The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. - Rafael Silva-Rocha; Hidde de Jong; Javier Tamames; Víctor de Lorenzo (BMC Syst. Biol., 2011)

Bacteria as Computers: Formalizing Transcriptional Regulatory Networks by Way of Digital Logic Circuits. - Rafael Silva-Rocha; Victor de Lorenzo (Int. J. Unconv. Comput., 2012)

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. - Rafael Silva-Rocha; Esteban Martínez-García; Belén Calles; Max Chavarría; Alejandro Arce-Rodríguez; Aitor de las Heras; A. David Páez-Espino; Gonzalo Durante-Rodríguez; Juhyun Kim; Pablo I. Nikel; Raúl Platero; Victor de Lorenzo (Nucleic Acids Res., 2013)

ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization. - Gustavo Tamasco; Manish Kumar; Karsten Zengler; Rafael Silva-Rocha; Ricardo Roberto da Silva (BMC Bioinform., 2022)