Kathleen Marchal

Publication Activity (10 Years)

Years Active: 2001-2022
Publications (10 Years): 8

Top Topics

Gene Ontology Terms

Gene Expression

Colorectal Cancer

Differentially Expressed

Top Venues

Nucleic Acids Res.

Publications

Dries Van Daele, Bram Weytjens, Luc De Raedt, Kathleen Marchal
OMEN: network-based driver gene identification using mutual exclusivity. Bioinform. 38 (12) (2022)
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 Gonzalez-Perez, 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 G. Gut, David Haan, Arif O. 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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578 (7793) (2020)
Camilo Andres Perez-Romero, Bram Weytjens, Dries Decap, Toon Swings, Jan Michiels, Dries De Maeyer, Kathleen Marchal
IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Mushthofa Mushthofa, Steven Schockaert, Ling-Hong Hung, Kathleen Marchal, Martine De Cock
Modeling multi-valued biological interaction networks using fuzzy answer set programming. Fuzzy Sets Syst. 345 (2018)
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
Simultaneous discovery of cancer subtypes and subtype features by molecular data integration. Bioinform. 32 (17) (2016)
Sergio Pulido-Tamayo, Jorge Duitama, Kathleen Marchal
EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Dries De Maeyer, Bram Weytjens, Joris Renkens, Luc De Raedt, Kathleen Marchal
PheNetic: network-based interpretation of molecular profiling data. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Jimmy Van den Eynden, Ana Carolina Fierro, Lieven P. C. Verbeke, Kathleen Marchal
SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering. BMC Bioinform. 16 (2015)
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
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. Nucleic Acids Res. 42 (Database-Issue) (2014)
Mushthofa Mushthofa, Gustavo Torres, Yves Van de Peer, Kathleen Marchal, Martine De Cock
ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. Bioinform. 30 (21) (2014)
Thanh Le Van, Matthijs van Leeuwen, Siegfried Nijssen, Ana Carolina Fierro, Kathleen Marchal, Luc De Raedt
Ranked Tiling. ECML/PKDD (2) (2014)
Qiang Fu, Ana Carolina Fierro, Pieter Meysman, Aminael Sánchez-Rodríguez, Klaas Vandepoele, Kathleen Marchal, Kristof Engelen
MAGIC: access portal to a cross-platform gene expression compendium for maize. Bioinform. 30 (9) (2014)
Lieven P. C. Verbeke, Lore Cloots, Piet Demeester, Jan Fostier, Kathleen Marchal
EPSILON: an eQTL prioritization framework using similarity measures derived from local networks. Bioinform. 29 (10) (2013)
Yao Yao, Kathleen Marchal, Yves Van de Peer
Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments. ECAL (2013)
Pushpike Jayantha Thilakarathne, Geert Verbeke, Kristof Engelen, Kathleen Marchal, Dan Lin
Identifying differentially expressed genes in the absence of replication. Int. J. Bioinform. Res. Appl. 9 (1) (2013)
Lyn Venken, Kathleen Marchal, Jozef Vanderleyden
Synthetic Biology and Microdevices: A Powerful Combination. ACM J. Emerg. Technol. Comput. Syst. 9 (4) (2013)
Guillermín Agüero-Chapín, Aminael Sánchez-Rodríguez, Pedro I. Hidalgo-Yanes, Yunierkis Pérez-Castillo, Reinaldo Molina Ruiz, Kathleen Marchal, Vitor Vasconcelos, Agostinho Antunes
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. IWBBIO (2013)
Marleen Claeys, Valerie Storms, Hong Sun, Tom Michoel, Kathleen Marchal
MotifSuite: workflow for probabilistic motif detection and assessment. Bioinform. 28 (14) (2012)
Thanh Le Van, Ana Carolina Fierro, Tias Guns, Matthijs van Leeuwen, Siegfried Nijssen, Luc De Raedt, Kathleen Marchal
Mining Local Staircase Patterns in Noisy Data. ICDM Workshops (2012)
Hui Zhao, Lore Cloots, Tim Van den Bulcke, Yan Wu, Riet De Smet, Valerie Storms, Pieter Meysman, Kristof Engelen, Kathleen Marchal
Query-based biclustering of gene expression data using Probabilistic Relational Models. BMC Bioinform. 12 (S-1) (2011)
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
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 5 (2011)
Pieter Meysman, Thanh Hai Dang, Kris Laukens, Riet De Smet, Yan Wu, Kathleen Marchal, Kristof Engelen
. Nucleic Acids Res. 39 (2) (2011)
Riet De Smet, Kathleen Marchal
An ensemble biclustering approach for querying gene expression compendia with experimental lists. Bioinform. 27 (14) (2011)
Tias Guns, Hong Sun, Kathleen Marchal, Siegfried Nijssen
Cis-regulatory module detection using constraint programming. BIBM (2010)
Riet De Smet, Kathleen Marchal
An ensemble method for querying gene expression compendia with experimental lists. BIBM (2010)
Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst. Biol. 3 (2009)
Pushpike Jayantha Thilakarathne, Geert Verbeke, Kristof Engelen, Kathleen Marchal
The Use of Mixed Models to Identify Differentially Expressed Genes when a Single Replicate per Biological Condition is Present. BIOCOMP (2009)
Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, Tom Michoel
Module networks revisited: computational assessment and prioritization of model predictions. Bioinform. 25 (4) (2009)
Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor, Kathleen Marchal
ViTraM: visualization of transcriptional modules. Bioinform. 25 (18) (2009)
Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor, Kathleen Marchal
-regulatory modules. BMC Bioinform. 10 (S-1) (2009)
Hong Sun, Tim Van den Bulcke, Bart De Moor, Karen Lemmens, Kristof Engelen, Kathleen Marchal
Layout and Post-Processing of Transcriptional Modules. IJCBS (2009)
Ana Carolina Fierro, Raphael Thuret, Kristof Engelen, Gilles Bernot, Kathleen Marchal, Nicolas Pollet
Evaluation of time profile reconstruction from complex two-color microarray designs. BMC Bioinform. 9 (2008)
Koenraad Van Leemput, Tim Van den Bulcke, Thomas Dhollander, Bart De Moor, Kathleen Marchal, Piet van Remortel
Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data. Artif. Life 14 (1) (2008)
Katrijn Van Deun, Kathleen Marchal, Willem J. Heiser, Kristof Engelen, Iven Van Mechelen
Joint mapping of genes and conditions via multidimensional unfolding analysis. BMC Bioinform. 8 (2007)
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
Validating module network learning algorithms using simulated data. BMC Bioinform. 8 (S-2) (2007)
Thomas Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal, Yves Moreau
Query-driven module discovery in microarray data. Bioinform. 23 (19) (2007)
Hui Zhao, Kristof Engelen, Bart De Moor, Kathleen Marchal
CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data. Bioinform. 23 (13) (2007)
Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal
A calibration method for estimating absolute expression levels from microarray data. Bioinform. 22 (10) (2006)
Pieter Monsieurs, Gert Thijs, Abeer A. Fadda, Sigrid C. J. De Keersmaecker, Jozef Vanderleyden, Bart De Moor, Kathleen Marchal
More robust detection of motifs in coexpressed genes by using phylogenetic information. BMC Bioinform. 7 (2006)
Tim Van den Bulcke, Koen Van Leemput, Bart Naudts, Piet van Remortel, Hongwu Ma, Alain Verschoren, Bart De Moor, Kathleen Marchal
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinform. 7 (2006)
Nathalie Pochet, Frizo A. L. Janssens, Frank De Smet, Kathleen Marchal, Ignace Vergote, Johan A. K. Suykens, Bart De Moor
M@CBETH: Optimizing Clinical Microarray Classification. CSB Workshops (2005)
Nathalie Pochet, Frizo A. L. Janssens, Frank De Smet, Kathleen Marchal, Johan A. K. Suykens, Bart De Moor
M@CBETH: a microarray classification benchmarking tool. Bioinform. 21 (14) (2005)
Tijl De Bie, Patrick Monsieurs, Kristof Engelen, Bart De Moor, Nello Cristianini, Kathleen Marchal
Discovering Transcriptional Modules from Motif, Chip-Chip and Microarray Data. Pacific Symposium on Biocomputing (2005)
Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal, Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys, Bart De Moor
INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis. Nucleic Acids Res. 31 (13) (2003)
Bart De Moor, Kathleen Marchal, Janick Mathys, Yves Moreau
Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars. Eur. J. Control 9 (2-3) (2003)
Kristof Engelen, Bert Coessens, Kathleen Marchal, Bart De Moor
MARAN: Normalizing Micro-array Data. Bioinform. 19 (7) (2003)
Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30 (1) (2002)
Gert Thijs, Yves Moreau, Frank De Smet, Janick Mathys, Magali Lescot, Stephane Rombauts, Pierre Rouzé, Bart De Moor, Kathleen Marchal
INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. Bioinform. 18 (2) (2002)
Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau
A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes. J. Comput. Biol. 9 (2) (2002)
Frank De Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, Yves Moreau
Adaptive quality-based clustering of gene expression profiles. Bioinform. 18 (5) (2002)
Yves Moreau, Frank De Smet, Gert Thijs, Kathleen Marchal, Bart De Moor
Functional bioinformatics of microarray data: from expression to regulation. Proc. IEEE 90 (11) (2002)
Gert Thijs, Kathleen Marchal, Magali Lescot, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau
A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes. RECOMB (2001)
Gert Thijs, Magali Lescot, Kathleen Marchal, Stephane Rombauts, Bart De Moor, Pierre Rouzé, Yves Moreau
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinform. 17 (12) (2001)