| 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 | 371 | 2019 |
| Gene expression changes and community turnover differentially shape the global ocean metatranscriptome G Salazar*, L Paoli*, A Alberti, J Huerta-Cepas, HJ Ruscheweyh, ... Cell 179 (5), 1068-1083. e21, 2019 | 294 | 2019 |
| Critical assessment of metagenome interpretation: the second round of challenges F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ... Nature methods 19 (4), 429-440, 2022 | 209 | 2022 |
| Biosynthetic potential of the global ocean microbiome L Paoli, HJ Ruscheweyh, CC Forneris, F Hubrich, S Kautsar, A Bhushan, ... Nature 607 (7917), 111–118, 2022 | 183 | 2022 |
| Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities SG Acinas, P Sánchez, G Salazar, FM Cornejo-Castillo, M Sebastián, ... Communications Biology 4 (1), 604, 2021 | 134* | 2021 |
| metaSNV: a tool for metagenomic strain level analysis PI Costea, R Munch, LP Coelho, L Paoli, S Sunagawa, P Bork PloS one 12 (7), e0182392, 2017 | 107 | 2017 |
| proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes DR Mende, I Letunic, OM Maistrenko, TSB Schmidt, A Milanese, L Paoli, ... Nucleic acids research 48 (D1), D621-D625, 2020 | 90 | 2020 |
| Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes RG Dorrell, T Azuma, M Nomura, G Audren de Kerdrel, L Paoli, S Yang, ... Proceedings of the National Academy of Sciences 116 (14), 6914-6923, 2019 | 87 | 2019 |
| Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean M Royo-Llonch, P Sánchez, C Ruiz-González, G Salazar, C Pedrós-Alió, ... Nature Microbiology 6 (12), 1561-1574, 2021 | 79* | 2021 |
| Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments HJ Ruscheweyh, A Milanese, L Paoli, N Karcher, Q Clayssen, MI Keller, ... Microbiome 10 (1), 212, 2022 | 30* | 2022 |
| Functional and evolutionary significance of unknown genes from uncultivated taxa Á Rodríguez del Río, J Giner-Lamia, CP Cantalapiedra, J Botas, Z Deng, ... Nature 626 (7998), 377-384, 2024 | 25 | 2024 |
| Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends CM Klinger, L Paoli, RJ Newby, MYW Wang, HD Carroll, JD Leblond, ... Genome biology and evolution 10 (4), 1019-1038, 2018 | 25 | 2018 |
| Phylogenetic estimation of community composition and novel eukaryotic lineages in Base Mine Lake: an oil sands tailings reclamation site in Northern Alberta E Richardson, D Bass, A Smirnova, L Paoli, P Dunfield, JB Dacks journal of eukaryotic microbiology 67 (1), 86-99, 2020 | 21 | 2020 |
| Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean C Hochart, L Paoli, HJ Ruscheweyh, G Salazar, E Boissin, S Romac, ... Nature Communications 14 (1), 3037, 2023 | 19 | 2023 |
| mOTUs: profiling taxonomic composition, transcriptional activity and strain populations of microbial communities HJ Ruscheweyh, A Milanese, L Paoli, A Sintsova, DR Mende, G Zeller, ... Current Protocols 1 (8), e218, 2021 | 17 | 2021 |
| 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 | 11 | 2022 |
| The defensome of complex bacterial communities A Beavogui, A Lacroix, N Wiart, J Poulain, TO Delmont, L Paoli, P Wincker, ... Nature Communications 15 (1), 2146, 2024 | 3 | 2024 |
| Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster Y Liu, T Brinkhoff, M Berger, A Poehlein, S Voget, L Paoli, S Sunagawa, ... Microbiome 11 (1), 265, 2023 | 3 | 2023 |
| Space, time and microdiversity: towards a resolution revolution in microbiomics L Paoli, S Sunagawa Environmental microbiology reports 13 (1), 31, 2021 | 2 | 2021 |
| Animal-associated marine Acidobacteria with a rich natural-product repertoire S Leopold-Messer, C Chepkirui, MFJ Mabesoone, J Meyer, L Paoli, ... Chem 9 (12), 3696-3713, 2023 | | 2023 |
