Web-based Data Collection for Uterine Adnexal Tumors: A Case Study. - Stein Aerts; Peter Antal; Dirk Timmerman; Bart De Moor; Yves Moreau (CBMS, 2002)

Computational detection of cis-regulatory modules. - Stein Aerts; Peter Van Loo; Gert Thijs; Yves Moreau; Bart De Moor (ECCB, 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)

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. - Stein Aerts; Peter Van Loo; Yves Moreau; Bart De Moor (Bioinform., 2004)

TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. - Stein Aerts; Peter Van Loo; Gert Thijs; Herbert Mayer; Rainer de Martin; Yves Moreau; Bart De Moor (Nucleic Acids Res., 2005)

Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus. - Michal Dabrowski; Stein Aerts; Bozena Kaminska (BMC Bioinform., 2006)

ORegAnno: an open-access community-driven resource for regulatory annotation. - Obi L. Griffith; Stephen B. Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica C. Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M. Gallo; et al. (Nucleic Acids Res., 2008)

ENDEAVOUR update: a web resource for gene prioritization in multiple species. - Léon-Charles Tranchevent; Roland Barriot; Shi Yu; Steven Van Vooren; Peter Van Loo; Bert Coessens; Bart De Moor; Stein Aerts; Yves Moreau (Nucleic Acids Res., 2008)

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections. - Rekin's Janky; Annelien Verfaillie; Hana Imrichová; Bram Van de Sande; Laura Standaert; Valerie Christiaens; Gert Hulselmans; Koen Herten; Marina Naval Sanchez; Delphine Potier; Dmitry Svetlichnyy; Zeynep Kalender Atak; et al. (PLoS Comput. Biol., 2014)

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. - Hana Imrichová; Gert Hulselmans; Zeynep Kalender Atak; Delphine Potier; Stein Aerts (Nucleic Acids Res., 2015)

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models. - Dmitry Svetlichnyy; Hana Imrichová; Mark Fiers; Zeynep Kalender Atak; Stein Aerts (PLoS Comput. Biol., 2015)

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks. - Thomas Moerman; Sara Aibar Santos; Carmen Bravo González-Blas; Jaak Simm; Yves Moreau; Jan Aerts; Stein Aerts (Bioinform., 2019)