Lucas Paoli
Lucas Paoli
School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Space, time and microdiversity: towards a resolution revolution in microbiomics
L Paoli, S Sunagawa
Environmental microbiology reports 13 (1), 31, 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
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