A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes. - Gert Thijs; Kathleen Marchal; Magali Lescot; Stephane Rombauts; Bart De Moor; Pierre Rouzé; Yves Moreau (RECOMB, 2001)

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. - Gert Thijs; Magali Lescot; Kathleen Marchal; Stephane Rombauts; Bart De Moor; Pierre Rouzé; Yves Moreau (Bioinform., 2001)

Adaptive quality-based clustering of gene expression profiles. - Frank De Smet; Janick Mathys; Kathleen Marchal; Gert Thijs; Bart De Moor; Yves Moreau (Bioinform., 2002)

INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. - Gert Thijs; Yves Moreau; Frank De Smet; Janick Mathys; Magali Lescot; Stephane Rombauts; Pierre Rouzé; Bart De Moor; Kathleen Marchal (Bioinform., 2002)

A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes. - Gert Thijs; Kathleen Marchal; Magali Lescot; Stephane Rombauts; Bart De Moor; Pierre Rouzé; Yves Moreau (J. Comput. Biol., 2002)

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. - Magali Lescot; Patrice Déhais; Gert Thijs; Kathleen Marchal; Yves Moreau; Yves Van de Peer; Pierre Rouzé; Stephane Rombauts (Nucleic Acids Res., 2002)

Functional bioinformatics of microarray data: from expression to regulation. - Yves Moreau; Frank De Smet; Gert Thijs; Kathleen Marchal; Bart De Moor (Proc. IEEE, 2002)

MARAN: Normalizing Micro-array Data. - Kristof Engelen; Bert Coessens; Kathleen Marchal; Bart De Moor (Bioinform., 2003)

Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars. - Bart De Moor; Kathleen Marchal; Janick Mathys; Yves Moreau (Eur. J. Control, 2003)

INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis. - Bert Coessens; Gert Thijs; Stein Aerts; Kathleen Marchal; Frank De Smet; Kristof Engelen; Patrick Glenisson; Yves Moreau; Janick Mathys; Bart De Moor (Nucleic Acids Res., 2003)

Advances in Cluster Analysis of Microarray Data. - Qizheng Sheng; Yves Moreau; Frank De Smet; Kathleen Marchal; Bart De Moor (Data Analysis and Visualization in Genomics and Proteomics, 2005)

M@CBETH: Optimizing Clinical Microarray Classification. - Nathalie Pochet; Frizo A. L. Janssens; Frank De Smet; Kathleen Marchal; Ignace Vergote; Johan A. K. Suykens; Bart De Moor (CSB Workshops, 2005)

Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data. - Tijl De Bie; Patrick Monsieurs; Kristof Engelen; Bart De Moor; Nello Cristianini; Kathleen Marchal (Pacific Symposium on Biocomputing, 2005)

M@CBETH: a microarray classification benchmarking tool. - Nathalie Pochet; Frizo A. L. Janssens; Frank De Smet; Kathleen Marchal; Johan A. K. Suykens; Bart De Moor (Bioinform., 2005)

A calibration method for estimating absolute expression levels from microarray data. - Kristof Engelen; Bart Naudts; Bart De Moor; Kathleen Marchal (Bioinform., 2006)

SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. - Tim Van den Bulcke; Koen Van Leemput; Bart Naudts; Piet van Remortel; Hongwu Ma; Alain Verschoren; Bart De Moor; Kathleen Marchal (BMC Bioinform., 2006)

More robust detection of motifs in coexpressed genes by using phylogenetic information. - Pieter Monsieurs; Gert Thijs; Abeer A. Fadda; Sigrid C. J. De Keersmaecker; Jozef Vanderleyden; Bart De Moor; Kathleen Marchal (BMC Bioinform., 2006)

Query-driven module discovery in microarray data. - Thomas Dhollander; Qizheng Sheng; Karen Lemmens; Bart De Moor; Kathleen Marchal; Yves Moreau (Bioinform., 2007)

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data. - Hui Zhao; Kristof Engelen; Bart De Moor; Kathleen Marchal (Bioinform., 2007)

Joint mapping of genes and conditions via multidimensional unfolding analysis. - Katrijn Van Deun; Kathleen Marchal; Willem J. Heiser; Kristof Engelen; Iven Van Mechelen (BMC Bioinform., 2007)

Validating module network learning algorithms using simulated data. - Tom Michoel; Steven Maere; Eric Bonnet; Anagha Joshi; Yvan Saeys; Tim Van den Bulcke; Koenraad Van Leemput; Piet van Remortel; Martin Kuiper; Kathleen Marchal; Yves Van de Peer (BMC Bioinform., 2007)

Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data. - Koenraad Van Leemput; Tim Van den Bulcke; Thomas Dhollander; Bart De Moor; Kathleen Marchal; Piet van Remortel (Artif. Life, 2008)

Evaluation of time profile reconstruction from complex two-color microarray designs. - Ana Carolina Fierro; Raphael Thuret; Kristof Engelen; Gilles Bernot; Kathleen Marchal; Nicolas Pollet (BMC Bioinform., 2008)

The Use of Mixed Models to Identify Differentially Expressed Genes when a Single Replicate per Biological Condition is Present. - Pushpike Jayantha Thilakarathne; Geert Verbeke; Kristof Engelen; Kathleen Marchal (BIOCOMP, 2009)

Layout and Post-Processing of Transcriptional Modules. - Hong Sun 002; Tim Van den Bulcke; Bart De Moor; Karen Lemmens; Kristof Engelen; Kathleen Marchal (IJCBS, 2009)

Module networks revisited: computational assessment and prioritization of model predictions. - Anagha Joshi; Riet De Smet; Kathleen Marchal; Yves Van de Peer; Tom Michoel (Bioinform., 2009)

ViTraM: visualization of transcriptional modules. - Hong Sun 002; Karen Lemmens; Tim Van den Bulcke; Kristof Engelen; Bart De Moor; Kathleen Marchal (Bioinform., 2009)

ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. - Hong Sun 002; Tijl De Bie; Valerie Storms; Qiang Fu 009; Thomas Dhollander; Karen Lemmens; Annemieke Verstuyf; Bart De Moor; Kathleen Marchal (BMC Bioinform., 2009)

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. - Tom Michoel; Riet De Smet; Anagha Joshi; Yves Van de Peer; Kathleen Marchal (BMC Syst. Biol., 2009)

Cis-regulatory module detection using constraint programming. - Tias Guns; Hong Sun 002; Kathleen Marchal; Siegfried Nijssen (BIBM, 2010)

An ensemble method for querying gene expression compendia with experimental lists. - Riet De Smet; Kathleen Marchal (BIBM, 2010)

An ensemble biclustering approach for querying gene expression compendia with experimental lists. - Riet De Smet; Kathleen Marchal (Bioinform., 2011)

Query-based biclustering of gene expression data using Probabilistic Relational Models. - Hui Zhao; Lore Cloots; Tim Van den Bulcke; Yan Wu; Riet De Smet; Valerie Storms; Pieter Meysman; Kristof Engelen; Kathleen Marchal (BMC Bioinform., 2011)

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. - Ines Thiele; Daniel R. Hyduke; Benjamin Steeb; Guy Fankam; Douglas K. Allen; Susanna Bazzani; Pep Charusanti; Feng-Chi Chen; Ronan M. T. Fleming; Chao A. Hsiung; Sigrid C. J. De Keersmaecker; Yu-Chieh Liao; et al. (BMC Syst. Biol., 2011)

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. - Pieter Meysman; Thanh Hai Dang; Kris Laukens; Riet De Smet; Yan Wu; Kathleen Marchal; Kristof Engelen (Nucleic Acids Res., 2011)

Mining Local Staircase Patterns in Noisy Data. - Thanh Le Van; Ana Carolina Fierro; Tias Guns; Matthijs van Leeuwen; Siegfried Nijssen; Luc De Raedt; Kathleen Marchal (ICDM Workshops, 2012)

MotifSuite: workflow for probabilistic motif detection and assessment. - Marleen Claeys; Valerie Storms; Hong Sun 002; Tom Michoel; Kathleen Marchal (Bioinform., 2012)

Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments. - Yao Yao; Kathleen Marchal; Yves Van de Peer (ECAL, 2013)

An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. - Guillermín Agüero-Chapín; Aminael Sánchez-Rodríguez; Pedro I. Hidalgo-Yanes; Yunierkis Pérez-Castillo; Reinaldo Molina Ruiz; Kathleen Marchal; Vítor V. Vasconcelos; Agostinho Antunes (IWBBIO, 2013)

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks. - Lieven P. C. Verbeke; Lore Cloots; Piet Demeester; Jan Fostier; Kathleen Marchal (Bioinform., 2013)

Identifying differentially expressed genes in the absence of replication. - Pushpike Jayantha Thilakarathne; Geert Verbeke; Kristof Engelen; Kathleen Marchal; Dan Lin 004 (Int. J. Bioinform. Res. Appl., 2013)

Synthetic Biology and Microdevices: A Powerful Combination. - Lyn Venken; Kathleen Marchal; Jozef Vanderleyden (ACM J. Emerg. Technol. Comput. Syst., 2013)

Ranked Tiling. - Thanh Le Van; Matthijs van Leeuwen; Siegfried Nijssen; Ana Carolina Fierro; Kathleen Marchal; Luc De Raedt (ECML/PKDD (2), 2014)

MAGIC: access portal to a cross-platform gene expression compendium for maize. - Qiang Fu 009; Ana Carolina Fierro; Pieter Meysman; Aminael Sánchez-Rodríguez; Klaas Vandepoele; Kathleen Marchal; Kristof Engelen (Bioinform., 2014)

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. - Mushthofa Mushthofa; Gustavo Torres; Yves Van de Peer; Kathleen Marchal; Martine De Cock (Bioinform., 2014)

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. - Pieter Meysman; Paolo Sonego; Luca Bianco; Qiang Fu 009; Daniela Ledezma-Tejeida; Socorro Gama-Castro; Veerle Liebens; Jan Michiels; Kris Laukens; Kathleen Marchal; Julio Collado-Vides; Kristof Engelen (Nucleic Acids Res., 2014)

SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering. - Jimmy Van den Eynden; Ana Carolina Fierro; Lieven P. C. Verbeke; Kathleen Marchal (BMC Bioinform., 2015)

PheNetic: network-based interpretation of molecular profiling data. - Dries De Maeyer; Bram Weytjens; Joris Renkens; Luc De Raedt; Kathleen Marchal (Nucleic Acids Res., 2015)

Simultaneous discovery of cancer subtypes and subtype features by molecular data integration. - Thanh Le Van; Matthijs van Leeuwen; Ana Carolina Fierro; Dries De Maeyer; Jimmy Van den Eynden; Lieven P. C. Verbeke; Luc De Raedt; Kathleen Marchal; Siegfried Nijssen (Bioinform., 2016)

EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. - Sergio Pulido-Tamayo; Jorge Duitama; Kathleen Marchal (Nucleic Acids Res., 2016)

Modeling multi-valued biological interaction networks using fuzzy answer set programming. - Mushthofa Mushthofa; Steven Schockaert; Ling-Hong Hung; Kathleen Marchal; Martine De Cock (Fuzzy Sets Syst., 2018)

IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations. - Camilo Andres Perez-Romero; Bram Weytjens; Dries Decap; Toon Swings; Jan Michiels; Dries De Maeyer; Kathleen Marchal (Nucleic Acids Res., 2019)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

OMEN: network-based driver gene identification using mutual exclusivity. - Dries Van Daele; Bram Weytjens; Luc De Raedt; Kathleen Marchal (Bioinform., 2022)

Prior Knowledge Injection into Deep Learning Models Predicting Gene Expression from Whole Slide Images. - Max Hallemeesch; Marija Pizurica; Paloma Rabaey; Olivier Gevaert; Thomas Demeester; Kathleen Marchal (CoRR, 2025)