Kathleen Marchal

56 papers B 1Misc 1Journal 44Unranked 9

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	ELLIPSIS: robust quantification of splicing in scRNA-seq. Bioinform. Marie Van Hecke, Niko Beerenwinkel, Thibault Lootens, Jan Fostier, Robrecht Raedt, Kathleen Marchal
2025	J	`jnl`	Prior Knowledge Injection into Deep Learning Models Predicting Gene Expression from Whole Slide Images. CoRR Max Hallemeesch, Marija Pizurica, Paloma Rabaey, Olivier Gevaert, Thomas Demeester, Kathleen Marchal
2022	J	`jnl`	OMEN: network-based driver gene identification using mutual exclusivity. Bioinform. Dries Van Daele, Bram Weytjens, Luc De Raedt, Kathleen Marchal
2020	J	`jnl`	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 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, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel González-Pérez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora
2019	J	`jnl`	IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations. Nucleic Acids Res. Camilo Andres Perez-Romero, Bram Weytjens, Dries Decap, Toon Swings, Jan Michiels, Dries De Maeyer, Kathleen Marchal
2018	J	`jnl`	Modeling multi-valued biological interaction networks using fuzzy answer set programming. Fuzzy Sets Syst. Mushthofa Mushthofa, Steven Schockaert, Ling-Hong Hung, Kathleen Marchal, Martine De Cock
2016	J	`jnl`	EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. Nucleic Acids Res. Sergio Pulido-Tamayo, Jorge Duitama, Kathleen Marchal
2016	J	`jnl`	Simultaneous discovery of cancer subtypes and subtype features by molecular data integration. Bioinform. 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
2015	J	`jnl`	PheNetic: network-based interpretation of molecular profiling data. Nucleic Acids Res. Dries De Maeyer, Bram Weytjens, Joris Renkens, Luc De Raedt, Kathleen Marchal
2015	J	`jnl`	SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering. BMC Bioinform. Jimmy Van den Eynden, Ana Carolina Fierro, Lieven P. C. Verbeke, Kathleen Marchal
2014	J	`jnl`	ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. Bioinform. Mushthofa Mushthofa, Gustavo Torres, Yves Van de Peer, Kathleen Marchal, Martine De Cock
2014	J	`jnl`	COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. Nucleic Acids Res. Pieter Meysman, Paolo Sonego, Luca Bianco, Qiang Fu, Daniela Ledezma-Tejeida, Socorro Gama-Castro, Veerle Liebens, Jan Michiels, Kris Laukens, Kathleen Marchal, Julio Collado-Vides, Kristof Engelen
2014	J	`jnl`	MAGIC: access portal to a cross-platform gene expression compendium for maize. Bioinform. Qiang Fu, Ana Carolina Fierro, Pieter Meysman, Aminael Sánchez-Rodríguez, Klaas Vandepoele, Kathleen Marchal, Kristof Engelen
2014	—	`conf`	Ranked Tiling. ECML/PKDD (2) Thanh Le Van, Matthijs van Leeuwen, Siegfried Nijssen, Ana Carolina Fierro, Kathleen Marchal, Luc De Raedt
2013	—	`conf`	An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. IWBBIO Guillermín Agüero-Chapín, Aminael Sánchez-Rodríguez, Pedro I. Hidalgo-Yanes, Yunierkis Pérez-Castillo, Reinaldo Molina Ruiz, Kathleen Marchal, Vítor V. Vasconcelos, Agostinho Antunes
2013	J	`jnl`	EPSILON: an eQTL prioritization framework using similarity measures derived from local networks. Bioinform. Lieven P. C. Verbeke, Lore Cloots, Piet Demeester, Jan Fostier, Kathleen Marchal
2013	J	`jnl`	Identifying differentially expressed genes in the absence of replication. Int. J. Bioinform. Res. Appl. Pushpike Jayantha Thilakarathne, Geert Verbeke, Kristof Engelen, Kathleen Marchal, Dan Lin
2013	J	`jnl`	Synthetic Biology and Microdevices: A Powerful Combination. ACM J. Emerg. Technol. Comput. Syst. Lyn Venken, Kathleen Marchal, Jozef Vanderleyden
2013	—	`conf`	Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments. ECAL Yao Yao, Kathleen Marchal, Yves Van de Peer
2012	—	`conf`	Mining Local Staircase Patterns in Noisy Data. ICDM Workshops Thanh Le Van, Ana Carolina Fierro, Tias Guns, Matthijs van Leeuwen, Siegfried Nijssen, Luc De Raedt, Kathleen Marchal
2012	J	`jnl`	MotifSuite: workflow for probabilistic motif detection and assessment. Bioinform. Marleen Claeys, Valerie Storms, Hong Sun, Tom Michoel, Kathleen Marchal
2011	J	`jnl`	A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 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, Kathleen Marchal, Monica L. Mo, Emre Özdemir, Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Sara Sigurbjörnsdóttir, Jonas Steinmann, Suresh Sudarsan, Neil Swainston, Inge M. Thijs, Karsten Zengler, Bernhard O. Palsson, Joshua N. Adkins, Dirk Bumann
2011	J	`jnl`	An ensemble biclustering approach for querying gene expression compendia with experimental lists. Bioinform. Riet De Smet, Kathleen Marchal
2011	J	`jnl`	Query-based biclustering of gene expression data using Probabilistic Relational Models. BMC Bioinform. Hui Zhao, Lore Cloots, Tim Van den Bulcke, Yan Wu, Riet De Smet, Valerie Storms, Pieter Meysman, Kristof Engelen, Kathleen Marchal
2011	J	`jnl`	Use of structural DNA properties for the prediction of transcription-factor binding sites in Nucleic Acids Res. Pieter Meysman, Thanh Hai Dang, Kris Laukens, Riet De Smet, Yan Wu, Kathleen Marchal, Kristof Engelen
2010	—	`conf`	An ensemble method for querying gene expression compendia with experimental lists. BIBM Riet De Smet, Kathleen Marchal
2010	—	`conf`	Cis-regulatory module detection using constraint programming. BIBM Tias Guns, Hong Sun, Kathleen Marchal, Siegfried Nijssen
2009	J	`jnl`	Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst. Biol. Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal
2009	—	`conf`	Layout and Post-Processing of Transcriptional Modules. IJCBS Hong Sun, Tim Van den Bulcke, Bart De Moor, Karen Lemmens, Kristof Engelen, Kathleen Marchal
2009	J	`jnl`	Module networks revisited: computational assessment and prioritization of model predictions. Bioinform. Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, Tom Michoel
2009	J	`jnl`	ModuleDigger: an itemset mining framework for the detection of BMC Bioinform. Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor, Kathleen Marchal
2009	—	`conf`	The Use of Mixed Models to Identify Differentially Expressed Genes when a Single Replicate per Biological Condition is Present. BIOCOMP Pushpike Jayantha Thilakarathne, Geert Verbeke, Kristof Engelen, Kathleen Marchal
2009	J	`jnl`	ViTraM: visualization of transcriptional modules. Bioinform. Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor, Kathleen Marchal
2008	J	`jnl`	Evaluation of time profile reconstruction from complex two-color microarray designs. BMC Bioinform. Ana Carolina Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal, Nicolas Pollet
2008	J	`jnl`	Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data. Artif. Life Koenraad Van Leemput, Tim Van den Bulcke, Thomas Dhollander, Bart De Moor, Kathleen Marchal, Piet van Remortel
2007	J	`jnl`	CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data. Bioinform. Hui Zhao, Kristof Engelen, Bart De Moor, Kathleen Marchal
2007	J	`jnl`	Joint mapping of genes and conditions via multidimensional unfolding analysis. BMC Bioinform. Katrijn Van Deun, Kathleen Marchal, Willem J. Heiser, Kristof Engelen, Iven Van Mechelen
2007	J	`jnl`	Query-driven module discovery in microarray data. Bioinform. Thomas Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal, Yves Moreau
2007	J	`jnl`	Validating module network learning algorithms using simulated data. BMC Bioinform. 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
2006	J	`jnl`	A calibration method for estimating absolute expression levels from microarray data. Bioinform. Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal
2006	J	`jnl`	More robust detection of motifs in coexpressed genes by using phylogenetic information. BMC Bioinform. Pieter Monsieurs, Gert Thijs, Abeer A. Fadda, Sigrid C. J. De Keersmaecker, Jozef Vanderleyden, Bart De Moor, Kathleen Marchal
2006	J	`jnl`	SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinform. Tim Van den Bulcke, Koen Van Leemput, Bart Naudts, Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor, Kathleen Marchal
2005	—	`ch.`	Advances in Cluster Analysis of Microarray Data. Data Analysis and Visualization in Genomics and Proteomics Qizheng Sheng, Yves Moreau, Frank De Smet, Kathleen Marchal, Bart De Moor
2005	Misc	`conf`	Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data. Pacific Symposium on Biocomputing Tijl De Bie, Patrick Monsieurs, Kristof Engelen, Bart De Moor, Nello Cristianini, Kathleen Marchal
2005	—	`conf`	M@CBETH: Optimizing Clinical Microarray Classification. CSB Workshops Nathalie Pochet, Frizo A. L. Janssens, Frank De Smet, Kathleen Marchal, Ignace Vergote, Johan A. K. Suykens, Bart De Moor
2005	J	`jnl`	M@CBETH: a microarray classification benchmarking tool. Bioinform. Nathalie Pochet, Frizo A. L. Janssens, Frank De Smet, Kathleen Marchal, Johan A. K. Suykens, Bart De Moor
2003	J	`jnl`	Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars. Eur. J. Control Bart De Moor, Kathleen Marchal, Janick Mathys, Yves Moreau
2003	J	`jnl`	INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res. Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal, Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys, Bart De Moor
2003	J	`jnl`	MARAN: Normalizing Micro-array Data. Bioinform. Kristof Engelen, Bert Coessens, Kathleen Marchal, Bart De Moor
2002	J	`jnl`	A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes. J. Comput. Biol. Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau
2002	J	`jnl`	Adaptive quality-based clustering of gene expression profiles. Bioinform. Frank De Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, Yves Moreau
2002	J	`jnl`	Functional bioinformatics of microarray data: from expression to regulation. Proc. IEEE Yves Moreau, Frank De Smet, Gert Thijs, Kathleen Marchal, Bart De Moor
2002	J	`jnl`	INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. Bioinform. Gert Thijs, Yves Moreau, Frank De Smet, Janick Mathys, Magali Lescot, Stephane Rombauts, Pierre Rouzé, Bart De Moor, Kathleen Marchal
2002	J	`jnl`	PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts
2001	B	`conf`	A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes. RECOMB Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau
2001	J	`jnl`	A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinform. Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau