João F. Matias Rodrigues
Postdoctoral Researcher
Christian von Mering's lab
Institute of Molecular Life Sciences
University of Zürich
Switzerland

Publications

• Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C (2017) MAPseq: bringing speed, accuracy and consistency to ribosomal RNA sequence analysis. Bioinformatics btx517

• Schmidt TSB, Matias Rodrigues JF, von Mering C (2017) A family of interaction-adjusted indices of community similarity. The ISME Journal 11, 791-807. Doi:10.1038/ismej.2016.139

• Tymecka-Mulik J, Boss L, Maciag-Dorszynska M, Matias Rodrigues JF, Gaffke L, Wosinski A, Cech GM, Szalewska-Palasz A, Wegrzyn G, Glinkowska MK (2017) Suppression of the Escherichia coli dnaA46 mutation by changes in the activities of the pyruvate-acetate node links DNA replication regulation to central carbon metabolism. PloS One Apr 27;12(4):e0176050. Doi: 10.1371/journal.pone.0176050

• SIB Swiss Institute of Bioinformatics Members (2016) The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Res. 44 D27-D37.

• Schmidt TSB, Matias Rodrigues JF, von Mering C (2015) Limits to robustness and reproducibility in the demarcation of operational taxonomic units. Environ Microbiol 17, 1689-706.

• Warinner C, Matias Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen LH, Samaniego Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis Jr CM, Collins MJ, Gilbert TP, Ruhli F, Cappellini E. (2014) Pathogens and host immunity in the ancient human oral cavity. Nature Genetics 46, 336-344. doi:10.1038/ng.2906

• Schmidt TSB, Matias Rodrigues JF, von Mering C (2014) Ecological Consistency of SSU rRNA-based Operational Taxonomic Units at a Global Scale. PLoS Comp Biol 10(4): e1003594. doi:10.1371/journal.pcbi.1003594

• Matias Rodrigues JF, von Mering C (2013) HPC-CLUST: clustering of large number of nucleotide sequences. Bioinformatics 2013:btt657

• Barve A, Matias Rodrigues JF, Wagner A (2013) Superessential reactions in metabolic networks and the evolution of drug resistance. Proc. Natl. Acad. Sci. 109(18):E1121-30. doi: 10.1073/pnas.1113065109

• Matias Rodrigues JF, Rankin DJ, Rossetti V, Wagner A, Bagheri HC (2013) Differences in cell division rates drive the evolution of terminal differentiation in microbes. PLoS Computational Biology 8(4):e1002468. doi: 10.1371/journal.pcbi.1002468

• Santos M, Matias Rodrigues JF, Wedekind C, Rankin DJ (2011) The emergence of human communication and the scale of competition. Evolution and Human Behavior doi:10.1016/j.evolhumbehav.2011.09.007

• Matias Rodrigues JF, Wagner A (2011) Genotype networks, innovation, and robustness in sulfur metabolism. BMC Systems Biology, 5: 39. doi:10.1186/1752-0509-5-39

• Samal A, Matias Rodrigues JF, Jost J, Martin OC, Wagner A (2010) Genotype networks in metabolic network spaces. BMC Systems Biology, 4(30) doi:10.1186/1752-0509-4-30

• Matias Rodrigues JF, Wagner A (2010) Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Computational Biology 5(12): e1000613. doi:10.1371/journal.pcbi.1000613

• Navarro-Barrientos JE, Cantero-Álvarez R, Matias Rodrigues JF and Schweitzer F (2007) Investments in random environments. Physica A, Vol. 387, Issues 8-9, pp. 2035-2046

• Battiston S, Rodrigues, J.F., Zeytinoglu H (2007) The Network of Inter-Regional Direct Investment Stocks across Europe. Advances in Complex Systems, Vol. 10, No. 1 pp. 29-51

• Santos FC, Rodrigues JF, Pacheco JM (2006) Graph topology plays an important role in the evolution of cooperation. Proc. Royal Soc. B 273, 1582

• Santos FC, Rodrigues JF, Pacheco JM (2005) Epidemic spreading and cooperation dynamics on homogeneous small-world networks. Physical Review E 72 (2005) 056128.