Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes. - Shao-Shan Huang; Debra L. Fulton; David J. Arenillas; Paul Perco; Shannan J. Ho Sui; James R. Mortimer; Wyeth W. Wasserman (APBC, 2006)

oPOSSUM: integrated tools for analysis of regulatory motif over-representation. - Shannan J. Ho Sui; Debra L. Fulton; David J. Arenillas; Andrew T. Kwon; Wyeth W. Wasserman (Nucleic Acids Res., 2007)

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation. - Malin C. Andersen; Pär G. Engström; Stuart Lithwick; David J. Arenillas; Per Eriksson; Boris Lenhard; Wyeth W. Wasserman; Jacob Odeberg (PLoS Comput. Biol., 2008)

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. - Elodie Portales-Casamar; David J. Arenillas; Jonathan S. Lim; Magdalena I. Swanson; Steven Jiang; Anthony McCallum; Stefan Kirov; Wyeth W. Wasserman (Nucleic Acids Res., 2009)

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. - Elodie Portales-Casamar; Supat Thongjuea; Andrew T. Kwon; David J. Arenillas; Xiaobei Zhao; Eivind Valen; Dimas Yusuf; Boris Lenhard; Wyeth W. Wasserman; Albin Sandelin (Nucleic Acids Res., 2010)

MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. - Antony Le Béchec; Elodie Portales-Casamar; Guillaume Vetter; Michèle Moes; Pierre-Joachim Zindy; Anne Saumet; David J. Arenillas; Charles Theillet; Wyeth W. Wasserman; Charles-Henri Lecellier; Evelyne Friederich (BMC Bioinform., 2011)

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers. - Andrew T. Kwon; Alice Yi Chou; David J. Arenillas; Wyeth W. Wasserman (PLoS Comput. Biol., 2011)

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. - Anthony Mathelier; Xiaobei Zhao; Allen W. Zhang; François Parcy; Rebecca Worsley-Hunt; David J. Arenillas; Sorana Buchman; Chih-Yu Chen; Alice Yi Chou; Hans Ienasescu; Jonathan S. Lim; Casper Shyr; et al. (Nucleic Acids Res., 2014)

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. - David J. Arenillas; Alistair R. R. Forrest; Hideya Kawaji; Timo Lassmann; Wyeth W. Wasserman; Anthony Mathelier (Bioinform., 2016)

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. - Anthony Mathelier; Oriol Fornes; David J. Arenillas; Chih-Yu Chen; Grégoire Denay; Jessica J. Y. Lee; Wenqiang Shi; Casper Shyr; Ge Tan; Rebecca Worsley-Hunt; Allen W. Zhang; François Parcy; et al. (Nucleic Acids Res., 2016)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. - Marina Lizio; Jayson Harshbarger; Imad Abugessaisa; Shuei Noguchi; Atsushi Kondo; Jessica Severin; Chris Mungall; David J. Arenillas; Anthony Mathelier; Yulia A. Medvedeva; Andreas Lennartsson; Finn Drabløs; et al. (Nucleic Acids Res., 2017)

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. - Aziz Khan 001; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime Abraham Castro-Mondragón; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada R. Kulkarni; Ge Tan; Damir Baranasic; David J. Arenillas; et al. (Nucleic Acids Res., 2018)

OnTarget: in silico design of MiniPromoters for targeted delivery of expression. - Oriol Fornes; Tamar Vered Av-Shalom; Andrea J. Korecki; Rachelle A. Farkas; David J. Arenillas; Anthony Mathelier; Elizabeth M. Simpson; Wyeth W. Wasserman (Nucleic Acids Res., 2023)