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2020 – today
- 2022
[j42]Dries Van Daele
, Bram Weytjens, Luc De Raedt, Kathleen Marchal:
OMEN: network-based driver gene identification using mutual exclusivity. Bioinform. 38(12): 3245-3251 (2022)- 2020
- [j41]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 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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020)
2010 – 2019
- 2019
- [j40]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): W151-W157 (2019) - 2018
- [j39]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: 63-82 (2018) - 2016
- [j38]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): 445-454 (2016) - [j37]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): W142-W146 (2016) - 2015
- [j36]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: 125:1-125:12 (2015) - [j35]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): W244-W250 (2015) - 2014
- [j34]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): 1316-1318 (2014) - [j33]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): 3086-3092 (2014) - [j32]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): 649-653 (2014) - [c11]Thanh Le Van, Matthijs van Leeuwen, Siegfried Nijssen, Ana Carolina Fierro, Kathleen Marchal, Luc De Raedt:
Ranked Tiling. ECML/PKDD (2) 2014: 98-113 - 2013
- [j31]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): 1308-1316 (2013) - [j30]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): 71-90 (2013) - [j29]Lyn Venken, Kathleen Marchal, Jozef Vanderleyden:
Synthetic Biology and Microdevices: A Powerful Combination. ACM J. Emerg. Technol. Comput. Syst. 9(4): 30:1-30:22 (2013) - [c10]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: 1234 - [c9]Guillermín Agüero-Chapín, Aminael Sánchez-Rodríguez, Pedro I. Hidalgo-Yanes, Yunierkis Pérez-Castillo, Reinaldo Molina Ruiz, Kathleen Marchal, Vítor V. Vasconcelos, Agostinho Antunes:
An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference. IWBBIO 2013: 155-156 - 2012
- [j28]Marleen Claeys, Valerie Storms, Hong Sun, Tom Michoel, Kathleen Marchal:
MotifSuite: workflow for probabilistic motif detection and assessment. Bioinform. 28(14): 1931-1932 (2012) - [c8]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: 139-146 - 2011
- [j27]Riet De Smet, Kathleen Marchal:
An ensemble biclustering approach for querying gene expression compendia with experimental lists. Bioinform. 27(14): 1948-1956 (2011) - [j26]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): S37 (2011) - [j25]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: 8 (2011) - [j24]Pieter Meysman, Thanh Hai Dang, Kris Laukens, Riet De Smet, Yan Wu, Kathleen Marchal, Kristof Engelen:
Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. Nucleic Acids Res. 39(2): 6 (2011) - 2010
- [c7]Riet De Smet, Kathleen Marchal:
An ensemble method for querying gene expression compendia with experimental lists. BIBM 2010: 314-318 - [c6]Tias Guns, Hong Sun, Kathleen Marchal, Siegfried Nijssen:
Cis-regulatory module detection using constraint programming. BIBM 2010: 363-368
2000 – 2009
- 2009
- [j23]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): 490-496 (2009) - [j22]Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor, Kathleen Marchal:
ViTraM: visualization of transcriptional modules. Bioinform. 25(18): 2450-2451 (2009) - [j21]Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor, Kathleen Marchal:
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. BMC Bioinform. 10(S-1) (2009) - [j20]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: 49 (2009) - [c5]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: 186-190 - [c4]Hong Sun, Tim Van den Bulcke, Bart De Moor, Karen Lemmens, Kristof Engelen, Kathleen Marchal:
Layout and Post-Processing of Transcriptional Modules. IJCBS 2009: 116-121 - 2008
- [j19]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): 49-63 (2008) - [j18]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) - 2007
- [j17]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): 1700-1701 (2007) - [j16]Thomas Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal, Yves Moreau:
Query-driven module discovery in microarray data. Bioinform. 23(19): 2573-2580 (2007) - [j15]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) - [j14]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) - 2006
- [j13]Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal:
A calibration method for estimating absolute expression levels from microarray data. Bioinform. 22(10): 1251-1258 (2006) - [j12]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: 43 (2006) - [j11]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: 160 (2006) - 2005
- [j10]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): 3185-3186 (2005) - [c3]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: 89-90 - [c2]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 - [p1]Qizheng Sheng, Yves Moreau, Frank De Smet, Kathleen Marchal, Bart De Moor:
Advances in Cluster Analysis of Microarray Data. Data Analysis and Visualization in Genomics and Proteomics 2005: 153-173 - 2003
- [j9]Kristof Engelen, Bert Coessens, Kathleen Marchal, Bart De Moor:
MARAN: Normalizing Micro-array Data. Bioinform. 19(7): 893-894 (2003) - [j8]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): 237-278 (2003) - [j7]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): 3468-3470 (2003) - 2002
- [j6]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): 331-332 (2002) - [j5]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): 735-746 (2002) - [j4]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): 447-464 (2002) - [j3]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): 325-327 (2002) - [j2]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): 1722-1743 (2002) - 2001
- [j1]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): 1113-1122 (2001) - [c1]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: 305-312
Coauthor Index
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