Selected publications

• Zeynep Kalender Atak*, Kim De Keersmaecker*, Valentina Gianfelici, Ellen Geerdens, Roel Vandepoel, Daphnie Pauwels, Michaël Porcu, Idoya Lahortiga, Vanessa Brys, Willy G. Dirks, Hilmar Quentmeier, Jacqueline Cloos, Harry Cuppens, Anne Uyttebroeck, Peter Vandenberghe, Jan Cools#, and Stein Aerts# (2012). High accuracy mutation detection in leukemia on a selected panel of cancer genes. PLoS ONE, in press.



• Stein Aerts (2012). Computational Strategies for the Genome-Wide Identification of cis-Regulatory Elements and Transcriptional Targets. Volume edited by Serge Plaza and Francois Payre "Transcriptional Switches During Development". Curr. Top. Dev. Biol. 98:121-45.



• Delphine Potier, Zeynep Kalender Atak, Marina Naval Sanchez, Carl Herrmann and Stein Aerts (2011). Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila Methods Mol Biol. 2012;786:291-314.



• Stein Aerts, Xiao-Jiang Quan, Annelies Claeys, Marina Naval Sanchez, Phillip Tate, Jiekun Yan, and Bassem Hassan (2010). Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification
  PLoS Biology 2010 Jul 27;8(7):e1000435.



• Stein Aerts*, Sven Vilain*, Shu Hu*, Leon-Charles Tranchevent*, Roland Barriot, Jiekun Yan, Yves Moreau, Bassem Hassan, and Xiao-Jiang Quan* (2009).
  Integrating Computational Biology and Forward Genetics in Drosophila
  PLoS Genetics 5(1): e1000351.



• Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L. Griffith, Paco Hulpiau, Steven J.M. Jones, Stephen B. Montgomery, Casey M. Bergman, The Open Regulatory Annotation Consortium (2008).
  Text-mining assisted regulatory annotation
  Genome Biology, 9:R31



• Stein Aerts, Jacques van Helden, Olivier Sand, Bassem Hassan (2007).
  Fine-tuning enhancer models to predict transcriptional targets across multiple genomes.
  PLoS ONE 2(11): e1115.



• Stein Aerts*, Diether Lambrechts*, Sunit Maity*, Peter Van Loo*, Bert Coessens*, Frederik De Smet, Leon-Charles Tranchevent, Bart De Moor, Peter Marynen, Bassem Hassan, Peter Carmeliet, Yves Moreau (2006).
  Gene prioritization through genomic data fusion.
  Nature Biotechnology24(5):537-544.



• Stein Aerts, Gert Thijs, Bert Coessens, Mik Staes, Yves Moreau and Bart De Moor (2003).
  TOUCAN: deciphering the cis-regulatory logic of coregulated genes
  Nucleic Acids Research, 31(6), 1753-1764. (pdf)