Kathleen Marchal

发表

Cis-regulatory module detection using constraint programming

Kathleen Marchal, Hong Sun, Tias Guns, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2002, Bioinform..

The Use of Mixed Models to Identify Differentially Expressed Genes when a Single Replicate per Biological Condition is Present

Kathleen Marchal, Geert Verbeke, Pushpike Jayantha Thilakarathne, 2009, BIOCOMP.

Functional bioinformatics of microarray data: from expression to regulation

Kathleen Marchal, Yves Moreau, Gert Thijs, 2002, Proc. IEEE.

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

Kathleen Marchal, Riet De Smet, K. Marchal, 2011, Bioinform..

A calibration method for estimating absolute expression levels from microarray data

Kathleen Marchal, Bart De Moor, Bart Naudts, 2006, Bioinform..

Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data

Kathleen Marchal, Bart De Moor, Koenraad Van Leemput, 2008, Artificial Life.

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

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2001, RECOMB.

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

Kathleen Marchal, Kristof Engelen, Pieter Meysman, 2014, Bioinform..

The Condition‐Dependent Transcriptional Network in Escherichia coli

Kathleen Marchal, Julio Collado-Vides, Kristof Engelen, 2009, Annals of the New York Academy of Sciences.

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

Kathleen Marchal, Bart De Moor, Yves Moreau, 2003, Nucleic Acids Res..

Benchmarking gene network inference algorithms using synthetic gene expression data

Kathleen Marchal, Koenraad Van Leemput, Bart De Moor, 2006 .

Computational reasoning on high-throughput omics results using interaction networks

Luc De Raedt, Dries De Maeyer, Kathleen Marchal, 2015 .

A validation strategy for ChIP-chip analysis using a genome-wide expression compendium

Kathleen Marchal, Riet De Smet, Hong Sun, 2010 .

ViTraM: visualization of transcriptional modules.

Kathleen Marchal, Hong Sun, Bart De Moor, 2009 .

Selecting and generating superior yeasts for Baking industry

Dries De Maeyer, Kathleen Marchal, Bo Zhu, 2014 .

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

Luc De Raedt, Dries De Maeyer, Kathleen Marchal, 2016, Bioinform..

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

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2002 .

Advances in Cluster Analysis of Microarray Data

Kathleen Marchal, Bart De Moor, Yves Moreau, 2005, Data Analysis and Visualization in Genomics and Proteomics.

Identifying differentially expressed genes in the absence of replication

Kathleen Marchal, Geert Verbeke, Dan Lin, 2013, Int. J. Bioinform. Res. Appl..

Reverse‐Engineering Transcriptional Modules from Gene Expression Data

Kathleen Marchal, Tom Michoel, Riet De Smet, 2009, Annals of the New York Academy of Sciences.

Interaction networks to analyze gene lists from omics data

Luc De Raedt, Dries De Maeyer, Kathleen Marchal, 2013 .

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

Kathleen Marchal, Martine De Cock, Steven Schockaert, 2018, Fuzzy Sets Syst..

Module networks revisited: computational assessment and prioritization of model predictions

Kathleen Marchal, Yves Van de Peer, Anagha Joshi, 2009, Bioinform..

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

Kathleen Marchal, Hong Sun, Qiang Fu, 2009, BMC Bioinformatics.

PheNetic: network-based interpretation of molecular profiling data

Luc De Raedt, Dries De Maeyer, Kathleen Marchal, 2015, Nucleic Acids Res..

Exploring the complementarity of eQTL mapping methods (poster)

Kathleen Marchal, Jan Fostier, Lieven Verbeke, 2012, ISMB 2012.

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

Kathleen Marchal, Stephane Rombauts, Yves Van de Peer, 2002, Nucleic Acids Res..

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

Kathleen Marchal, Martine De Cock, Yves Van de Peer, 2014, Bioinform..

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

Lore Cloots, Kathleen Marchal, Piet Demeester, 2013, Bioinform..

Synthetic Biology and Microdevices: A Powerful Combination

Kathleen Marchal, Jozef Vanderleyden, Lyn Venken, 2013, JETC.

A query-based framework to validate ChIP-chip targets

Kathleen Marchal, Riet De Smet, Hong Sun, 2009 .

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

Kathleen Marchal, Gilles Bernot, Kristof Engelen, 2008, BMC Bioinformatics.

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

Kathleen Marchal, Lieven P. C. Verbeke, Ana Carolina Fierro, 2015, BMC Bioinformatics.

Gene Regulation Bioinformatics of Microarray Data

Kathleen Marchal, Bart De Moor, Gert Thijs, 2007 .

CHALLENGES OF SYSTEMS BIOLOGY: COMMUNITY EFFORTS TO HARNESS BIOLOGICAL COMPLEXITY

Kathleen Marchal, Yves Van de Peer, Tom Michoel, 2009, CMSB 2009.

M@CBETH: optimizing clinical microarray classification

Kathleen Marchal, Johan A. K. Suykens, Bart De Moor, 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins

Kathleen Marchal, Geert Verbeke, Kristof Engelen, 2009, Statistical applications in genetics and molecular biology.

Evaluation of existing motif detection tools on their ability to retrieve regulatory motifs in sequence data

Kathleen Marchal, Bart De Moor, Valerie Storms, 2009 .

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

Kathleen Marchal, Yves Van de Peer, Anagha Joshi, 2009, BMC Systems Biology.

"Omics" Result Interpretation Using Interaction Networks

Luc De Raedt, Kathleen Marchal, Bram Weytjens, 2013 .

An ensemble method for querying gene expression compendia with experimental lists

Kathleen Marchal, Riet De Smet, K. Marchal, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Conditional Random Fields Feature Subset Selection Based on Genetic Algorithms for Phosphorylation Site Prediction

Kathleen Marchal, Thanh Hai Dang, Kristof Engelen, 2009, 2009 International Conference on Knowledge and Systems Engineering.

Validation of ChIP-chip targets by query-driven biclustering

Kathleen Marchal, Kristof Engelen, Riet De Smet, 2009 .

Cross-platform expression compendia

Kathleen Marchal, Qiang Fu, Kristof Engelen, 2008 .

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

Kathleen Marchal, Martine De Cock, Yves Van de Peer, 2012 .

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

Kathleen Marchal, Jorge Duitama, Sergio Pulido-Tamayo, 2016, Nucleic Acids Res..

Layout and Post-Processing of Transcriptional Modules

Kathleen Marchal, Hong Sun, Bart De Moor, 2009, 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing.

MotifSuite: workflow for probabilistic motif detection and assessment

Kathleen Marchal, Hong Sun, Tom Michoel, 2012, Bioinform..

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

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2001, Bioinform..

PheNetic: "Omics" Interpretation Using Interaction Networks

Luc De Raedt, Dries De Maeyer, Kathleen Marchal, 2014 .

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

Lore Cloots, Kathleen Marchal, Hui Zhao, 2011, BMC Bioinformatics.

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

Kathleen Marchal, Bart De Moor, Gert Thijs, 2006, BMC Bioinformatics.

A generator of biologically plausible synthetic gene expression data for design and analysis of structure learning algorithms

Kathleen Marchal, Bart De Moor, Koenraad Van Leemput, 2005 .

Query-driven module discovery in microarray data

Kathleen Marchal, Bart De Moor, Yves Moreau, 2007, Bioinform..

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

Kathleen Marchal, Hui Zhao, Bart De Moor, 2007, Bioinform..

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

Kathleen Marchal, Thanh Hai Dang, Yan Wu, 2010, Nucleic Acids Res..

M@cbeth: a Microarray Classification Benchmarking Tool

Kathleen Marchal, Johan A. K. Suykens, Bart De Moor, 2005 .

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

Kathleen Marchal, Ronan M. T. Fleming, Neil Swainston, 2011, BMC Systems Biology.

Proximity-based cis-regulatory module detection using constraint programming for itemset mining

Luc De Raedt, Kathleen Marchal, Hong Sun, 2010 .

Running head: A Calibration Method for Microarray Data

Kathleen Marchal, Bart De Moor, Bart De Moor, 2006 .

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

Kathleen Marchal, Piet Demeester, Jan Fostier, 2015, PloS one.

Mechanistic interpretation of gene lists using interaction networks

Luc De Raedt, Dries De Maeyer, Kathleen Marchal, 2013 .

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

Kathleen Marchal, Assia Saltykova, Wesley Mattheus, 2019, Front. Microbiol..

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

Kathleen Marchal, Bart De Moor, Koenraad Van Leemput, 2006, BMC Bioinformatics.

ModuleVisualization: a tool for visualizing gene module network

Kathleen Marchal, Hong Sun, Bart De Moor, 2008 .

Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data

Nello Cristianini, Kathleen Marchal, Bart De Moor, 2004, Pacific Symposium on Biocomputing.

Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars

Kathleen Marchal, Bart De Moor, Yves Moreau, 2003, Eur. J. Control.

Cross-checking experimental results with publicly available gene expression data: a query-driven approach

Kathleen Marchal, Riet De Smet, Hong Sun, 2010 .

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

Kathleen Marchal, Qiang Fu, Luca Bianco, 2013, Nucleic Acids Res..

Adaptive quality-based clustering of gene expression profiles

Kathleen Marchal, Bart De Moor, Yves Moreau, 2002, Bioinform..

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

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2001, RECOMB.

Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments

Kathleen Marchal, Yves Van de Peer, Yao Yao, 2013, ECAL.

Mining Local Staircase Patterns in Noisy Data

Luc De Raedt, Kathleen Marchal, Tias Guns, 2012, 2012 IEEE 12th International Conference on Data Mining Workshops.

MARAN: Normalizing Micro-array Data

Kathleen Marchal, Bart De Moor, Kristof Engelen, 2003, Bioinform..

Quantitative analysis of a bacterial gene expression by using the gusA reporter system in a non-steady state continuous culture

Kathleen Marchal, Jan Van Impe, Bart De Moor, 2001, ISMB 2001.

Facilitating ChIP-chip-based reconstruction of regulatory networks by combining omics data

Kathleen Marchal, Kristof Engelen, Riet De Smet, 2008 .

Ranked Tiling

Luc De Raedt, Kathleen Marchal, Siegfried Nijssen, 2014, ECML/PKDD.

Validating module network learning algorithms using simulated data

Kathleen Marchal, Yvan Saeys, Koenraad Van Leemput, 2007, BMC Bioinformatics.

Joint mapping of genes and conditions via multidimensional unfolding analysis

Kathleen Marchal, Willem J. Heiser, Iven Van Mechelen, 2007, BMC Bioinformatics.

Identifying Common Structural DNA Properties in Transcription Factor Binding Site Sets of the LacI-GalR Family

Kathleen Marchal, Kristof Engelen, Pieter Meysman, 2013 .

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

Lore Cloots, Kathleen Marchal, K. Marchal, 2011, Current opinion in microbiology.

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

Kathleen Marchal, Jos Vanderleyden, Sigrid C J De Keersmaecker, 2010, Future microbiology.

Delineation of the Salmonella enterica Serovar Typhimurium HilA Regulon through Genome-Wide Location and Transcript Analysis

Kathleen Marchal, Hui Zhao, Kristof Engelen, 2007, Journal of bacteriology.

MARAN : normalizing microarray data

Kathleen Marchal, Bart De Moor, Kristof Engelen, 2003 .

Guidelines for Optimisation of a Multiplex Oligonucleotide Ligation-PCR for Characterisation of Microbial Pathogens in a Microsphere Suspension Array

Kathleen Marchal, Sophie Bertrand, Sigrid C J De Keersmaecker, 2015, BioMed research international.

Characterizing transcriptional modules in Escherichia coli inferred from gene expression data

Kathleen Marchal, Anagha Joshi, Tom Michoel, 2009 .

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

Kathleen Marchal, Aminael Sánchez-Rodríguez, Jorge Duitama, 2014, BMC Genomics.

Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes1

Kathleen Marchal, Stephane Rombauts, Magali Lescot, 2003, Plant Physiology.

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

Kathleen Marchal, Aminael Sánchez-Rodríguez, Jos Vanderleyden, 2014, BMC Genomics.

A novel approach to identifying regulatory motifs in distantly related genomes

Kathleen Marchal, Gert Thijs, Bart De Moor, 2005, Genome Biology.

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

Kathleen Marchal, Ilse Smets, Kristel Bernaerts, 2002, Biotechnology and bioengineering.

Cluster analysis of microarray data

Kathleen Marchal, Yves Moreau, Filip De Smet, 2004 .

Network-Based Analysis of eQTL Data to Prioritize Driver Mutations

Kathleen Marchal, Bram Weytjens, Luc De Raedt, 2016, Genome biology and evolution.

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

Kathleen Marchal, Jan Fostier, Aminael Sánchez-Rodríguez, 2015, Nucleic acids research.

COMPARISON OF DIFFERENT METHODOLOGIES TO IDENTIFY DIFFERENTIALLY EXPRESSED GENES IN TWO-SAMPLE cDNA MICROARRAYS

Kathleen Marchal, Bart De Moor, Stein Aerts, 2002 .

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

Kathleen Marchal, Jan Michiels, Jos Vanderleyden, 2002, Genome Biology.

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

Kathleen Marchal, Janick Mathys, Kristof Engelen, 2004, Molecular 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:-

Kathleen Marchal, Sophie Bertrand, Assia Saltykova, 2018, PLoS ONE.

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

Lore Cloots, Kathleen Marchal, Joris Renkens, 2013, Molecular bioSystems.

ProBic: identification of overlapping biclusters using Probabilistic Relational Models, applied to simulated gene expression data.

Kathleen Marchal, Hui Zhao, Bart De Moor, 2001 .

Pathway and network analysis of more than 2,500 whole cancer genomes

Kathleen Marchal, Alfonso Valencia, Icgc, 2018, bioRxiv.

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

Kathleen Marchal, Tias Guns, Siegfried Nijssen, 2012, Nucleic acids research.

Chemical Synthesis of (S)-4,5-Dihydroxy-2,3-pentanedione, a Bacterial Signal Molecule Precursor, and Validation of Its Activity in Salmonella typhimurium*

Kathleen Marchal, Jos Vanderleyden, Sigrid C J De Keersmaecker, 2005, Journal of Biological Chemistry.

Omics derived networks in bacteria

Lore Cloots, Kathleen Marchal, Aminael Sánchez-Rodríguez, 2013 .

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

Kathleen Marchal, Bram Weytjens, Sergio Pulido-Tamayo, 2016, Scientific Reports.

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

Kathleen Marchal, Annemieke Verstuyf, Guy Eelen, 2007, Cancer research.

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

Kathleen Marchal, Kristof Engelen, J. Winderickx, 2008, FEMS yeast research.

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

Kathleen Marchal, Bart De Moor, Stephane Rombauts, 2000 .

Comparison of the PhoPQ Regulon in Escherichia coli and Salmonella typhimurium

Kathleen Marchal, Bart De Moor, Frank De Smet, 2005, Journal of Molecular Evolution.

Brominated Furanones Inhibit Biofilm Formation by Salmonella enterica Serovar Typhimurium

Kathleen Marchal, Hui Zhao, Jeremy Levin, 2008, Applied and Environmental Microbiology.

Pacific Symposium on Biocomputing (PSB)

Nello Cristianini, Kathleen Marchal, Kristof Engelen, 2005 .

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

Kathleen Marchal, Kristof Engelen, Kris Laukens, 2010, Journal of proteome research.

DNA Structural Properties in the Classification of Genomic Transcription Regulation Elements

Kathleen Marchal, Kristof Engelen, Pieter Meysman, 2012, Bioinformatics and biology insights.

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

Kathleen Marchal, Jos Vanderleyden, Sigrid C J De Keersmaecker, 2006, Molecular microbiology.

Inferring Transcriptional Networks by Mining 'Omics' Data

Kathleen Marchal, Yves Van de Peer, Tim Van den Bulcke, 2006 .

Expression Divergence between Escherichia coli and Salmonella enterica serovar Typhimurium Reflects Their Lifestyles

Kathleen Marchal, Kristof Engelen, Pieter Meysman, 2013, Molecular biology and evolution.