| Pathogens and host immunity in the ancient human oral cavity C Warinner, JFM Rodrigues, R Vyas, C Trachsel, N Shved, J Grossmann, ... Nature genetics 46 (4), 336-344, 2014 | 690 | 2014 |
| Graph topology plays a determinant role in the evolution of cooperation FC Santos, JF Rodrigues, JM Pacheco Proceedings of the Royal Society B: Biological Sciences 273 (1582), 51-55, 2006 | 431 | 2006 |
| Epidemic spreading and cooperation dynamics on homogeneous small-world networks FC Santos, JF Rodrigues, JM Pacheco Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 72 (5 …, 2005 | 349 | 2005 |
| Evolutionary plasticity and innovations in complex metabolic reaction networks JF Matias Rodrigues, A Wagner PLoS computational biology 5 (12), e1000613, 2009 | 148 | 2009 |
| MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis JF Matias Rodrigues, TSB Schmidt, J Tackmann, C von Mering Bioinformatics 33 (23), 3808-3810, 2017 | 129 | 2017 |
| Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale TSB Schmidt, JF Matias Rodrigues, C von Mering PLoS computational biology 10 (4), e1003594, 2014 | 128 | 2014 |
| Limits to robustness and reproducibility in the demarcation of operational taxonomic units TSB Schmidt, JF Matias Rodrigues, C von Mering Environmental microbiology 17 (5), 1689-1706, 2015 | 126 | 2015 |
| Rapid inference of direct interactions in large-scale ecological networks from heterogeneous microbial sequencing data J Tackmann, JFM Rodrigues, C von Mering Cell systems 9 (3), 286-296. e8, 2019 | 120 | 2019 |
| Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity OM Maistrenko, DR Mende, M Luetge, F Hildebrand, TSB Schmidt, SS Li, ... The ISME journal 14 (5), 1247-1259, 2020 | 103 | 2020 |
| Genotype networks in metabolic reaction spaces A Samal, JF Matias Rodrigues, J Jost, OC Martin, A Wagner BMC systems biology 4, 1-21, 2010 | 78 | 2010 |
| The network of inter-regional direct investment stocks across Europe S Battiston, JF Rodrigues, H Zeytinoglu Advances in Complex Systems 10 (01), 29-51, 2007 | 74 | 2007 |
| HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences JF Matias Rodrigues, C von Mering Bioinformatics 30 (2), 287-288, 2014 | 70 | 2014 |
| Superessential reactions in metabolic networks A Barve, JFM Rodrigues, A Wagner Proceedings of the National Academy of Sciences 109 (18), E1121-E1130, 2012 | 70 | 2012 |
| A family of interaction-adjusted indices of community similarity TSB Schmidt, JF Matias Rodrigues, C Von Mering The ISME journal 11 (3), 791-807, 2017 | 53 | 2017 |
| The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases SIB Swiss Institute of Bioinformatics Members Nucleic acids research 44 (D1), D27-D37, 2016 | 51 | 2016 |
| Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites J Tackmann, N Arora, TSB Schmidt, JFM Rodrigues, C von Mering Microbiome 6, 1-16, 2018 | 40 | 2018 |
| Genotype networks, innovation, and robustness in sulfur metabolism JF Matias Rodrigues, A Wagner BMC Systems Biology 5, 1-13, 2011 | 38 | 2011 |
| proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes A Fullam, I Letunic, TSB Schmidt, QR Ducarmon, N Karcher, S Khedkar, ... Nucleic acids research 51 (D1), D760-D766, 2023 | 27 | 2023 |
| Suppression of the Escherichia coli dnaA46 mutation by changes in the activities of the pyruvate-acetate node links DNA replication regulation to central carbon … J Tymecka-Mulik, L Boss, M Maciąg-Dorszyńska, JF Matias Rodrigues, ... PLoS One 12 (4), e0176050, 2017 | 24 | 2017 |
| The Evolution of Ecological Diversity in Acidobacteria J Sikorski, V Baumgartner, K Birkhofer, RS Boeddinghaus, B Bunk, ... Frontiers in Microbiology 13, 715637, 2022 | 23 | 2022 |