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Mathieu Almeida · SciRah

Researcher profile · Semantic Scholar

Mathieu Almeida

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Mathieu Almeida — researcher profile on SciRah

h-index: 17
Works: 47
Citations: 13K

Most-cited papers

A metagenome-wide association study of gut microbiota in type 2 diabetes
J. Qin, Ying-Rui Li, Zhi-Ming Cai, Sheng-Hui Li +52 more
2012Nature6,309 citations Open access
Semantic Scholar
Richness of human gut microbiome correlates with metabolic markers
Emmanuelle Le Chatelier, T. Nielsen, J. Qin, Edi Prifti +37 more
2013Nature4,349 citations Open access
Semantic Scholar
Dietary intervention impact on gut microbial gene richness
Aurélie Cotillard, S. Kennedy, L. Kong, Edi Prifti +14 more
2013Nature1,735 citations
Semantic Scholar
Microbial ecology perturbation in human IgA deficiency
J. Fadlallah, Hela El Kafsi, D. Sterlin, C. Juste +24 more
2018Science Translational Medicine268 citations Open access
Semantic Scholar
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data
Florian Plaza Oñate, E. Le Chatelier, Mathieu Almeida, Alessandra C. L. Cervino +4 more
2017bioRxiv114 citations Open access
Semantic Scholar
Benchmarking second and third-generation sequencing platforms for microbial metagenomics
V. Meslier, B. Quinquis, K. Da Silva, Florian Plaza Oñate +4 more
2022Scientific Data93 citations Open access
Semantic Scholar
Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products
Mathieu Almeida, Agnès Hébert, Anne-Laure Abraham, Simon Rasmussen +12 more
2014BMC Genomics74 citations Open access
Semantic Scholar
Comparative methods for fecal sample storage to preserve gut microbial structure and function in an in vitro model of the human colon
C. Deschamps, E. Fournier, O. Uriot, Frédérique Lajoie +9 more
2020Applied Microbiology and Biotechnology60 citations
Semantic Scholar
The Bacterial and Viral Complexity of Postinfectious Hydrocephalus in Uganda
J. Paulson, Brent L. Williams, C. Hehnly, N. Mishra +48 more
2020Science Translational Medicine44 citations Open access
Semantic Scholar
Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM8232
C. Delorme, Claire Bartholini, M. Luraschi, N. Pons +5 more
2011Journal of Bacteriology40 citations Open access
Semantic Scholar
Accurate taxonomy assignments in cheeses ecosystems via a metagenomic approach
Charlie Pauvert, Anne-Laure Abraham, Mathieu Almeida, N. Pons +4 more
201535 citations Open access
Semantic Scholar
Global compositional and functional states of the human gut microbiome in health and disease
Sunjae Lee, T. Portlock, E. Le Chatelier, F. Garcia-Guevara +29 more
2024Genome Research34 citations Open access
Semantic Scholar
MetaCompass: Reference-guided Assembly of Metagenomes
Tu Luan, V. Cepeda, Bo Liu, Z. Bowen +7 more
2017bioRxiv34 citations Open access
Semantic Scholar
Transient colonizing microbes promote gut dysbiosis and functional impairment
Sunjae Lee, V. Meslier, G. Bidkhori, F. Garcia-Guevara +20 more
2024npj Biofilms and Microbiomes33 citations Open access
Semantic Scholar
Cross talk between Paneth and tuft cells drives dysbiosis and inflammation in the gut mucosa
Nathalie Coutry, Julie Nguyen, Salima Soualhi, F. Gerbe +21 more
2023Proceedings of the National Academy of Sciences of the United States of America29 citations Open access
Semantic Scholar
Complete Genome Sequence of the Commensal Streptococcus salivarius Strain JIM8777
É. Guédon, C. Delorme, N. Pons, C. Cruaud +13 more
2011Journal of Bacteriology20 citations Open access
Semantic Scholar
Corrigendum: Dietary intervention impact on gut microbial gene richness
Aurélie Cotillard, S. Kennedy, L. Kong, Edi Prifti +15 more
2013Nature18 citations Open access
Semantic Scholar
In Vitro Modelling of Oral Microbial Invasion in the Human Colon
L. Etienne-Mesmin, V. Meslier, O. Uriot, E. Fournier +12 more
2022bioRxiv17 citations Open access
Semantic Scholar
The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism
G. Bidkhori, Sunjae Lee, L. Edwards, E. Le Chatelier +11 more
2021bioRxiv11 citations Open access
Semantic Scholar
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs
K. Da Silva, N. Pons, M. Berland, Florian Plaza Oñate +2 more
2021bioRxiv10 citations Open access
Semantic Scholar
Complete Genome Sequences of the Human Pathogen Paenibacillus thiaminolyticus Mbale and Type Strain P. thiaminolyticus NRRL B-4156
C. Hehnly, Li-Jun Zhang, J. Paulson, Mathieu Almeida +6 more
2020Microbiology Resource Announcements10 citations Open access
Semantic Scholar
Capturing the most wanted taxa through cross-sample correlations
Mathieu Almeida, Mihai Pop, E. Le Chatelier, Edi Prifti +3 more
2016The ISME Journal9 citations Open access
Semantic Scholar
Recovery of Metagenome-Assembled Genomes from a Human Fecal Sample with Pacific Biosciences High-Fidelity Sequencing
Florian Plaza Oñate, H. Roume, Mathieu Almeida
2022Microbiology Resource Announcements8 citations Open access
Semantic Scholar
Privacy-Preserving Federated Survival Support Vector Machines for Cross-Institutional Time-To-Event Analysis: Algorithm Development and Validation
Julian Späth, Zeno Sewald, Niklas Probul, M. Berland +8 more
2024JMIR AI7 citations Open access
Semantic Scholar
Global and temporal state of the human gut microbiome in health and disease
S. Shoaie, Sunjae Lee, Mathieu Almeida, G. Bidkhori +28 more
20217 citations Open access
Semantic Scholar
The Bacterial and Viral Complexity of Postinfectious Hydrocephalus in Uganda
J. Paulson, Brent L. Williams, C. Hehnly, N. Mishra +48 more
2020medRxiv7 citations Open access
Semantic Scholar
Complete Genome Sequence of the Clinical Streptococcus salivarius Strain CCHSS3
C. Delorme, É. Guédon, N. Pons, C. Cruaud +12 more
2011Journal of Bacteriology7 citations Open access
Semantic Scholar
Bacterial Consumption of T4 Phages
J. Godon, Ariane Bize, Hoang Ngo, L. Cauquil +3 more
2021Microorganisms6 citations Open access
Semantic Scholar
Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut – Le Microbiote Français Study
Chloe Connan, S. Fromentin, M. Benallaoua, Anne-Sophie Alvarez +14 more
2024JMIR Research Protocols5 citations Open access
Semantic Scholar
Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products
Mathieu Almeida, Agnès Hébert, Anne-Laure Abraham, S. Rasmussen +12 more
2014BMC Genomics5 citations Open access
Semantic Scholar
Complete Genome Sequence of the Pigmented Streptococcus thermophilus Strain JIM 8232
C. Delorme, Claire Bartholini, M. Luraschi, N. Pons +5 more
20114 citations
Semantic Scholar
Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics
V. Meslier, E. Menozzi, A. David, C. Morabito +10 more
2023Biomolecules2 citations Open access
Semantic Scholar
High-Throughput Sequencing as a Tool for Exploring the Human Microbiome
Mathieu Almeida, Mihai Pop
20152 citations
Semantic Scholar
A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning
H. Nielsen, Mathieu Almeida, A. Juncker, Simon Rasmussen +4 more
20142 citations
Semantic Scholar
From genomics to metagenomics: benchmark of variation graphs
K. Da Silva, N. Pons, M. Berland, F. Oñate +2 more
20191 citations
Semantic Scholar
Complete Genome Sequence of the Clinical Streptococcus salivarius Strain CCHSS 3
C. Delorme, É. Guédon, N. Pons, C. Cruaud +12 more
20111 citations
Semantic Scholar
Multi-center Medical Data Mining with FL-Net - A One-stop Shop for Federated Learning
Simon Süwer, Juliane Klemm, E. Acitelli, Mathieu Almeida +38 more
20260 citations
Semantic Scholar
Fedflow: cloud orchestration for federated learning with the FeatureCloud platform
Lukas Weilguny, Niklas Probul, Ya-Ni Ren, Nicolas Pons +2 more
2026Bioinformatics Advances0 citations Open access
Semantic Scholar
Enhanced Computational and Experimental Approaches for Comparative Analysis of the Human Mycobiome
Neelu Begum, Sunjae Lee, Mathieu Almeida, Lars Engstrand +5 more
2025bioRxiv0 citations Open access
Semantic Scholar
Correction: Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut – Le Microbiote Français Study
Chloe Connan, S. Fromentin, M. Benallaoua, Anne-Sophie Alvarez +14 more
2025JMIR Research Protocols0 citations Open access
Semantic Scholar
Transient Colonising Microbes Promote Gut Dysbiosis and Disease Pathology
Sunjae Lee, V. Meslier, G. Bidkhori, L. Etienne-Mesmin +14 more
2022Social Science Research Network0 citations Open access
Semantic Scholar
Bacterial predation on T4 phages
J. Godon, Ariane Bize, Hoang Ngo, L. Cauquil +3 more
2021bioRxiv0 citations Open access
Semantic Scholar
Reference-guided Assembly of Metagenomic Sequences
V. Cepeda, Bo Liu, Mathieu Almeida, C. Hill +1 more
20160 citations
Semantic Scholar
A shotgun metagenomic method to characterise low abundant species and assign precisely taxonomy in complex microbial ecosystems
Anne-Laure Abraham, Mathieu Almeida, N. Pons, Charlie Pauvert +3 more
2014European Conference on Computational Biology0 citations
Semantic Scholar
1363 CHARACTERIZATION OF THE GUT MICROBIOTA BY QUANTITATIVE METAGENOMICS: A PROMISING TOOL FOR RISK STRATIFICATION IN NAFLD PATIENTS
V. Ratziu, M. Pichaud, L. Fedchuk, F. Levenez +9 more
20130 citations Open access
Semantic Scholar
Prevalence of streptococci in the intestinal flora
Mathieu Almeida, N. Pons, E. Achouri, Séverine Layec +8 more
20120 citations
Semantic Scholar
Complete Genome Sequence of the Clinical Streptococcus salivarius Strain CCHSS3 (cid:1)
C. Delorme, É. Guédon, N. Pons, C. Cruaud +12 more
20110 citations
Semantic Scholar

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