João F. Matias Rodrigues

Joao Rodrigues

 

Institute of Molecular Life Sciences
University of Zurich
Y55-L-56
Winterthurerstrasse 190
CH-8057 Zurich
Switzerland
Phone: +41 44 63 53148
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Curriculum Vitae

  • current - PostDoc at Christian von Mering's lab, Institute of Molecular Life Sciences, University of Zürich.
  • 2011 - Doctorate at Andreas Wagner's lab, Institute of Evolutionary Biology and Environmental Studies, University of Zürich.
  • 2004 - Degree in physics at the University of Lisbon.

Research Interests

  • Analysis and modeling of microbial interactions and ecology.
  • Modeling the evolution of microbial metabolic networks.
  • Evolution of cooperation, multicellularity and symbiosis.

Publications

Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C (2017) MAPseq: bringing speed, accuracy and consistency to ribosomal RNA sequence analysis. Bioinformatics. 2017: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, Maciąg-Dorszyńska M, Matias Rodrigues JF, Gaffke L, Wosinski A, Cech GM, Szalewska-Pałasz A, Węgrzyn 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 2017 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. Environmental Microbiology. 17, 1689–706.

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

Warinner C, Matias Rodrigues JF, Vyas R, et al. (2014) Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. doi: 10.1038/ng.2906.

Matias Rodrigues JF, von Mering C. (2013) HPC-CLUST: Distributed hierarchical clustering for very large sets of nucleotide sequences. Bioinformatics, (Epub ahead of print). doi: 10.1093/bioinformatics/btt657

Barve A, Matias Rodrigues JF, Wagner A. (2012) 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. (2012) 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 D. (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. (2009) Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Computational Biology 5(12): e1000613. doi: 10.1371/journal.pcbi.1000613

Santos FC, Rodrigues JF, Pacheco JM. (2006) Graph topology plays a determinant role in the evolution of cooperation. Proc. Royal Soc. B 273, 1582. doi: 10.1098/rspb.2005.3272

Santos FC, Rodrigues JF, Pacheco JM. (2005) Epidemic spreading and cooperation dynamics on homogeneous small-world networks. Physical Review E 72 (2005) 056128. doi: 10.1103/PhysRevE.72.056128