SARS-CoV-2 lineage-dependent temporal phylogenetic distribution and viral load in immunocompromised and immunocompetent individuals K Zafilaza, A Fauchois, V Leducq, R Coppée, R Guilbaud, AMF Yusti, ... Virology Journal 22 (1), 118 , 2025 2025
CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure L Chivot, N Mathieux, A Cosson, A Bridier-Nahmias, L Favennec, JC Gelly, ... Bioinformatics 41 (4), btaf166 , 2025 2025 Citations: 3
Genomic evidence of Escherichia coli gut population diversity translocation in leukemia patients J Marin, V Walewski, T Braun, S Dziri, M Magnan, E Denamur, ... Msphere 9 (10), e00530-24 , 2024 2024
Viral whole genome sequencing reveals high variations in APOBEC3 editing between HPV risk categories VM Ferré, R Coppée, FA Gbeasor‐Komlanvi, S Vacher, ... Journal of Medical Virology 96 (10), e70002 , 2024 2024 Citations: 1
Variability in cell division among anatomical sites shapes Escherichia coli antibiotic survival in a urinary tract infection mouse model A Amoura, C Pistien, C Chaligné, S Dion, M Magnan, A Bridier-Nahmias, ... Cell host & microbe 32 (6), 900-912. e4 , 2024 2024 Citations: 5
Higher levels of SARS-CoV-2 genetic variation in immunocompromised patients: a retrospective case-control study R Guilbaud, AM Franco Yusti, V Leducq, K Zafilaza, A Bridier-Nahmias, ... The Journal of Infectious Diseases 229 (4), 1041-1049 , 2024 2024 Citations: 11
Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases C D’humières, M Delavy, L Alla, F Ichou, E Gauliard, A Ghozlane, ... Microbiome 12 (1), 50 , 2024 2024 Citations: 21
Escherichia coli extra-intestinal population translocation in leukemia patients J Marin, V Walewski, S Dziri, M Magnan, E Denamur, E Carbonnelle, ... bioRxiv, 2024.01. 26.577459 , 2024 2024
Towards the reconstruction of a global TB history using a new pipeline “TB-Annotator G Senelle, MR Sahal, K La, T Billard-Pomares, J Marin, F Mougari, ... Tuberculosis 143, 102376 , 2023 2023 Citations: 6
Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger H Jacquier, B Assao, F Chau, O Guindo, B Condamine, M Magnan, ... Journal of Infection 87 (3), 199-209 , 2023 2023 Citations: 9
Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020 R Coppée, F Blanquart, A Jary, V Leducq, VM Ferré, AM Franco Yusti, ... Elife 12, e82538 , 2023 2023 Citations: 8
Perturbation and resilience of the gut microbiome up to three months after β-lactams exposure in healthy volunteers suggest an important role of endogenous β-lactamases C d'Humières, M Delavy, L Alla, F Ichou, A Ghozlane, F Levenez, ... 2023
Temporal dynamics of RSV shedding and genetic diversity in adults during the COVID-19 pandemic in a French hospital, early 2021 R Coppée, HR Chenane, A Bridier-Nahmias, C Tcherakian, E Catherinot, ... Virus research 323, 198950 , 2023 2023 Citations: 13
Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation J Do Vale, D Roux, A Bridier Nahmias, M Salmona, S Mercier-Delarue, ... F1000Research 11, 1246 , 2022 2022
Phylodynamics of SARS-CoV-2 transmissions in France, Europe and the world during 2020 R Coppée, F Blanquart, A Jary, V Leducq, VM Ferré, AM Franco Yusti, ... medRxiv, 2022.08. 10.22278636 , 2022 2022 Citations: 2
Faecal carriage of ESBL-producing Escherichia coli in a remote region of Niger H Jacquier, B Assao, F Chau, O Guindo, B Condamine, M Magnan, ... bioRxiv, 2022.07. 07.499258 , 2022 2022 Citations: 2
Modeling the bacterial dynamics in the gut microbiota following an antibiotic‐induced perturbation J Guk, A Bridier‐Nahmias, M Magnan, N Grall, X Duval, O Clermont, ... CPT: Pharmacometrics & Systems Pharmacology 11 (7), 906-918 , 2022 2022 Citations: 7
The growing chaos of tuberculosis population genomics at the era of'Big Data’: sorting out the wheat from the chaff C Sola, G Senelle, K La, T Billard-Pomares, J Marin, A Bridier-Nahmias, ... Annual Congress of the European Society of Mycobacteriology , 2022 2022 Citations: 1
Microbiome pulmonaire et pneumonie acquise sous ventilation mécanique M Fromentin, J Mullaert, A Bridier-Nahmias, S Mercier-Delarue, J Do Vale, ... Médecine et Maladies Infectieuses Formation 1 (2), S13 , 2022 2022
Azithromycin Resistance in Shiga Toxin-Producing Escherichia coli in France between 2004 and 2020 and Detection of mef (C)- mph (G) Genes E Bizot, A Cointe, P Bidet, P Mariani-Kurkdjian, CA Hobson, C Courroux, ... Antimicrobial Agents and Chemotherapy 66 (2), e01949-21 , 2022 2022 Citations: 8
MOST CITED SCHOLAR PUBLICATIONS
ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping J Beghain, A Bridier-Nahmias, H Le Nagard, E Denamur, O Clermont Microbial genomics 4 (7), e000192 , 2018 2018 Citations: 712
Characterization and rapid identification of phylogroup G in Escherichia coli , a lineage with high virulence and antibiotic resistance potential O Clermont, OVA Dixit, B Vangchhia, B Condamine, S Dion, ... Environmental microbiology 21 (8), 3107-3117 , 2019 2019 Citations: 318
JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs G Beauclair, A Bridier-Nahmias, JF Zagury, A Saïb, A Zamborlini Bioinformatics 31 (21), 3483-3491 , 2015 2015 Citations: 236
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectiousness among three immunocompromised patients: from prolonged viral shedding to SARS-CoV-2 … H Tarhini, A Recoing, A Bridier-Nahmias, M Rahi, C Lambert, P Martres, ... The Journal of infectious diseases 223 (9), 1522-1527 , 2021 2021 Citations: 186
An RNA polymerase III subunit determines sites of retrotransposon integration A Bridier-Nahmias, A Tchalikian-Cosson, JA Baller, R Menouni, H Fayol, ... Science 348 (6234), 585-588 , 2015 2015 Citations: 95
Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size M Ghalayini, A Launay, A Bridier-Nahmias, O Clermont, E Denamur, ... Applied and environmental microbiology 84 (6), e02377-17 , 2018 2018 Citations: 86
Ceftriaxone and cefotaxime have similar effects on the intestinal microbiota in human volunteers treated by standard-dose regimens C Burdet, N Grall, M Linard, A Bridier-Nahmias, M Benhayoun, ... Antimicrobial agents and chemotherapy 63 (6), 10.1128/aac. 02244-18 , 2019 2019 Citations: 72
Emergence of E484K mutation following bamlanivimab monotherapy among high-risk patients infected with the alpha variant of SARS-CoV-2 N Peiffer-Smadja, A Bridier-Nahmias, VM Ferré, C Charpentier, M Garé, ... Viruses 13 (8), 1642 , 2021 2021 Citations: 58
Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress G Servant, B Pinson, A Tchalikian-Cosson, F Coulpier, S Lemoine, ... Nucleic acids research 40 (12), 5271-5282 , 2012 2012 Citations: 52
Escherichia coli O80 hybrid pathotype strains producing Shiga toxin and ESBL: molecular characterization and potential therapeutic options A Cointe, A Birgy, A Bridier-Nahmias, P Mariani-Kurkdjian, V Walewski, ... Journal of Antimicrobial Chemotherapy 75 (3), 537-542 , 2020 2020 Citations: 24
Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases C D’humières, M Delavy, L Alla, F Ichou, E Gauliard, A Ghozlane, ... Microbiome 12 (1), 50 , 2024 2024 Citations: 21
Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targets nucleosomal DNA near the H2A/H2B interface A Bridier-Nahmias, P Lesage Mobile DNA 3 (1), 22 , 2012 2012 Citations: 16
Escherichia coli genomic diversity within extraintestinal acute infections argues for adaptive evolution at play A Bridier-Nahmias, A Launay, A Bleibtreu, M Magnan, V Walewski, ... MSphere 6 (1), 10.1128/msphere. 01176-20 , 2021 2021 Citations: 15
Temporal dynamics of RSV shedding and genetic diversity in adults during the COVID-19 pandemic in a French hospital, early 2021 R Coppée, HR Chenane, A Bridier-Nahmias, C Tcherakian, E Catherinot, ... Virus research 323, 198950 , 2023 2023 Citations: 13
Higher levels of SARS-CoV-2 genetic variation in immunocompromised patients: a retrospective case-control study R Guilbaud, AM Franco Yusti, V Leducq, K Zafilaza, A Bridier-Nahmias, ... The Journal of Infectious Diseases 229 (4), 1041-1049 , 2024 2024 Citations: 11
Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger H Jacquier, B Assao, F Chau, O Guindo, B Condamine, M Magnan, ... Journal of Infection 87 (3), 199-209 , 2023 2023 Citations: 9
Nosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020 V Leducq, A Jary, A Bridier-Nahmias, L Daniel, K Zafilaza, F Damond, ... Scientific reports 12 (1), 1094 , 2022 2022 Citations: 9
Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020 R Coppée, F Blanquart, A Jary, V Leducq, VM Ferré, AM Franco Yusti, ... Elife 12, e82538 , 2023 2023 Citations: 8
Azithromycin Resistance in Shiga Toxin-Producing Escherichia coli in France between 2004 and 2020 and Detection of mef (C)- mph (G) Genes E Bizot, A Cointe, P Bidet, P Mariani-Kurkdjian, CA Hobson, C Courroux, ... Antimicrobial Agents and Chemotherapy 66 (2), e01949-21 , 2022 2022 Citations: 8
Modeling the bacterial dynamics in the gut microbiota following an antibiotic‐induced perturbation J Guk, A Bridier‐Nahmias, M Magnan, N Grall, X Duval, O Clermont, ... CPT: Pharmacometrics & Systems Pharmacology 11 (7), 906-918 , 2022 2022 Citations: 7
