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List of works by Kathleen Marchal

1-((2,4-Dichlorophenethyl)Amino)-3-Phenoxypropan-2-ol Kills Pseudomonas aeruginosa through Extensive Membrane Damage. ⬇️

scientific article published on 8 February 2018

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

scientific article published on 22 December 2006

A Comparative Transcriptome Analysis of Rhizobium etli Bacteroids: Specific Gene Expression During Symbiotic Nongrowth

article

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

scientific article

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

scientific article

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

scientific article published in December 2001

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

scientific article

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

scientific article published on 25 November 2019

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

scientific article

A novel approach to identifying regulatory motifs in distantly related genomes

scientific article published on 30 December 2005

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

scientific article

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

scientific article published on 15 July 2014

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

scientific article published on 6 November 2015

Adaptive quality-based clustering of gene expression profiles.

scientific article published in May 2002

Advantages and limitations of current network inference methods

scientific article

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

scientific article published in October 2010

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

scientific article

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

scientific article published on 18 May 2011

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

scientific article published in March 2004

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

scientific article

Associating expression and genomic data using co-occurrence measures

scientific article published on 09 May 2019

Association of the Vascular Endothelial Growth Factor Gene Polymorphisms (-460C/T, +405G/C and +936T/C) with Endometriosis: A Meta-Analysis

article

Brominated furanones inhibit biofilm formation by Salmonella enterica serovar Typhimurium

scientific article

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

scientific article

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

scientific article

COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia ⬇️

scientific article published on July 14, 2011

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

scientific article

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

scientific article

Characterization of an Azospirillum brasilense Tn5 mutant with enhanced N(2) fixation: the effect of ORF280 on nifH expression.

scientific article published on February 2000

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

scientific article

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

scientific article published on 24 March 2005

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

scientific article published on 09 March 2020

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

scientific article

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

scientific article published on 06 July 2020

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

scientific article published on 2 July 2015

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:.

scientific article

Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium

scientific article published in April 2005

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

scientific article

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

scientific article

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

scientific article published on 04 May 2007

Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept

scientific article published on 18 December 2019

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

scientific article published on 06 May 2019

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

scientific article

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

scientific article published on 28 April 2020

Dynamics of the Saccharomyces cerevisiae transcriptome during bread dough fermentation.

scientific article published on 20 September 2013

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

scientific article published on 16 April 2013

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

scientific article

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

scientific article published on 12 January 2017

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

scientific article

Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa ⬇️

scientific article

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

scientific article

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

scientific article

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

scientific article published on 20 February 2013

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

scientific article

FabR regulates Salmonella biofilm formation via its direct target FabB.

scientific article

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

scientific article published on 11 December 2016

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

article

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

scientific article published on 18 May 2015

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

scientific article published on 10 November 2006

Genetic and physical map of the pLAFR1 vector

scientific article

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

scientific article published on 22 April 2011

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

scientific article

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

scientific article published in February 2003

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

scientific article

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

scientific article published on 28 August 2008

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

scientific article published on 22 June 2021

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

scientific article

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

scientific article published on 01 July 2019

INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling

scientific article published in February 2002

Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology.

scientific article published on 13 September 2012

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

scientific article published on 01 December 2018

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

scientific article

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

scientific article

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

scientific article

Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia

scientific article (publication date: 27 January 2014)

Inferring the transcriptional network of Bacillus subtilis

scientific article published on 28 July 2009

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

scientific article

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

scientific article

Joint mapping of genes and conditions via multidimensional unfolding analysis

scientific article

M@CBETH: a microarray classification benchmarking tool

scientific article published on 12 May 2005

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

scientific article published on 8 January 2014

MARAN: normalizing micro-array data ⬇️

scientific article published on May 1, 2003

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

scientific article

Meta Analysis of Gene Expression Data within and Across Species

scientific article

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

scientific article

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

scientific article

Module networks revisited: computational assessment and prioritization of model predictions

scientific article

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

scientific article

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

scientific article published on 3 January 2018

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

scientific article published on 20 March 2006

MotifSuite: workflow for probabilistic motif detection and assessment

scientific article published on 15 May 2012

Network-Based Analysis of eQTL Data to Prioritize Driver Mutations

scientific article

Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations.

scientific article published on 28 August 2017

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

scientific article

Nucleosomes affect local transformation efficiency.

scientific article published on 16 August 2012

Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance.

scientific article published on 4 June 2015

Organellar carbon metabolism is coordinated with distinct developmental phases of secondary xylem

scientific article published on 25 March 2019

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

scientific article

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration

scientific article

Pathway and network analysis of more than 2500 whole cancer genomes

scientific article published on 05 February 2020

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.

scientific article published in September 2004

PheNetic: network-based interpretation of molecular profiling data

scientific article

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

scientific article

Photoreceptor-mediated bending towards UV-B in Arabidopsis.

scientific article published on 7 April 2014

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

scientific article

Predicting the clinical behavior of ovarian cancer from gene expression profiles.

scientific article published in January 2006

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

scientific article

Query-driven module discovery in microarray data.

scientific article

Reverse-engineering transcriptional modules from gene expression data

scientific article

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

scientific article

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

scientific article

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

scientific article published in October 2002

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

scientific article

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

scientific article published on 23 April 2015

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

scientific article

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

scientific article published in June 2006

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

scientific article

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

scientific article published on 13 July 2010

The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources

scientific article published on 30 October 2018

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

scientific article

The Effect of a Sertoli Cell-Selective Knockout of the Androgen Receptor on Testicular Gene Expression in Prepubertal Mice

article

The condition-dependent transcriptional network in Escherichia coli

scientific article published in March 2009

The effect of orthology and coregulation on detecting regulatory motifs

scientific article

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

scientific article published on January 2004

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

scientific article

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

scientific article

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

scientific article

Ultraviolet-B radiation stimulates downward leaf curling in Arabidopsis thaliana

scientific article published on 17 December 2014

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

scientific article published on 15 March 2012

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

scientific article published on 4 November 2010

Using ribosomal protein genes as reference: a tale of caution

scientific article (publication date: 2008)

Validating module network learning algorithms using simulated data

scientific article

ViTraM: visualization of transcriptional modules

scientific article published on 8 July 2009

Vitamin D3 Induces Tolerance in Human Dendritic Cells by Activation of Intracellular Metabolic Pathways

scientific article published on 4 February 2015

Whole Slide Imaging-Based Prediction of TP53 Mutations Identifies an Aggressive Disease Phenotype in Prostate Cancer

scientific article published in September 2023

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