| Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii S Miquel, M Leclerc, R Martin, F Chain, M Lenoir, S Raguideau, S Hudault, ... MBio 6 (2), 10.1128/mbio. 00300-15, 2015 | 260 | 2015 |
| DESMAN: a new tool for de novo extraction of strains from metagenomes C Quince, TO Delmont, S Raguideau, J Alneberg, AE Darling, G Collins, ... Genome biology 18, 1-22, 2017 | 184 | 2017 |
| STRONG: metagenomics strain resolution on assembly graphs C Quince, S Nurk, S Raguideau, R James, OS Soyer, JK Summers, ... Genome biology 22, 1-34, 2021 | 90 | 2021 |
| Gene duplication drives genome expansion in a major lineage of Thaumarchaeota PO Sheridan, S Raguideau, C Quince, J Holden, L Zhang, ... Nature communications 11 (1), 5494, 2020 | 64 | 2020 |
| Population-level impacts of antibiotic usage on the human gut microbiome K Lee, S Raguideau, K Sirén, F Asnicar, F Cumbo, F Hildebrand, ... Nature Communications 14 (1), 1191, 2023 | 38 | 2023 |
| Impact of sulfamethoxazole on a riverine microbiome C Borsetto, S Raguideau, E Travis, DW Kim, DH Lee, A Bottrill, R Stark, ... Water Research 201, 117382, 2021 | 23 | 2021 |
| Inferring aggregated functional traits from metagenomic data using constrained non-negative matrix factorization: Application to fiber degradation in the human gut microbiota S Raguideau, S Plancade, N Pons, M Leclerc, B Laroche PLoS computational biology 12 (12), e1005252, 2016 | 19 | 2016 |
| Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere G Muscatt, S Hilton, S Raguideau, G Teakle, IDEA Lidbury, ... Microbiome 10 (1), 181, 2022 | 18 | 2022 |
| High-quality metagenome assembly from long accurate reads with metaMDBG G Benoit, S Raguideau, R James, AM Phillippy, R Chikhi, C Quince Nature Biotechnology, 1-6, 2024 | 11 | 2024 |
| Stimulation of distinct rhizosphere bacteria drives phosphorus and nitrogen mineralization in oilseed rape under field conditions IDEA Lidbury, S Raguideau, C Borsetto, ARJ Murphy, A Bottrill, S Liu, ... Msystems 7 (4), e00025-22, 2022 | 11 | 2022 |
| De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning C Quince, S Connelly, S Raguideau, J Alneberg, SG Shin, G Collins, ... BioRxiv, 073825, 2016 | 8 | 2016 |
| Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium prausnitzii. mBio 6: e00300-15 S Miquel, M Leclerc, R Martin, F Chain, M Lenoir, S Raguideau, S Hudault, ... | 8 | 2015 |
| Efficient high-quality metagenome assembly from long accurate reads using minimizer-space de Bruijn graphs G Benoit, S Raguideau, R James, AM Phillippy, R Chikhi, C Quince bioRxiv, 2023 | 7 | 2023 |
| Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Commun 11: 5494 PO Sheridan, S Raguideau, C Quince, J Holden, L Zhang, C Thames, ... | 7 | 2020 |
| Reproducible spatial structure formation and stable community composition in the cyanosphere predicts metabolic interactions SJ Duxbury, S Raguideau, J Rosko, K Cremin, M Coates, C Quince, ... | 5* | 2022 |
| Four functional profiles for fibre and mucin metabolism in the human gut microbiome S Labarthe, S Plancade, S Raguideau, F Plaza Oñate, E Le Chatelier, ... Microbiome 11 (1), 231, 2023 | 2 | 2023 |
| Novel microbial syntrophies identified by longitudinal metagenomics S Raguideau, A Trego, F Farrell, G Collins, C Quince, OS Soyer BioRxiv, 2021.07. 05.451125, 2021 | 2 | 2021 |
| Impact of trimethoprim on the river microbiome and antimicrobial resistance J Delaney, S Raguideau, J Holden, L Zhang, HJ Tipper, GL Hill, ... bioRxiv, 2020.06. 05.133348, 2020 | 2 | 2020 |
| Metagenomics Strain Resolution on Assembly Graphs. preprint C Quince, S Nurk, S Raguideau, R James, OS Soyer, JK Summers, ... Bioinformatics, September, 2020 | 2 | 2020 |
| Meta-exoproteomics identifies active plant-microbe interactions operating in the rhizosphere IDEA Lidbury, S Raguideau, S Liu, ARJ Murphy, R Stark, C Borsetto, ... bioRxiv, 2021.09. 01.458574, 2021 | 1 | 2021 |
