Bioinformatics

My theoretical work is often inspired by problems from bioinformatics. My contributions in this area pertain to integrative biology (in particular the identification of transcriptional modules), the study of the evolution of gene families, and disease gene hunting.

Publications: 
Title Authors Status Year
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Mieke Verstuyf, Bart De Moor, Kathleen Marchal journal paper 2009
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli Karen Lemmens, Tijl De Bie, Thomas Dhollander, Sigrid De Keersmaecker, Inge Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jozef Vanderleyden, Julio Collado-Vides, Kristof Engelen and Kathleen Marchal journal paper 2009
The Condition-Dependent Transcriptional Network in Escherichia Coli Karen Lemmens, Tijl De Bie, Thomas Dhollander, Pieter Monsieurs, Bart De Moor, Julio Collado-Vides, Kristof Engelen, Kathleen Marchal journal paper 2009
Integrating Microarray and Proteomics Data to Predict the Response of Cetuximab in Patients with Rectal Cancer Anneleen Daemen, Olivier Gevaert, Tijl De Bie, Annelies Debucquoy, Jean-Pascal Machiels, Bart De Moor, Karin Haustermans conference paper 2008
Kernel-Based Data Fusion for Gene Prioritization Tijl De Bie, Leon-Charles Tranchevent, Liesbeth van Oeffelen, Yves Moreau journal paper 2007
Kernel clustering for knowledge discovery in clinical microarray data analysis Nathalie Pochet, Fabian Ojeda, Frank De Smet, Tijl De Bie, Johan Suykens, Bart De Moor book chapter 2006
CAFE: a computational tool for the study of gene family evolution Tijl De Bie, Nello Cristianini, Jeffery Demuth, Matthew Hahn journal paper 2006
Inferring transcriptional module networks from ChIP-chip-, motif- and microarray data Karen Lemmens, Thomas Dhollander, Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Joris Winderickx, Bart De Moor, Kathleen Marchal journal paper 2006
The Evolution of Mammalian Gene Families Jeffery Demuth, Tijl De Bie, Jason Stajich, Nello Cristianini, Matthew Hahn journal paper 2006
Discovering Transcriptional Modules from Motif, ChIP-chip and Microarray Data Tijl De Bie, Pieter Monsieurs, Kristof Engelen, Bart De Moor, Nello Cristianini, Kathleen Marchal conference paper 2005
Estimating the tempo and mode of gene family evolution from comparative genomic data Matthew Hahn, Tijl De Bie, Jason Stajich, Chi Nguyen, Nello Cristianini journal paper 2005
Semi-supervised learning based on kernel methods and graph cut algorithms Tijl De Bie phd thesis 2005
A Statistical Framework for Genomic Data Fusion Gert Lanckriet, Tijl De Bie, Nello Cristianini, Michael Jordan, William Stafford Noble journal paper 2004