| Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation PM Rosado, DCA Leite, GAS Duarte, RM Chaloub, G Jospin, ... The ISME journal 13 (4), 921-936, 2019 | 355 | 2019 |
| Complementary roles of wood-inhabiting fungi and bacteria facilitate deadwood decomposition V Tláskal, V Brabcová, T Větrovský, M Jomura, R López-Mondéjar, ... Msystems 6 (1), 10.1128/msystems. 01078-20, 2021 | 98 | 2021 |
| Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals T Keller-Costa, A Lago-Lestón, JP Saraiva, R Toscan, SG Silva, ... Microbiome 9, 1-21, 2021 | 59 | 2021 |
| TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes FB Corrêa, JP Saraiva, PF Stadler, UN da Rocha Nucleic acids research 48 (D1), D626-D632, 2020 | 50 | 2020 |
| Machine learning-assisted identification of bioindicators predicts medium-chain carboxylate production performance of an anaerobic mixed culture B Liu, H Sträuber, J Saraiva, H Harms, SG Silva, JC Kasmanas, ... Microbiome 10 (1), 48, 2022 | 27 | 2022 |
| iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6 O Dias, J Saraiva, C Faria, M Ramirez, F Pinto, I Rocha Frontiers in Microbiology 10, 1283, 2019 | 24 | 2019 |
| Biotransformation of hexachlorocyclohexanes contaminated biomass for energetic utilization demonstrated in continuous anaerobic digestion system S Lian, M Nikolausz, I Nijenhuis, UN da Rocha, B Liu, FB Corrêa, ... Journal of hazardous materials 384, 121448, 2020 | 22 | 2020 |
| PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning LM Oliveira Monteiro, JP Saraiva, R Brizola Toscan, PF Stadler, ... Environmental Microbiome 17 (1), 7, 2022 | 14 | 2022 |
| Mining synergistic microbial interactions: a roadmap on how to integrate multi-omics data JP Saraiva, A Worrich, C Karakoç, R Kallies, A Chatzinotas, F Centler, ... Microorganisms 9 (4), 840, 2021 | 13 | 2021 |
| Complementary roles of wood-inhabiting fungi and bacteria facilitate deadwood decomposition. mSystems 6 V Tláskal, V Brabcová, T Větrovský, M Jomura, R López-Mondéjar, ... | 13 | 2021 |
| Complementary roles of wood-inhabiting fungi and bacteria facilitate deadwood decomposition. mSystems, 6 (1), e01078-20 V Tláskal, V Brabcová, T Větrovský, M Jomura, R López-Mondéjar, ... | 13 | 2021 |
| Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes JP Saraiva, A Bartholomäus, RB Toscan, P Baldrian, U Nunes da Rocha Molecular Ecology Resources 23 (5), 1066-1076, 2023 | 11 | 2023 |
| MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes MK Nata’ala, AP Avila Santos, J Coelho Kasmanas, A Bartholomäus, ... Environmental Microbiome 17 (1), 57, 2022 | 11 | 2022 |
| Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood V Tláskal, V Brabcová, T Větrovský, R López-Mondéjar, LMO Monteiro, ... Scientific data 8 (1), 198, 2021 | 11 | 2021 |
| MuDoGeR: Multi-domain genome recovery from metagenomes made easy UN da Rocha, JC Kasmanas, R Kallies, JP Saraiva, RB Toscan, ... bioRxiv, 2022.06. 21.496983, 2022 | 8 | 2022 |
| Combining flow cytometry and metagenomics improves recovery of metagenome-assembled genomes in a cell culture from activated sludge N Abdulkadir, JP Saraiva, F Schattenberg, RB Toscan, F Borim Correa, ... Microorganisms 11 (1), 175, 2023 | 7 | 2023 |
| Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in … S Magnúsdóttir, JP Saraiva, A Bartholomäus, M Soheili, RB Toscan, ... Frontiers in Microbiology 14, 1037845, 2023 | 6 | 2023 |
| Combination of classifiers identifies fungal-specific activation of lysosome genes in human monocytes JP Leonor Fernandes Saraiva, C Zubiria-Barrera, TE Klassert, ... Frontiers in Microbiology 8, 2366, 2017 | 6 | 2017 |
| Fungal biomarker discovery by integration of classifiers JP Saraiva, M Oswald, A Biering, D Röll, C Assmann, T Klassert, M Blaess, ... BMC genomics 18, 1-11, 2017 | 5 | 2017 |
| Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge … N Abdulkadir, JP Saraiva, J Zhang, S Stolte, O Gillor, H Harms, U Rocha Microbiology spectrum 12 (3), e02918-23, 2024 | 4 | 2024 |