Signal search analysis server. - Giovanna Ambrosini; Viviane Praz; Vidhya Jagannathan; Philipp Bucher (Nucleic Acids Res., 2003)

ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites. - Thomas J. Cradick; Giovanna Ambrosini; Christian Iseli; Philipp Bucher; Anton P. McCaffrey (BMC Bioinform., 2011)

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. - René Dreos; Giovanna Ambrosini; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2013)

Principles of ChIP-seq Data Analysis Illustrated with Examples. - Giovanna Ambrosini; René Dreos; Philipp Bucher (IWBBIO, 2014)

Transcription factor binding and nucleosome positioning are alternative pathways for transcription start site selection in eukaryotic promoters. - René Dreos; Giovanna Ambrosini; Philipp Bucher (IWBBIO, 2014)

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools. - René Dreos; Giovanna Ambrosini; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2015)

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters. - René Dreos; Giovanna Ambrosini; Philipp Bucher (PLoS Comput. Biol., 2016)

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. - René Dreos; Giovanna Ambrosini; Romain Groux; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2017)

SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity. - Sunil Kumar; Giovanna Ambrosini; Philipp Bucher (Nucleic Acids Res., 2017)

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix. - Giovanna Ambrosini; Romain Groux; Philipp Bucher (Bioinform., 2018)

MGA repository: a curated data resource for ChIP-seq and other genome annotated data. - René Dreos; Giovanna Ambrosini; Romain Groux; Rouaïda Cavin Périer; Philipp Bucher (Nucleic Acids Res., 2018)

EPD in 2020: enhanced data visualization and extension to ncRNA promoters. - Patrick Meylan; René Dreos; Giovanna Ambrosini; Romain Groux; Philipp Bucher (Nucleic Acids Res., 2020)