| Extensive transmission of microbes along the gastrointestinal tract TSB Schmidt, MR Hayward, LP Coelho, SS Li, PI Costea, AY Voigt, ... eLife 8, e42693, 2019 | 376 | 2019 |
| Microbial abundance, activity and population genomic profiling with mOTUs2 A Milanese, DR Mende, L Paoli, G Salazar, HJ Ruscheweyh, M Cuenca, ... Nature communications 10 (1), 1014, 2019 | 348 | 2019 |
| The superfamily of heme–copper oxygen reductases: Types and evolutionary considerations FL Sousa, RJ Alves, MA Ribeiro, JB Pereira-Leal, M Teixeira, MM Pereira Biochimica et Biophysica Acta (BBA)-Bioenergetics 1817 (4), 629-637, 2012 | 206 | 2012 |
| A genomic signature and the identification of new sporulation genes AB Abecasis, M Serrano, R Alves, L Quintais, JB Pereira-Leal, ... Journal of bacteriology 195 (9), 2101-2115, 2013 | 140 | 2013 |
| A faecal microbiota signature with high specificity for pancreatic cancer E Kartal, TSB Schmidt, E Molina-Montes, S Rodríguez-Perales, J Wirbel, ... Gut 71 (7), 1359-1372, 2022 | 129 | 2022 |
| Combinatorial, additive and dose-dependent drug–microbiome associations SK Forslund, R Chakaroun, M Zimmermann-Kogadeeva, L Markó, ... Nature 600 (7889), 500-505, 2021 | 121 | 2021 |
| Microbiome and metabolome features of the cardiometabolic disease spectrum S Fromentin, SK Forslund, K Chechi, J Aron-Wisnewsky, R Chakaroun, ... Nature medicine 28 (2), 303-314, 2022 | 110 | 2022 |
| Staphylococcus aureus Survives with a Minimal Peptidoglycan Synthesis Machine but Sacrifices Virulence and Antibiotic Resistance P Reed, ML Atilano, R Alves, E Hoiczyk, X Sher, NT Reichmann, ... Plos pathogens 11 (5), e1004891, 2015 | 105 | 2015 |
| Towards the biogeography of prokaryotic genes LP Coelho, R Alves, ÁR Del Río, PN Myers, CP Cantalapiedra, ... Nature 601 (7892), 252-256, 2022 | 98 | 2022 |
| Loss of genetic redundancy in reductive genome evolution AG Mendonça, RJ Alves, JB Pereira-Leal PLoS computational biology 7 (2), e1001082, 2011 | 96 | 2011 |
| Antibiotics-induced monodominance of a novel gut bacterial order F Hildebrand, L Moitinho-Silva, S Blasche, MT Jahn, TI Gossmann, ... Gut 68 (10), 1781-1790, 2019 | 70 | 2019 |
| Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications B Mészáros, H Sámano-Sánchez, J Alvarado-Valverde, J Čalyševa, ... Science signaling 14 (665), eabd0334, 2021 | 68 | 2021 |
| A bioinformatics classifier and database for heme-copper oxygen reductases FL Sousa, RJ Alves, JB Pereira-Leal, M Teixeira, MM Pereira PLoS One 6 (4), e19117, 2011 | 62 | 2011 |
| NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language LP Coelho, R Alves, P Monteiro, J Huerta-Cepas, AT Freitas, P Bork Microbiome 7, 1-10, 2019 | 58 | 2019 |
| Bioinformatics projects supporting life-sciences learning in high schools I Marques, P Almeida, R Alves, MJ Dias, A Godinho, JB Pereira-Leal PLoS computational biology 10 (1), e1003404, 2014 | 32 | 2014 |
| Extensive transmission of microbes along the gastrointestinal tract. Elife 8 TS Schmidt, MR Hayward, LP Coelho, SS Li, PI Costea, AY Voigt, J Wirbel, ... eLife Sciences Publications Ltd, 2019 | 18 | 2019 |
| Microbial abundance, activity and population genomic profiling with mOTUs2. Nat Commun 10: 1014 A Milanese, DR Mende, L Paoli, G Salazar, HJ Ruscheweyh, M Cuenca, ... | 16 | 2019 |
| metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes T Van Rossum, PI Costea, L Paoli, R Alves, R Thielemann, S Sunagawa, ... Bioinformatics 38 (4), 1162-1164, 2022 | 10 | 2022 |
| ELIXIR Software Management Plan for Life Sciences R Alves, D Bampalikis, LJ Castro, JMF González, J Harrow, M Kuzak, ... BioHackrXiv, 2021 | 9 | 2021 |
| inTB-a data integration platform for molecular and clinical epidemiological analysis of tuberculosis P Soares, RJ Alves, AB Abecasis, C Penha-Gonçalves, MGM Gomes, ... BMC bioinformatics 14, 1-8, 2013 | 9 | 2013 |
