Domain Fishing: a first step in protein comparative modelling. - Bruno Contreras-Moreira; Paul A. Bates (Bioinform., 2002)

Comparative footprinting of DNA-binding proteins. - Bruno Contreras-Moreira; Julio Collado-Vides (ISMB (Supplement of Bioinformatics), 2006)

TFmodeller: comparative modelling of protein-DNA complexes. - Bruno Contreras-Moreira; Pierre-Alain Branger; Julio Collado-Vides (Bioinform., 2007)

Prediction of TF target sites based on atomistic models of protein-DNA complexes. - Vladimir Espinosa Angarica; Abel González Pérez; Ana Tereza Ribeiro de Vasconcelos; Julio Collado-Vides; Bruno Contreras-Moreira (BMC Bioinform., 2008)

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. - Socorro Gama-Castro; Verónica Jiménez-Jacinto; Martín Peralta-Gil; Alberto Santos-Zavaleta; Mónica I. Peñaloza-Spínola; Bruno Contreras-Moreira; Juan Segura-Salazar; Luis Muñiz-Rascado; Irma Martínez-Flores; Heladia Salgado; César Bonavides-Martínez; Cei Abreu-Goodger; et al. (Nucleic Acids Res., 2008)

primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. - Bruno Contreras-Moreira; Bernardo Sachman-Ruiz; Iraís Figueroa-Palacios; Pablo Vinuesa (Nucleic Acids Res., 2009)

Interface Similarity Improves Comparison of DNA-Binding Proteins: The Homeobox Example. - Álvaro Sebastián; Carlos P. Cantalapiedra; Bruno Contreras-Moreira (JBI, 2010)

3D-footprint: a database for the structural analysis of protein-DNA complexes. - Bruno Contreras-Moreira (Nucleic Acids Res., 2010)

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. - Álvaro Sebastián; Bruno Contreras-Moreira (Bioinform., 2014)

RSAT 2015: Regulatory Sequence Analysis Tools. - Alejandra Medina-Rivera; Matthieu Defrance; Olivier Sand; Carl Herrmann; Jaime Abraham Castro-Mondragón; Jeremy Delerce; Sébastien Jaeger; Christophe Blanchet; Pierre Vincens; Christophe Caron; Daniel M. Staines; Bruno Contreras-Moreira; et al. (Nucleic Acids Res., 2015)

RSAT 2018: regulatory sequence analysis tools 20th anniversary. - Nga Thi Thuy Nguyen; Bruno Contreras-Moreira; Jaime Abraham Castro-Mondragón; Walter Santana-Garcia; Raul Ossio; Carla Daniela Robles-Espinoza; Mathieu Bahin; Samuel Collombet; Pierre Vincens; Denis Thieffry; Jacques van Helden; Alejandra Medina-Rivera; et al. (Nucleic Acids Res., 2018)

Ensembl Genomes 2020 - enabling non-vertebrate genomic research. - Kevin L. Howe; Bruno Contreras-Moreira; Nishadi De Silva; Gareth Maslen; Wasiu A. Akanni; James E. Allen; Jorge Álvarez-Jarreta; Matthieu Barba; Dan M. Bolser; Lahcen Cambell; Manuel Carbajo; Marc Chakiachvili; et al. (Nucleic Acids Res., 2020)

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. - Marcela K. Tello-Ruiz; Sushma Naithani; Parul Gupta; Andrew Olson; Sharon Wei; Justin Preece; Yinping Jiao; Bo Wang 117; Kapeel Chougule; Priyanka Garg; Justin Elser; Sunita Kumari; et al. (Nucleic Acids Res., 2021)

RSAT 2022: regulatory sequence analysis tools. - Walter Santana-Garcia; Jaime Abraham Castro-Mondragón; Mónica Padilla-Gálvez; Nga Thi Thuy Nguyen; Ana Elizondo-Salas; Najla Ksouri; François Gerbes; Denis Thieffry; Pierre Vincens; Bruno Contreras-Moreira; Jacques van Helden; Morgane Thomas-Chollier; et al. (Nucleic Acids Res., 2022)

The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. - Nishadi De Silva; Jyothish Bhai; Marc Chakiachvili; Bruno Contreras-Moreira; Carla A. Cummins; Adam Frankish; Astrid Gall; Thiago Augusto Lopes Genez; Kevin L. Howe; Sarah E. Hunt; Fergal J. Martin; Benjamin Moore; et al. (Nucleic Acids Res., 2022)

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. - Andrew D. Yates; James E. Allen; M. Ridwan Amode; Andrey G. Azov; Matthieu Barba; Andrés Becerra; Jyothish Bhai; Lahcen I. Campbell; Manuel Carbajo Martinez; Marc Chakiachvili; Kapeel Chougule; Mikkel B. Christensen; et al. (Nucleic Acids Res., 2022)