Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks. - João F. Matias Rodrigues; Andreas Wagner (PLoS Comput. Biol., 2009)

Genotype networks in metabolic reaction spaces. - Areejit Samal; João F. Matias Rodrigues; Jürgen Jost; Olivier C. Martin; Andreas Wagner (BMC Syst. Biol., 2010)

Genotype networks, innovation, and robustness in sulfur metabolism. - João F. Matias Rodrigues; Andreas Wagner (BMC Syst. Biol., 2011)

Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes. - João F. Matias Rodrigues; Daniel J. Rankin; Valentina Rossetti; Andreas Wagner; Homayoun C. Bagheri (PLoS Comput. Biol., 2012)

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. - João F. Matias Rodrigues; Christian von Mering (Bioinform., 2014)

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale. - Thomas S. B. Schmidt; João F. Matias Rodrigues; Christian von Mering (PLoS Comput. Biol., 2014)

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. - João F. Matias Rodrigues; Thomas S. B. Schmidt; Janko Tackmann; Christian von Mering (Bioinform., 2017)

Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments. - Annika L. Gable; Damian Szklarczyk; David Lyon; João F. Matias Rodrigues; Christian von Mering (Briefings Bioinform., 2022)

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. - Anthony Fullam; Ivica Letunic; Thomas S. B. Schmidt; Quinten R. Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn 004; Martin Larralde; Oleksandr M. Maistrenko; Lukas Malfertheiner; Alessio Milanese; João F. Matias Rodrigues; et al. (Nucleic Acids Res., 2023)