTS METHODS

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

Leveraging comprehensive cancer systems genetic data to uncover the modus operandi of driver mutations

Maarten LarmuseauKathleen MarchalTijl De Bie

Metagenomics to detect and characterize viruses in food samples at genome level? Lessons learnt from a norovirus study

Florence BuytaersBavo VerhaegenMathieu GandJolien D'aesKevin VannesteNancy H. C. RoosensKathleen MarchalSarah DenayerSigrid C. J. De Keersmaecker

A1 Journal Article in FOODS

OMEN : network-based driver gene identification using mutual exclusivity

Dries Van DaeleBram WeytjensLuc De RaedtKathleen Marchal

A1 Journal Article in BIOINFORMATICS

2021

A bioinformatics whole-genome sequencing workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and in silico approaches

Bert BogaertsThomas DelcourtKarine SoetaertSamira BoarbiPieter-Jan CeyssensRaf WinandJulien Van BraekelSigrid C. J. De KeersmaeckerNancy H. C. RoosensKathleen Marchal et al.

A1 Journal Article in JOURNAL OF CLINICAL MICROBIOLOGY

A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products

Florence E. BuytaersMarie-Alice FraitureBas BerbersEls VandermassenStefan HoffmanNina PapazovaKevin VannesteKathleen MarchalNancy H. C. RoosensSigrid C. J. De Keersmaecker

A2 Journal Article in FOOD CHEMISTRY: MOLECULAR SCIENCES

Application of a strain- level shotgun metagenomics approach on food samples : resolution of the source of a Salmonella food-borne outbreak

Florence BuytaersAssia SaltykovaWesley MattheusValeska LaisnezBavo VerhaegenNancy H. C. RoosensKevin VannesteNaiima HammamiBrigitte PochetVera Cantaert et al.

A1 Journal Article in MICROBIAL GENOMICS

Development of a data-intensive centralized system for surveillance and outbreak investigation of bacterial pathogens using whole-genome sequencing

Bert BogaertsKathleen MarchalKevin VannesteSigrid De Keersmaecker

DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil

Harry LernerBasak OzturkAnja B. DohrmannJoice ThomasKathleen MarchalRene De MotWim DehaenChristoph C. TebbeDirk Springael

A1 Journal Article in FEMS MICROBIOLOGY ECOLOGY

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

Luca RendersKathleen MarchalJan Fostier

A1 Journal Article in ISCIENCE

Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations

Bert BogaertsRaf WinandJulien Van BraekelStefan HoffmanNancy H. C. RoosensSigrid C. J. De KeersmaeckerKathleen MarchalKevin Vanneste

A1 Journal Article in MICROBIAL GENOMICS

First detection of a plasmid-encoded New-Delhi metallo-beta-lactamase-1 (NDM-1) producing Acinetobacter baumannii using whole genome sequencing, isolated in a clinical setting in Benin

Carine YehouenouBert BogaertsKevin VannesteNancy H. C. RoosensSigrid C. J. De KeersmaeckerKathleen MarchalDissou AffolabiReza SoleimaniHector Rodriguez-VillalobosFrancoise Van Bambeke et al.

A1 Journal Article in ANNALS OF CLINICAL MICROBIOLOGY AND ANTIMICROBIALS

Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes

Razgar Seyed RahmaniTao ShiDongzhi ZhangXiaoping GouJing YiGiles MiclotteKathleen MarchalJia Li

A1 Journal Article in BMC GENOMICS

Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals

Arne ClaeysTom LuijtsKathleen MarchalJimmy Van den Eynden

A1 Journal Article in PLOS Genetics

Multifocality in prostate cancer : implications for PAM50 subtyping using an index lesion-only approach

Kim Van der EeckenMaarten LarmuseauJan VanwelkenhuyzenNicolaas LumenKathleen MarchalJo Van DorpePiet OstBram De LaereSofie Verbeke

Network-based analysis to identify drivers of metastatic prostate cancer using GoNetic

Louise de Schaetzen van BrienenGiles MiclotteMaarten LarmuseauJimmy Van den EyndenKathleen Marchal

A1 Journal Article in CANCERS

Phylogenomic investigation of increasing fluoroquinolone resistance among Belgian cases of shigellosis between 2013 and 2018 indicates both travel-related imports and domestic circulation

Bert BogaertsRaf WinandJulien Van BraekelWesley MattheusSigrid C. J. De KeersmaeckerNancy H. C. RoosensKathleen MarchalKevin VannestePieter-Jan Ceyssens

A1 Journal Article in MICROORGANISMS

Towards real-time and affordable strain-level metagenomics-based foodborne outbreak investigations using Oxford nanopore sequencing technologies

Florence BuytaersAssia SaltykovaSarah DenayerBavo VerhaegenKevin VannesteNancy H. C. RoosensDenis PierardKathleen MarchalSigrid C. J. De Keersmaecker

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods

Bert BogaertsStéphanie NouwsBavo VerhaegenSarah DenayerJulien Van BraekelRaf WinandQiang FuFlorence CrombéDenis PiérardKathleen Marchal et al.

A1 Journal Article in MICROBIAL GENOMICS

Whole genome sequencing provides an added value to the investigation of staphylococcal food poisoning outbreaks

Stéphanie NouwsBert BogaertsBavo VerhaegenSarah DenayerLasse LaeremansKathleen MarchalNancy H. C. RoosensKevin VannesteSigrid C. J. De Keersmaecker

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Whole-genome sequencing-based antimicrobial resistance characterization and phylogenomic investigation of 19 multidrug-resistant and extended-spectrum beta-lactamase-positive escherichia coli strains collected from hospital patients in Benin in 2019

Carine Laurence YehouenouBert BogaertsSigrid C. J. De KeersmaeckerNancy H. C. RoosensKathleen MarchalEdmond TchiakpeDissou AffolabiAnne SimonFrancis Moise DossouKevin Vanneste et al.

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

2020

A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium

Mathieu GandWesley MattheusNancy RoosensKatelijne DierickKathleen MarchalSophie BertrandSigrid C. J. De Keersmaecker

A1 Journal Article in FOOD MICROBIOLOGY

A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay

Mathieu GandWesley MattheusNancy HC RoosensKatelijne DierickKathleen MarchalSigrid CJ De KeersmaeckerSophie Bertrand

A1 Journal Article in FOOD MICROBIOLOGY

A practical method to implement strain-level metagenomics-based foodborne outbreak investigation and source tracking in routine

Florence BuytaersAssia SaltykovaSarah DenayerBavo VerhaegenKevin VannesteNancy H. C. RoosensDenis PiérardKathleen MarchalSigrid C. J. De Keersmaecker

A1 Journal Article in MICROORGANISMS

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Esther RheinbayMorten Muhlig NielsenFederico AbascalJeremiah A WalaOfer ShapiraGrace TiaoHenrik HornshøjJulian M HessRandi Istrup JuulZiao Lin et al.

A1 Journal Article in NATURE

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

David Mas-PonteRory JohnsonFederico AbascalSamirkumar B. AminGary D. BaderJonathan BarenboimRameen BeroukhimJohanna BertlKeith A. BoroevichSoren Brunak et al.

A1 Journal Article in COMMUNICATIONS BIOLOGY

Combined burden and functional impact tests for cancer driver discovery using DriverPower

Shimin ShuaiSteven GallingerLincoln Steinthe PCAWG Drivers and Functional Interpretation Working GroupKathleen MarchalSergio Pulido-Tamayo

A1 Journal Article in NATURE COMMUNICATIONS

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus

Bas BerbersAssia SaltykovaCristina Garcia-GraellsPatrick PhilippFabrice ArellaKathleen MarchalRaf WinandKevin VannesteNancy H. C. RoosensSigrid C. J. De Keersmaecker

A1 Journal Article in SCIENTIFIC REPORTS

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

Culture-independent analysis of linuron-mineralizing microbiota and functions in on-farm biopurification systems via DNA-stable isotope probing : comparison with enrichment culture

Harry LernerBaşak ÖztürkAnja B. DohrmannJoice ThomasKathleen MarchalRené De MotWim DehaenChristoph C. TebbeDirk Springael

A1 Journal Article in ENVIRONMENTAL SCIENCE & TECHNOLOGY

Development of a genoserotyping system for the identification of Salmonella serotypes

Mathieu GandKathleen MarchalSigrid De KeersmaeckerSophie Bertrand

Development of an NGS-based workflow for improved monitoring of circulating plasmids in support of risk assessment of antimicrobial resistance gene dissemination

Bas BerbersPieter-Jan CeyssensPierre BogaertsKevin VannesteNancy RoosensKathleen MarchalSigrid C.J. De Keersmaecker

A1 Journal Article in ANTIBIOTICS-BASEL

Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants

Tao ShiRazgar Seyed RahmaniPaul F. GuggerMuhua WangHui LiYue ZhangZhizhong LiQingfeng WangYves Van de PeerKathleen Marchal et al.

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

First detection of a plasmid located carbapenem resistant bla(VIM-1) gene in E. coli isolated from meat products at retail in Belgium in 2015

Cristina Garcia-GraellsBas BerbersBavo VerhaegenKevin VannesteKathleen MarchalNancy H. C. RoosensNadine BotteldoornSigrid C. J. De Keersmaecker

A1 Journal Article in INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Image-based dynamic phenotyping reveals genetic determinants of filamentation-mediated beta-lactam tolerance

Taiyeb ZahirDorien WilmaertsSabine FrankeBram WeytjensRafael CamachoKathleen MarchalJohan HofkensMaarten FauvartJan Michielsen

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates

Stephanie NouwsBert BogaertsBavo VerhaegenSarah DenayerDenis PierardKathleen MarchalNancy H. C. RoosensKevin VannesteSigrid C. J. De Keersmaecker

A1 Journal Article in SCIENTIFIC REPORTS

Integrative pathway enrichment analysis of multivariate omics data

Marta PaczkowskaJonathan BarenboimNardnisa SintupisutNatalie S FoxHelen ZhuDiala Abd-RabboMiles W MeePaul C BoutrosJüri Reimandthe PCAWG Drivers and Functional Interpretation Working Group et al.

A1 Journal Article in NATURE COMMUNICATIONS

Pan-cancer analysis of whole genomes

Peter J. CampbellGad GetzJan O. KorbelJoshua M. StuartJennifer L. JenningsLincoln D. SteinMarc D. PerryHardeep K. Nahal-BoseB. F. Francis OuelletteConstance H. Li et al.

A1 Journal Article in NATURE

Pathway and network analysis of more than 2500 whole cancer genomes

Matthew A ReynaDavid HaanMarta PaczkowskaLieven VerbekeMiguel VazquezAbdullah KahramanSergio Pulido-TamayoJonathan BarenboimLina WadiPriyanka Dhingra et al.

A1 Journal Article in NATURE COMMUNICATIONS

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Matthew H. BaileyWilliam U. MeyersonLewis Jonathan DursiLiang-Bo WangGuanlan DongWen-Wei LiangAmila WeerasingheShantao LiYize LiSean Kelso et al.

A1 Journal Article in NATURE COMMUNICATIONS

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (vol 11, 4748, 2020)

Matthew H. BaileyWilliam U. MeyersonLewis Jonathan DursiLiang-Bo WangGuanlan DongWen-Wei LiangAmila WeerasingheShantao LiYize LiSean Kelso et al.

Sex differences in oncogenic mutational processes

Constance H. LiStephenie D. ProkopecRen X. SunFouad YousifNathaniel SchmitzPaul C. BoutrosSergio Pulido TamayoKathleen MarchalLieven Verbeke[missing] PCAWG Tumour Subtypes and Clinical Translation et al.

A1 Journal Article in NATURE COMMUNICATIONS

Strain-level metagenomic data analysis of enriched in vitro and in silico spiked food samples : paving the way towards a culture-free foodborne outbreak investigation using STEC as a case study

Assia SaltykovaFlorence BuytaersSarah DenayerBavo VerhaegenDenis PiérardNancy H. C. RoosensKathleen MarchalSigrid C. J. De Keersmaecker

A1 Journal Article in INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a national reference laboratory in a smaller country

Stéphanie NouwsBert BogaertsBavo VerhaegenSarah DenayerFlorence CrombéKlara De RauwDenis PiérardKathleen MarchalKevin VannesteNancy H. C. Roosens et al.

A1 Journal Article in FOODS

2019

Associating expression and genomic data using co-occurrence measures

Maarten LarmuseauLieven VerbekeKathleen Marchal

A1 Journal Article in BIOLOGY DIRECT

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Michael P. MendenDennis WangMike J. MasonBence SzalaiKrishna C. BulusuYuanfang GuanThomas YuJaewoo KangMinji JeonRuss Wolfinger et al.

A1 Journal Article in NATURE COMMUNICATIONS

Detailed evaluation of data analysis tools for subtyping of bacterial isolates based on whole genome sequencing : Neisseria meningitidis as a proof of concept

Assia SaltykovaWesley MattheusSophie BertrandNancy HC RoosensKathleen MarchalSigrid CJ De Keersmaecker

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java

Mathieu GandWesley MattheusAssia SaltykovaNancy RoosensKatelijne DierickKathleen MarchalSigrid C. J. De KeersmaeckerSophie Bertrand

A1 Journal Article in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

IAMBEE : a web-service for the identification of adaptive pathways from parallel evolved clonal populations

Camilo Andrés Pérez RomeroBram WeytjensDries DecapToon SwingsJan MichielsDries De MaeyerKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Managing evidence in food safety and nutrition

Ermanno CavalliMary GilsenanJane Van DorenDanica Grahek-OgdenJane RichardsonFabrizio AbbinanteClaudia CascioPaul DevalierNikolai BrunIgor Linkov et al.

A1 Journal Article in EFSA JOURNAL

Organellar carbon metabolism is co-ordinated with distinct developmental phases of secondary xylem

Desré PinardAna Carolina Elisa Fierro GutierrezKathleen MarchalAlexander A MyburgEshchar Mizrachi

A1 Journal Article in NEW PHYTOLOGIST

2018

1-((2,4-Dichlorophenethyl)amino)3-phenoxypropan-2-ol kills Pseudomonas aeruginosa through extensive membrane damage

Valerie DefraineVeerle LiebensEvelien LoosToon SwingsBram WeytjensCarolina FierroKathleen MarchalLiam SharkeyAlex J O'NeillRomu Corbau et al.

A1 Journal Article in FRONTIERS IN MICROBIOLOGY

Catabolic task division between two near-isogenic subpopulations co-existing in a herbicide-degrading bacterial consortium : consequences for the interspecies consortium metabolic model

Pieter AlbersCédric LoodBasak ÖzturkBenjamin HoremansRob LavigneVera van NoortRené De MotKathleen MarchalAminael Sanchez-RodriguezDirk Springael

A1 Journal Article in ENVIRONMENTAL MICROBIOLOGY

Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5], 12:i:-

Assia SaltykovaVéronique WuytsWesley MattheusSophie BertrandNancy HC RoosensKathleen MarchalSigrid De Keersmaecker

A1 Journal Article in PLOS ONE

Identification of novel genes involved in acetic acid tolerance of Saccharomyces cerevisiae using pooled-segregant RNA sequencing

Miguel Fernández-NiñoSergio Pulido TamayoDespina StefanoskaCamilo Andrés Pérez RomeroDaniel González-RamosAntonius JA van MarisKathleen MarchalElke NevoigtSteve Swinnen

A1 Journal Article in FEMS YEAST RESEARCH

Modeling multi-valued biological interaction networks using fuzzy answer set programming

Mushthofa MushthofaSteven SchockaertLing-Hong HungKathleen MarchalMartine De Cock

A1 Journal Article in FUZZY SETS AND SYSTEMS

Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics

Pieter AlbersBram WeytjensRené De MotKathleen MarchalDirk Springael

A1 Journal Article in MICROBIOLOGYOPEN

Network-based modelling for omics data

Mushthofa MushthofaMartine De CockKathleen Marchal

The Crabtree effect shapes the Saccharomyces cerevisiae lag phase during the switch between different carbon sources

Gemma Perez-SamperBram CerulusAbbas JarianiLieselotte VermeerschNuria Barrajon SimancasMarkus MM BisschopsJoost van den BrinkDaniel Solis-EscalanteBrigida GalloneDries De Maeyer et al.

A1 Journal Article in MBIO

2017

Early differences in islets from prediabetic NOD mice : combined microarray and proteomic analysis

Inne CrèvecoeurValborg GudmundsdottirSaurabh VigFernanda Marques Câmara SodréWannes D’HertogAna Carolina Elisa Fierro GutierrezLeentje Van LommelConny GysemansKathleen MarchalEtienne Waelkens et al.

A1 Journal Article in DIABETOLOGIA

Effect of genomic distance on coexpression of coregulated genes in E. coli

Lucia PannierEnrique MerinoKathleen MarchalJulio Collado-Vides

A1 Journal Article in PLOS ONE

Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains

Sam CrauwelsFilip Van OpstaeleBarbara Jaskula-GoirisJan SteenselsChristel VerrethLien BosmansCaroline PaulussenBeatriz Herrera-MalaverRonnie de JongeJessika De Clippeleer et al.

A1 Journal Article in FEMS YEAST RESEARCH

Molecular subtyping of Salmonella Typhimurium with multiplex oligonucleotide ligation-PCR (MOL-PCR)

Véronique WuytsWesley MattheusNancy HC RoosensKathleen MarchalSophie BertrandSigrid CJ De Keersmaecker

Bookchapter in Diagnostic bacteriology : methods and protocols

Network-based identification of adaptive pathways in evolved ethanol-tolerant bacterial populations

Toon SwingsBram WeytjensThomas SchalckCamille BonteNatalie VerstraetenJan MichielsKathleen Marchal

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Network-based identification of driver pathways in clonal systems

Bram WeytjensKathleen MarchalJos Vanderleyden

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

Eshchar MizrachiLieven VerbekeNanette ChristieAna Carolina Elisa Fierro GutierrezShawn D MansfieldMark F DavisErica GjersingGerald A TuskanMarc Van MontaguYves Van de Peer et al.

A1 Journal Article in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles of systems biology, no. 14 : [...] Network analysis of woody biomass

Eshchar MizrachiLieven VerbekeYves Van de PeerKathleen MarchalAlexander A Myburg

Editorial material

The evolutionary significance of polyploidy

Yves Van de PeerEshchar MizrachiKathleen Marchal

A1 Journal Article in NATURE REVIEWS GENETICS

2016

Adaptive self-organizing organisms using a bio-inspired gene regulatory network controller: for the aggregation of evolutionary robots under a changing environment

Yao YaoKathleen MarchalYves Van de Peer

Bookchapter in Handbook of research on design, control and modeling of swarm robotics

Elucidation of the mode of action of a new antibacterial compound active against Staphylococcus aureus and Pseudomonas aeruginosa

Evelien GeritsEline BlommaertAnna LippellAlex J O'NeillBram WeytjensDries De MaeyerAna Carolina FierroKathleen MarchalArnaud MarchandPatrick Chaltin et al.

A1 Journal Article in PLOS ONE

Emergent adaptive behaviour of GRN-controlled simulated robots in a changing environment

Yao YaoVeronique StormeKathleen MarchalYves Van de Peer

A1 Journal Article in PEERJ

Exploiting natural selection to study adaptive behavior

Sergio Pulido TamayoKathleen MarchalJan FostierJos Vanderleyden

EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

Sergio Pulido TamayoJorge DuitamaKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

FabR regulates Salmonella biofilm formation via its direct target FabB

Kim HermansStefanie RoberfroidInge M ThijsGwendoline KintDavid De CosterKathleen MarchalJos VanderleydenSigrid CJ De KeersmaeckerHans P Steenackers

A1 Journal Article in BMC GENOMICS

Network-based analysis of eQTL data to prioritize driver mutations

Dries De MaeyerBram WeytjensLuc De RaedtKathleen Marchal

A1 Journal Article in GENOME BIOLOGY AND EVOLUTION

Network-based omics data analysis

Dries De MaeyerJos VanderleydenKathleen Marchal

Network-guided data integration and gene prioritization

Lieven VerbekeJan FostierKathleen Marchal

Optimized MOL-PCR for characterization of microbial pathogens

Véronique WuytsNancy HC RoosensSophie BertrandKathleen MarchalSigrid CJ De Keersmaecker

Bookchapter in Current protocols in cytometry

Simultaneous discovery of cancer subtypes and subtype features by molecular data integration

Thanh Le VanMatthijs van LeeuwenAna Carolina Elisa Fierro GutierrezDries De MaeyerJimmy Van den EyndenLieven VerbekeLuc De RaedtKathleen MarchalSiegfries Nijssen

A1 Journal Article in BIOINFORMATICS

SSA-ME Detection of cancer driver genes using mutual exclusivity by small subnetwork analysis

Sergio Pulido TamayoBram WeytjensDries De MaeyerKathleen Marchal

A1 Journal Article in SCIENTIFIC REPORTS

2015

A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium

Véronique WuytsWesley MattheusNancy HC RoosensKathleen MarchalSophie BertrandSigrid CJ De Keersmaecker

A1 Journal Article in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Adaptation to high ethanol reveals complex evolutionary pathways

Karin VoordeckersJacek KominekAnupam DasAdriana Espinosa-CantúDries De MaeyerAhmed ArslanMichiel Van PeeElisa van der ZandeWim MeertYudi Yang et al.

A1 Journal Article in PLOS GENETICS

Adaptation to high ethanol reveals complex evolutionary pathways

Karin VoordeckersJacek KominekAnupam DasAdriana Espinosa-CantuDries De MaeyerKathleen MarchalAlexander DeLunaRob JelierKevin Verstrepen

Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains

S CrauwelsA Van AsscheRonnie de JongeAR BornemanC VerrethP TroelsG De SamblanxKathleen MarchalYves Van de PeerKA Willems et al.

A1 Journal Article in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

Guidelines for optimisation of a multiplex oligonucleotide ligation-PCR for characterisation of microbial pathogens in a microsphere suspension array

Véronique WuytsNancy HC RoosensSophie BertrandKathleen MarchalSigrid CJ De Keersmaecker

A1 Journal Article in BIOMED RESEARCH INTERNATIONAL

Identifying prokaryotic consortia that live in close interactions with algae

Assia SaltykovaSergio Pulido-TamayoMarie PazoutovaStefan A RensingTomoaki NishiyamaYves Van de PeerKathleen MarchalStephane Rombauts

Obg and membrane depolarization are part of a microbial bet-hedging strategy that leads to antibiotic tolerance

Natalie VerstraetenWouter Joris KnapenCyrielle Ines KintVeerle LiebensBram Van den BerghLiselot DewachterJoran Elie MichielsQiang FuCharlotte Claudia DavidAna Carolina Fierro et al.

A1 Journal Article in MOLECULAR CELL

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

PheNetic : network-based interpretation of molecular profiling data

Dries De MaeyerBram WeytjensJoris RenkensLuc De RaedtKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Small-scale fermentation assay reveals differences in sugar consumption and (off)flavour production across Brettanomyces bruxellensis strains

Sam CrauwelsFilip Van OpstaeleBarbara Jaskula-GoirisChristel VerrethJessika De ClippeleerKathleen MarchalGorik De SamblanxKris WillemsKevin VerstrepenGuido Aerts et al.

SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering

Jimmy Van den EyndenAna Carolina Elisa Fierro GutierrezLieven VerbekeKathleen Marchal

A1 Journal Article in BMC BIOINFORMATICS

Studying the relationship between drug resistance and genomic variations in Leishmania donovani using a network-based method

MR Ticlla CcenhuaS Pulido-TamayoH ImamuraLieven VerbekeJ CottonJ-C DujardinKathleen Marchal

The usefulness of whole genome sequencing for outbreak investigation of food pathogens, Salmonella Enteritidis as a case study

Véronique WuytsSarah DenayerNancy HC RoosensWesley MattheusSophie BertrandKathleen MarchalKatelijne DierickSigrid CJ De Keersmaecker

Ultraviolet-B radiation stimulates downward leaf curling in Arabidopsis thaliana

Ana Carolina Elisa Fierro GutierrezOlivier LerouxBarbara De ConinckBruno PA CammueKathleen MarchalEls PrinsenDominique Van Der StraetenFilip Vandenbussche

A1 Journal Article in PLANT PHYSIOLOGY AND BIOCHEMISTRY

User‐friendly WGS analysis of Salmonella Enteritidis PT4 outbreaks

Véronique WuytsSarah DenayerNancy HC RoosensWesley MattheusSophie BertrandKathleen MarchalKatelijne DierickSigrid CJ De Keersmaecker

Vitamin D3 induces tolerance in human dendritic cells by activation of intracellular metabolic pathways

Gabriela Bomfim FerreiraAn-Sofie VanherwegenGuy EelenAna Carolina Fierro GutíerrezLeentje Van LommelKathleen MarchalLieve VerlindenAnnemieke VerstuyfTatiane NogueiraMaria Georgiadou et al.

A1 Journal Article in CELL REPORTS

Whole genome sequence analysis of Salmonella Enteritidis PT4 outbreaks from a national reference laboratory’s viewpoint

Véronique WuytsSarah DenayerNancy HC RoosensWesley MattheusSophie BertrandKathleen MarchalKatelijne DierickSigrid CJ De Keersmaecker

A2 Journal Article in PLOS CURRENTS OUTBREAKS

2014

A network-based approach to identify substrate classes of bacterial glycosyltransferases

Aminael Sánchez-RodríguezHanne LP TytgatJoris WinderickxJos VanderleydenSarah LebeerKathleen Marchal

A1 Journal Article in BMC GENOMICS

A putative de-N-acetylase of the PIG-L superfamily affects fluoroquinolone tolerance in Pseudomonas aeruginosa

Veerle LiebensValerie DefraineAnnelies Van der LeydenValerie N De GrooteCarolina FierroSerge BeullensNatalie VerstraetenCyrielle KintAnn JansEmanuela Frangipani et al.

A1 Journal Article in PATHOGENS AND DISEASE

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

Mushthofa MushthofaGustavo Adolfo Torres TorresYves Van de PeerKathleen MarchalMartine De Cock

A1 Journal Article in BIOINFORMATICS

Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing

Sam CrauwelsBo ZhuJan SteenselsPieter BusschaertGorik De SamblanxKathleen MarchalKris A WillemsKevin J VerstrepenBart Lievens

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia

Pieter MeysmanPaolo SonegoLuca BiancoQiang FuDaniela Ledezma-TejeidaSocorro Gama-CastroVeerle LiebensJan MichielsKris LaukensKathleen Marchal et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Genome-scale co-expression network comparison across escherichia coli and salmonella enterica serovar typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles

P ZarrinehA Sanchez-RodriguezN HosseinkhanZ NarimaniKathleen MarchalA Masoudi-Nejad

A1 Journal Article in PLOS ONE

Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast

Jorge DuitamaAminael Sánchez-RodriguezAnnelies GoovaertsSergio Pulido TamayoGeorg HubmannMaria R Foulquié-MorenoJohan M TheveleinKelvin J VerstrepenKathleen Marchal

A1 Journal Article in BMC GENOMICS

Improving the adaptability of simulated evolutionary swarm robots in dynamically changing environments

Yao YaoKathleen MarchalYves Van de Peer

A1 Journal Article in PLOS ONE

Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia

Ivan IshchukovYan WuSandra Van PuyveldeJos VanderleydenKathleen Marchal

A1 Journal Article in BMC MICROBIOLOGY

MAGIC: access portal to a cross-platform gene expression compendium for maize

Qiang FuAna Carolina Elisa Fierro GutierrezPieter MeysmanAminael Sanchez RodriguezKlaas VandepoeleKathleen MarchalKristof Engelen

A1 Journal Article in BIOINFORMATICS

Path finding in biological networks

Lore ClootsDries De MaeyerKathleen Marchal

Bookchapter in Springer handbook of bio-/neuroinformatics

Phenotypical and molecular responses of Arabidopsis thaliana roots as a result of inoculation with the auxin-producing bacterium Azospirillum brasilense

Stijn SpaepenStijn BossuytKristof EngelenKathleen MarchalJos Vanderleyden

A1 Journal Article in NEW PHYTOLOGIST

Photoreceptor-mediated bending towards UV-B in Arabidopsis

Filip VandenbusscheKimberley TilbrookAna Carolina FierroKathleen MarchalDirk PoelmanDominique Van Der StraetenRoman Ulm

A1 Journal Article in MOLECULAR PLANT

Thanh Le VanMatthijs Van LeeuwenSiegfried NijssenAna Carolina FierroKathleen MarchalLuc De Raedt

2013

An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference

Guillermin Agüero-ChapinAminael Sánchez-RodríguezPedro I Hidalgo-YanesYunierkis Pérez-CastilloReinaldo Molina-RuizKathleen MarchalVitor VasconcelosAgostinho Antunes

Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation

Elham AslankoohiBo ZhuMohammad Naser RezaeiKarin VoordeckersDries De MaeyerKathleen MarchalEmmie DornezChristophe M CourtinKevin J Verstrepen

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Lieven VerbekeLore ClootsPiet DemeesterJan FostierKathleen Marchal

A1 Journal Article in BIOINFORMATICS

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

Lieven VerbekePiet DemeesterJan FostierKathleen Marchal

Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles

Pieter MeysmanAminael Sánchez-RodríguezQiang FuKathleen MarchalKristof Engelen

A1 Journal Article in MOLECULAR BIOLOGY AND EVOLUTION

Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family

Pieter MeysmanKathleen MarchalKristof Engelen

A1 Journal Article in CURRENT BIOINFORMATICS

Identifying differentially expressed genes in the absence of replication

Pushpke J ThilakarathneGeert VerbekeKristof EngelenKathleen MarchalDan Lin

A2 Journal Article in INTERNATIONAL JOURNAL OF BIOINFORMATICS RESEARCH AND APPLICATIONS

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

Lieven VerbekeAC FierroJimmy Van den EyndenPiet DemeesterJan FostierKathleen Marchal

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Pablo MeyerGeoffrey SiwoDanny ZeeviEilon SharonRaquel NorelEran SegalGustavo Stolovitzkythe DREAM6 consortiumYvan SaeysKathleen Marchal

A1 Journal Article in GENOME RESEARCH

MLVA as a tool for public health surveillance of human Salmonella Typhimurium : prospective study in Belgium and evaluation of MLVA loci stability

Véronique WuytsWesley MattheusGuillaume De Laminne de BexChrista WildemauweNancy HC RoosensKathleen MarchalSigrid CJ De KeersmaeckerSophie Bertrand

A1 Journal Article in PLOS ONE

Omics derived networks in bacteria

Aminael Sánchez-RodríguezLore ClootsKathleen Marchal

A1 Journal Article in CURRENT BIOINFORMATICS

PheNetic: network-based interpretation of unstructured gene lists in E. coli

Dries De MaeyerJoris RenkensLore ClootsLuc De RaedtKathleen Marchal

A1 Journal Article in MOLECULAR BIOSYSTEMS

Synthetic biology and microdevices : a powerful combination

Lyn VenkenKathleen MarchalJos Vanderleyden

A1 Journal Article in ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS

2012

A combined approach to study the protein glycosylation potential of Lactobacillus rhamnosus GG (LGG)

Hanne LP TytgatAminael Sánchez-RodríguezGeert SchoofsTine LA VerhoevenSigrid CJ De KeersmaeckerKathleen MarchalJos VanderleydenSarah Lebeer

A4 Journal Article in COMMUNICATIONS IN AGRICULTURAL AND APPLIED BIOLOGICAL SCIENCES

An ASP-based simulation method for finding all synchronous and asynchronous attractors in genetic regulatory networks

Gustavo Adolfo Torres TorresKathleen MarchalYves Van de PeerMartine De Cock

Association of the vascular endothelial growth factor gene polymorphisms (-460C/T,+405G/C and+936T/C) with endometriosis: a meta-analysis

Shaohua XuWei WuHong SunJing LuBeilei YuanYankai XiaBart De MoorKathleen MarchalXinru WangPeizhen Xu et al.

A1 Journal Article in ANNALS OF HUMAN GENETICS

Directed module detection in a large-scale expression compendium

Qiang FuKaren LemmensAminael Sánchez-RodríguezInge M ThijsPieter MeysmanHong SunAna Carolina FierroKristof EngelenKathleen Marchal

Bookchapter in Bacterial molecular networks : methods and protocols

DNA structural properties in the classification of genomic transcription

Pieter MeysmanKathleen MarchalKristof Engelen

A2 Journal Article in BIOINFORMATICS AND BIOLOGY INSIGHTS

Exploring the complementarity of eQTL mapping methods (poster)

Lieven VerbekeKathleen MarchalJan Fostier

Follicle stimulating hormone receptor G-29A, 919A > G, 2039A > G polymorphism and the risk of male infertility: A meta-analysis

Wei WuHongquan CaiHong SunJing LuDan ZhaoYufeng QinXiumei HanXiaobing NiuChuncheng LuYankai Xia et al.

A1 Journal Article in GENE

Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology

Karin VoordeckersDries De MaeyerElisa van der ZandeMarcelo D VincesWim MeertLore ClootsOwen RyanKathleen MarchalKevin J Verstrepen

A1 Journal Article in MOLECULAR MICROBIOLOGY

Mining local staircase patterns in noisy data

Thanh Le VanAna Carolina FierroTias GunsMatthijs Van LeeuwenSiegfried NijssenLuc De RaedtKathleen Marchal

MotifSuite: workflow for probabilistic motif detection and assessment

Marleen ClaeysValerie StormsHong SunTom MichoelKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Nucleosomes affect local transformation efficiency

Elham AslankoohiKarin VoordeckersHong SunAminael Sanchez-RodriguezElisa van der ZandeKathleen MarchalKevin J Verstrepen

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Predicting long term behavior of genetic regulatory networks with answer set programming

Gustavo Adolfo Torres TorresKathleen MarchalYves Van de PeerMartine De Cock

Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection

Hong SunTias GunsAna Carolina FierroLieven ThorrezSiegfried NijssenKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2011

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

Ines ThieleDaniel R HydukeBenjamin SteebGuy FankamDouglas K AllenSusanna BazzaniPep CharusantiFeng-Chi ChenRonan MT FlemingChao A Hsiung et al.

A1 Journal Article in BMC SYSTEMS BIOLOGY

A comparative transcriptome analysis of Rhizobium etli bacteroids: specific gene expression during symbiotic nongrowth

Maarten VercruysseMaarten FauvartSerge BeullensKristien BraekenLore ClootsKristof EngelenKathleen MarchalJan Michiels

A1 Journal Article in MOLECULAR PLANT-MICROBE INTERACTIONS

An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference

Guillermin Aguero-ChapinAminael Sánchez-RodríguezPedro I Hidalgo-YanesYunierkis Pérez-CastilloReinaldo Molina-RuizKathleen MarchalVitor VasconcelosAgostinho Antunes

A1 Journal Article in PLOS ONE

An ensemble biclustering approach for querying gene expression compendia with experimental lists

Riet De SmetKathleen Marchal

A1 Journal Article in BIOINFORMATICS

COLOMBOS : access port for cross-platform bacterial expression compendia

Kristof EngelenQiang FuPieter MeysmanAminael Sánchez-RodríguezRiet De SmetKaren LemmensAna Carolina FierroKathleen Marchal

A1 Journal Article in PLOS ONE

COMODO : an adaptive coclustering strategy to identify conserved coexpression modules between organisms

Peyman ZarrinehAna C FierroAminael Sánchez-RodríguezBart De MoorKristof EngelenKathleen Marchal

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Genome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil

Maarten FauvartAminael Sánchez-RodríguezSerge BeullensKathleen MarchalJan Michiels

A1 Journal Article in JOURNAL OF BACTERIOLOGY

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

Lore ClootsKathleen Marchal

A1 Journal Article in CURRENT OPINION IN MICROBIOLOGY

Query-based biclustering of gene expression data using Probabilistic Relational Models

Hui ZhaoLore ClootsTim Van den BulckeYan WuRiet De SmetValerie StormsPieter MeysmanKristof EngelenKathleen Marchal

A1 Journal Article in BMC BIOINFORMATICS

Stress response regulators identified through genome-wide transcriptome analysis of the (p) ppGpp-dependent response in Rhizobium etli

Maarten VercruysseMaarten FauvartAnn JansSerge BeullensKristien BraekenLore ClootsKristof EngelenKathleen MarchalJan Michiels

A1 Journal Article in GENOME BIOLOGY

Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response

Sandra Van PuyveldeLore ClootsKristof EngelenFrederik DasKathleen MarchalJos VanderleydenStijn Spaepen

A1 Journal Article in MICROBIAL ECOLOGY

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli

Pieter MeysmanHai Dang ThanhKris LaukensRiet De SmetYan WuKathleen MarchalKristof Engelen

A1 Journal Article in NUCLEIC ACIDS RESEARCH

2010

Advantages and limitations of current network inference methods

Riet De SmetKathleen Marchal

A1 Journal Article in NATURE REVIEWS MICROBIOLOGY

Alternative experimental design with an applied normalization scheme can improve statistical power in 2D-DIGE experiments

Kristof EngelenAlejandro SifrimBabs Van de PlasKris LaukensLutgarde ArckensKathleen Marchal

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

An ensemble method for querying gene expression compendia with experimental lists

Riet De SmetKathleen Marchal

Cis-regulatory module detection using constraint programming

Tias GunsHong SunKathleen MarchalSiegfried Nijssen

Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array

Maarten VercruysseMaarten FauvartLore ClootsKristof EngelenInge M ThijsKathleen MarchalJan Michiels

A1 Journal Article in BMC GENOMICS

Integration of 'omics' data: does it lead to new insights into host-microbe interactions?

Gwendoline KintCarolina FierroKathleen MarchalJos VanderleydenSigrid CJ De Keersmaecker

A1 Journal Article in FUTURE MICROBIOLOGY

Module network inference from a cancer gene expression data set identifies microRNA regulated modules

Eric BonnetMarianthi TatariAnagha Madhusudan JoshiTom MichoelKathleen MarchalGeert BerxYves Van de Peer

A1 Journal Article in PLOS ONE

Regulation of cystathionine beta synthase by 1α,25-dihydroxyvitamin D₃

Carsten KriebitzschLieve VerlindenGuy EelenKathleen MarchalBart De MoorIne BeullensMark Van CampRoger BouillonAnnemieke Verstuyf

Regulation of semaphorin 3 family members and their receptors by 1α,25-dihydroxyvitamin D₃

Lieve VerlindenCarsten KriebitzschGuy EelenIne BeullensMark Van CampBiauw Keng TanBart De MoorKathleen MarchalRoger BouillonAnnemieke Verstuyf

Systems microbiology : gaining insights in transcriptional networks

Riet De SmetKaren LemmensAna Carolina FierroKathleen Marchal

Bookchapter in Infectious disease informatics

The AI-2-dependent regulator LsrR has a limited regulon in Salmonella Typhimurium

Inge M ThijsHui ZhaoAmi De WeerdtKristof EngelenDavid De CosterGeert SchoofsMichael McClellandJos VanderleydenKathleen MarchalSigrid CD De Keersmaecker

A1 Journal Article in CELL RESEARCH

The effect of orthology and coregulation on detecting regulatory motifs

Valerie StormsMarleen ClaeysAmiael SanchezBart De MoorAnnemieke VerstuyfKathleen Marchal

A1 Journal Article in PLOS ONE

The potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

Animael Sanchez-RodriguezCindy MartensKristof EngelenYves Van de PeerKathleen Marchal

A1 Journal Article in BMC EVOLUTIONARY BIOLOGY

The small regulatory RNA molecule MicA is involved in Salmonella enterica serovar Typhimurium biofilm formation

Gwendoline KintDavid De CosterKathleen MarchalJos VanderleydenSigrid CJ De Keersmaecker

A1 Journal Article in BMC MICROBIOLOGY

2009

A nonlinear mixed-effects model for estimating calibration intervals for unknown concentrations in two-color microarray data with spike-ins

Pushpike J ThilakarathneGeert VerbekeKristof EngelenKathleen Marchal

A1 Journal Article in STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Tom MichoelRiet De SmetAnagha Madhusudan JoshiYves Van de PeerKathleen Marchal

A1 Journal Article in BMC Systems Biology

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

Karen LemmensTijl De BieThomas DhollanderSigrid CJ De KeersmaeckerInge M ThijsGeert SchoofsAmi De WeerdtBart De MoorJos VanderleydenJulio Collado-Vides et al.

A1 Journal Article in GENOME BIOLOGY

Inferring the transcriptional network of Bacillus subtilis

Abeer FaddaAna Carolina FierroKaren LemmensPieter MonsieursKristof EngelenKathleen Marchal

A1 Journal Article in MOLECULAR BIOSYSTEMS

Layout and post-processing of transcriptional modules

Hong SunTim Van den BulckeBart De MoorKaren LemmensKristof EngelenKathleen Marchal

Microarray analysis of MCF-7 breast cancer cells treated with 1,25-dihydroxyvitamin D-3 or a 17-methyl-D-ring analog

Els VanoirbeekGuy EelenLieve VerlindenKathleen MarchalKristof EngelenBart De MoorIne BeullensSuzanne MarcelisPierre De ClercqRoger Bouillon et al.

A1 Journal Article in ANTICANCER RESEARCH

Module networks revisited: computational assessment and prioritization of model predictions

Anagha Madhusudan JoshiRiet De SmetKathleen MarchalYves Van de PeerTom Michoel

A1 Journal Article in BIOINFORMATICS

ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules

Hong SunTijl De BieValerie StormsQiang FuThomas DhollanderKaren LemmensAnnemieke VerstuyfBart De MoorKathleen Marchal

A1 Journal Article in BMC BIOINFORMATICS

Reverse-engineering transcriptional modules from gene expression data

Tom MichoelRiet De SmetAnagha Madhusudan JoshiKathleen MarchalYves Van de Peer

A1 Journal Article in Annals of the New York Academy of Sciences

The condition-dependent transcriptional network in Escherichia coli

Karen LemmensTijl De BieThomas DhollanderPieter MonsieursBart De MoorJulio Collado-VidesKristof EngelenKathleen Marchal

A1 Journal Article in Annals of the New York Academy of Sciences

The use of mixed models to identify differentially expressed genes when a single replicate per biological condition is present

PJ ThilakarathneG VerbekeK EngelenKathleen Marchal

ViTraM: visualization of transcriptional modules

Hong SunKaren LemmensTim Van den BulckeKristof EngelenBart De MoorKathleen Marchal

A1 Journal Article in BIOINFORMATICS

2008

Bacterial networking

Kathleen MarchalSigrid CJ De Keersmaecker

Brominated furanones inhibit biofilm formation by Salmonella enterica serovar Typhimurium

Joost CA JanssensHans SteenackersStijn RobijnsEdith GellensJeremy LevinHui ZhaoKim HermansDavid De CosterTine L VerhoevenKathleen Marchal et al.

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluation of time profile reconstruction from complex two-color microarray designs

Ana C FierroRaphael ThuretKristof EngelenGilles BernotKathleen MarchalNicolas Pollet

A1 Journal Article in BMC BIOINFORMATICS

Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data

Koenraad Van LeemputTim Van den BulckeThomas DhollanderBart De MoorKathleen MarchalPiet van Remortel

A1 Journal Article in ARTIFICIAL LIFE

Expression of the BRCA1-interacting protein Brip1/BACH1/FANCJ is driven by E2F and correlates with human breast cancer malignancy

G EelenI Vanden BemptL VerlindenM DrijkoningenA SmeetsP NevenMR ChristiaensKathleen MarchalR BouillonA Verstuyf

A1 Journal Article in ONCOGENE

Genome-wide expression analysis reveals TORC1-dependent and -independent functions of Sch9

Bart SmetsPepijn De SnijderKristof EngelenEva JoossensRuben GhillebertKarin ThevissenKathleen MarchalJoris Winderickx

A1 Journal Article in FEMS YEAST RESEARCH

Meta analysis of gene expression data within and across species

Ana Carolina FierroFilip VandenbusscheKristof EngelenYves Van de PeerKathleen Marchal

A1 Journal Article in CURRENT GENOMICS

Microarray analysis of MCF-7 breast cancer cells treated with 1,25-(OH)(2)D-3 or the analog WY1112

Els VanoirbeekGuy EelenIne BeullensMark Van CampKristof EngelenKathleen MarchalPierre De ClercqM VandewalleRoger BouillonAnnemieke Verstuyf

Using ribosomal protein genes as reference : a tale of caution

Lieven ThorrezKatrijn Van DeunLéon-Charles TrancheventLeentje Van LommelKristof EngelenKathleen MarchalYves MoreauIven Van MechelenFrans Schuit

A1 Journal Article in PLOS ONE

2007

1α,25-Dihydroxyvitamin D₃-induced down-regulation of the checkpoint proteins, Chk1 and Claspin, is mediated by the pocket proteins p107 and p130

Lieve VerlindenGuy EelenRuth Van HellemontKristof EngelenIne BeullensMark Van CampKathleen MarchalChantal MathieuRoger BouillonAnnemieke Verstuyf

A1 Journal Article in JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data

Hui ZhaoKristof EngelenBart De MoorKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Combining omics data to unravel the regulatory network controlling Salmonella invasion of epithelial cells

Inge M ThijsSigrid CJ De KeersmaeckerA FaddaKristof EngelenH ZhaoM McClellandKathleen MarchalJos Vanderleyden

A4 Journal Article in COMMUNICATIONS IN AGRICULTURAL AND APPLIED BIOLOGICAL SCIENCES

Delineation of the Salmonella enterica serovar Typhimurium HilA regulon through genome-wide location and transcript analysis

Inge MV ThijsSigrid CJ De KeersmaeckerAbeer A FaddaKristof EngelenHui ZhaoMichael McClellandKathleen MarchalJos Vanderleyden

A1 Journal Article in JOURNAL OF BACTERIOLOGY

Divergence of regulatory sequences in duplicated fish genes

R Van HellemontTine BlommeYves Van de PeerKathleen Marchal

Bookchapter in Gene and protein evolution

Functional analysis of luxS in the probiotic strain Lactobacillus rhamnosus GG reveals a central metabolic role important for growth and biofilm formation

Sarah LebeerSigrid CJ De KeersmaeckerTine LA VerhoevenAbeer A FaddaKathleen MarchalJos Vanderleyden

A1 Journal Article in JOURNAL OF BACTERIOLOGY

Gene regulation bioinformatics of microarray data

Gert ThijsFrank De SmetYves MoreauKathleen MarchalBart De Moor

Bookchapter in Genomics and proteomics engineering in medicine and biology

GeneReg: integration of experimental data on the DNA transcription process

David PastorKaren LemmensÁlvaro Cortés-CalabuigKathleen MarchalMarc DeneckerBart De Moor

Joint mapping of genes and conditions via multidimensional unfolding analysis

Katrijn Van DeunKathleen MarchalWillem J HeiserKristof EngelenIven Van Mechelen

A1 Journal Article in BMC BIOINFORMATICS

Query-driven module discovery in microarray data

Thomas DhollanderQizheng ShengKaren LemmensBart De MoorKathleen MarchalYves Moreau

A1 Journal Article in BIOINFORMATICS

The E2F-regulated gene Chk1 is highly expressed in triple-negative estrogen receptor-/progesterone receptor-/HER-2-breast carcinomas

Lieve VerlindenIsabelle Vanden BemptGuy EelenMaria DrijkoningenIlse VerlindenKathleen MarchalChristiane De Wolf-PeetersMarie-Rose ChristiaensLuc MichielsRoger Bouillon et al.

A1 Journal Article in CANCER RESEARCH

Validating module network learning algorithms using simulated data

Tom MichoelSteven MaereEric BonnetAnagha Madhusudan JoshiYvan SaeysTim Van den BulckeKoenraad Van LeemputPiet Van RemortelMartin KuiperKathleen Marchal et al.

A1 Journal Article in BMC BIOINFORMATICS

2006

A calibration method for estimating absolute expression levels from microarray data

Kristof EngelenBart NaudtsBart De MoorKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Inferring transcriptional modules from ChIP-chip, motif and microarray data

Karen LemmensThomas DhollanderTijl De BiePieter MonsieursKristof EngelenBart SmetsJoris WinderickxBart De MoorKathleen Marchal

A1 Journal Article in GENOME BIOLOGY

Inferring transcriptional networks by mining 'omics' data

Tim Van den BulckeKaren LemmensYves Van de PeerKathleen Marchal

A1 Journal Article in CURRENT BIOINFORMATICS

Integration of omics data: how well does it work for bacteria?

Sigrid CJ De KeersmaeckerInge MV ThijsJos VanderleydenKathleen Marchal

A1 Journal Article in MOLECULAR MICROBIOLOGY

More robust detection of motifs in coexpressed genes by using phylogenetic information

Pieter MonsieursGert ThijsAbeer A FaddaSigrid CJ De KeersmaeckerJos VanderleydenBart De MoorKathleen Marchal

A1 Journal Article in BMC BIOINFORMATICS

Predicting the clinical behavior of ovarian cancer from gene expression profiles

F De SmetNL PochetK EngelenT Van GorpP Van HummelenKathleen MarchalF AmantD TimmermanBL De MoorIB Vergote

A1 Journal Article in INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid

Sigrid CJ De KeersmaeckerTine LA VerhoevenJos DesairKathleen MarchalJos VanderleydenIstván Nagy

A1 Journal Article in FEMS MICROBIOLOGY LETTERS

SynTReN : a generator of synthetic gene expression data for design and analysis of structure learning algorithms

Tim Van den BulckeKoenraad Van LeemputBart NaudtsPiet van RemortelHongwu MaAlain VerschorenBart De MoorKathleen Marchal

A1 Journal Article in BMC BIOINFORMATICS

The effect of a sertoli cell-selective knockout of the androgen receptor on testicular gene expression in prepubertal mice

Evi DenoletKarel De GendtJoke AllemeerschKristof EngelenKathleen MarchalPaul Van HummelenKaren AL TanRichard M SharpePhilippa TK SaundersJohannes V Swinnen et al.

A1 Journal Article in MOLECULAR ENDOCRINOLOGY

2005

A novel approach to identifying regulatory motifs in distantly related genomes

Ruth Van HellemontPieter MonsieursGert ThijsBart De MoorYves Van de PeerKathleen Marchal

A1 Journal Article in GENOME BIOLOGY

Advances in cluster analysis of microarray data

Qizheng ShengYves MoreauFrank De SmetKathleen MarchalBart De Moor

Bookchapter in Data analysis and visualization in genomics and proteomics

Characterization of the condensin component Cnap1 and protein kinase Melk as novel E2F target genes down-regulated by 1,25-dihydroxyvitamin D3

Lieve VerlindenGuy EelenIne BeullensMark Van CampPaul Van HummelenKristof EngelenRuth Van HellemontKathleen MarchalBart De MoorFloris Foijer et al.

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

Chemical synthesis of (S)-4,5-dihydroxy-2,3-pentanedione, a bacterial signal molecule precursor, and validation of its activity in Salmonella Typhimurium

Sigrid CJ De KeersmaeckerCsaba VarszegiNadja van BoxelLothar W HabelKristine MetzgerRuth DanielsKathleen MarchalDirk De VosJos Vanderleyden

A1 Journal Article in JOURNAL OF BIOLOGICAL CHEMISTRY

Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium

Pieter MonsieursSigrid CJ De KeersmaeckerWilliam W NavarreMartin W BaderFrank De SmetMichael McClellandFerric C FangBart De MoorJos VanderleydenKathleen Marchal

A1 Journal Article in JOURNAL OF MOLECULAR EVOLUTION

Discovering transcriptional modules from motif, chip-chip and microarray data

Tijl De BiePieter MonsieursKristof EngelenBart De MoorNello CristianiniKathleen Marchal

Identifying new drug targets to combat pathogenic infections: an interdisciplinary approach

Ilse SmetsAstrid CappuynsKristel BernaertsNadja Van BoxelKathleen SonckSigrid De KeersmaeckerPieter MonsieursTim Van den BulckeKathleen MarchalJanick Mathys et al.

M@CBETH: a microarray classification benchmarking tool

Nathalie LMM PochetFrizo AL JanssensFrank De SmetKathleen MarchalJohan AK SuykensBart LR De Moor

A1 Journal Article in BIOINFORMATICS

M@CBETH: optimizing clinical microarray classification

NLMM PochetFAL JanssensF De SmetKathleen MarchalIB VergoteJAK SuykensBLR De Moor

Microarray analysis and motif detection reveal new targets of the Salmonella enterica serovar Typhimurium HilA regulatory protein, including hilA itself

Sigrid CJ De KeersmaeckerKathleen MarchalTine LA VerhoevenKristof EngelenJos VanderleydenCorrella S Detweiler

A1 Journal Article in JOURNAL OF BACTERIOLOGY

PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability

Johnny RoosenKristof EngelenKathleen MarchalJanick MathysGerard GriffioenElisabetta CameroniJohan M TheveleinClaudio De VirgilioBart De MoorJoris Winderickx

A1 Journal Article in MOLECULAR MICROBIOLOGY

2004

Annotation of the pRhico plasmid of Azospirillum brasilense reveals its role in determining the outer surface composition

Els VanbleuKathleen MarchalMark LambrechtJanick MathysJos Vanderleyden

A1 Journal Article in FEMS MICROBIOLOGY LETTERS

Computational biology and toxicogenomics

Kathleen MarchalFrank De SmetKristof EngelenBart De Moor

Bookchapter in Predictive toxicology

Differential regulation of the insulin-like growth factor II mRNA-binding protein genes by architectural transcription factor HMGA2

Jan R BrantsTorik AY AyoubiKiran ChadaKathleen MarchalWim JM Van de VenMarleen MR Petit

A1 Journal Article in FEBS LETTERS

Genetic and physical map of the pLAFR1 vector

E VanbleuKathleen MarchalJ Vanderleyden

A1 Journal Article in DNA SEQUENCE

In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection

Kathleen MarchalSigrid De KeersmaeckerPieter MonsieursNadja van BoxelKaren LemmensGert ThijsJos VanderleydenBart De Moor

A1 Journal Article in GENOME BIOLOGY

Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters

G DirixP MonsieursB DombrechtR DanielsKathleen MarchalJ VanderleydenJ Michiels

A1 Journal Article in PEPTIDES

Screening genomes of Gram-positive bacteria for double-glycine-motif-containing peptides

G DirixP MonsieursKathleen MarchalJ VanderleydenJ Michiels

Editorial material

The effects of 1α,25-dihydroxyvitamin D₃ on the expression of DNA replication genes

Guy EelenLieve VerlindenMark van CampPaul van HummelenKathleen MarchalBart de MoorChantal MathieuGeert CarmelietRoger BouillonAnnemieke Verstuyf

A1 Journal Article in JOURNAL OF BONE AND MINERAL RESEARCH

2003

Bioinformatics: organisms from Venus, technology from Jupiter, algorithms from Mars

Bart De MoorKathleen MarchalJanick MathysYves Moreau

A1 Journal Article in EUROPEAN JOURNAL OF CONTROL

Computational approaches to identify promoters and cis-regulatory elements in plant genomes

Stephane RombautsKobe FlorquinMagali LescotKathleen MarchalPierre RouzéYves Van de Peer

A1 Journal Article in PLANT PHYSIOLOGY

Genome-specific higher-order background models to improve motif detection

Kathleen MarchalGert ThijsSigrid De KeersmaeckerPieter MonsieursBart De MoorJos Vanderleyden

A1 Journal Article in TRENDS IN MICROBIOLOGY

INCLUSive : a web portal and service registry for microarray and regulatory sequence analysis

Bert CoessensGert ThijsStein AertsKathleen MarchalFrank De SmetKristof EngelenPatrick GlenissonYves MoreauJanick MathysBart De Moor

A1 Journal Article in NUCLEIC ACIDS RESEARCH

MARAN: normalizing micro-array data

Kristof EngelenBert CoessensKathleen MarchalBart De Moor

A1 Journal Article in BIOINFORMATICS

2002

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes

Gert ThijsKathleen MarchalMagali LescotStephane RombautsBart De MoorPierre RouzéYves Moreau

A1 Journal Article in JOURNAL OF COMPUTATIONAL BIOLOGY

Adaptive quality-based clustering of gene expression profiles

Frank De SmetJanick MathysKathleen MarchalGert ThijsBart De MoorYves Moreau

A1 Journal Article in BIOINFORMATICS

Comparison of different methodologies to identify differentially expressed genes in two-sample cDNA microarrays

Kathleen MarchalKristof EngelenJos De BrabanterStein AertBart De MoorTurik AyoubiPaul Van Hummelen

A1 Journal Article in JOURNAL OF BIOLOGICAL SYSTEMS

Functional bioinformatics of microarray data: from expression to regulation

Yves MoreauFrank De SmetGert ThijsKathleen MarchalBart De Moor

A1 Journal Article in PROCEEDINGS OF THE IEEE

INCLUSive: INtegrated Clustering, Upstream of sequence retrieval and motif Sampling

Gert ThijsYves MoreauFrank De SmetJanick MathysMagali LescotStephane RombautsPierre RouzéBart De MoorKathleen Marchal

A1 Journal Article in BIOINFORMATICS

Integrating quality-based clustering of microarray data with Gibbs sampling for the discovery of regulatory motifs

Yves MoreauGert ThijsKathleen MarchalFrank De SmetJanick MathysMagali LescotStephane RombautsPierre RouzéBart De Moor

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Magali LescotPatrice DéhaisGert ThijsKathleen MarchalYves MoreauYves Van de PeerPierre RouzéStephane Rombauts

A1 Journal Article in NUCLEIC ACIDS RESEARCH

Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales

Bruno DombrechtKathleen MarchalJos VanderleydenJan Michiels

A1 Journal Article in GENOME BIOLOGY

Sensitivity function-based model reduction: a bacterial gene expression case study

Ilse SmetsKristel BernaertsJun SunKathleen MarchalJos VanderleydenJan Van Impe

A1 Journal Article in BIOTECHNOLOGY AND BIOENGINEERING

The PlantCARE database and tools for in silico search of plant cis-acting regulatory elements

Stephane RombautsMagali LescotGert ThijsKathleen MarchalYves MoreauPatrice DéhaisYves Van de PeerPierre Rouzé

2001

A Gibbs sampling method to detect over-represented motifs in upstream regions of co-expressed genes

Gert ThijsKathleen MarchalYves Moreau

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling

Gert ThijsMagali LescotKathleen MarchalStephane RombautsBart De MoorPierre RouzéYves Moreau

A1 Journal Article in BIOINFORMATICS

In silico search of plant cis-acting regulatory elements

Magali LescotStephane RombautsGert ThijsKathleen MarchalBart De MoorYves MoreauPierre Rouzé

Quantitative analysis of bacterial gene expression by using the gusA reporter gene system

Jun SunIlse SmetsKristel BernaertsJan Van ImpeJos VanderleydenKathleen Marchal

A1 Journal Article in APPLIED AND ENVIRONMENTAL MICROBIOLOGY

2000

Characterization of an Azospirillum brasilense Tn5 mutant with enhanced N₂ fixation: the effect of ORF280 on nifH expression

LF ReversLM PassagliaKathleen MarchalJ FrazzonCG BlahaJ VanderleydenIS Schrank

A1 Journal Article in FEMS MICROBIOLOGY LETTERS

Detection of cis-acting regulatory elements in plants : a GIBBS sampling approach

Gert ThijsStephane RombautsMagali LescotKathleen MarchalBart De MoorYves MoreauPierre Rouzé

The 'oxygen paradox' of dinitrogen-fixing bacteria

Kathleen MarchalJos Vanderleyden

A1 Journal Article in BIOLOGY AND FERTILITY OF SOILS

The cytochrome cbb3 (cytochrome C) terminal oxidase of A. brasilense Sp7

Kathleen MarchalJ SunV KeijersH HaakerJ Vanderleyden

1998

A cytochrome cbb3 (cytochrome c) terminal oxidase in Azospirillum brasilense Sp7 supports microaerobic growth

Kathleen MarchalJun SunVeerle KeijersHuub HaakerJos Vanderleyden

A1 Journal Article in JOURNAL OF BACTERIOLOGY

1997

Evidence for a cbb 3-type cytochrome C terminal oxidase in Azospirillum brasilense Sp7

Kathleen MarchalV KeijersH HaakerJ Vanderleyden