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Alexandre Almeida
Researcher at European Bioinformatics Institute
Publications - 70
Citations - 3504
Alexandre Almeida is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Metagenomics & Microbiome. The author has an hindex of 17, co-authored 57 publications receiving 1677 citations. Previous affiliations of Alexandre Almeida include Pierre-and-Marie-Curie University & Wellcome Trust Sanger Institute.
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Journal ArticleDOI
A new genomic blueprint of the human gut microbiota
Alexandre Almeida,Alex L. Mitchell,Miguel Boland,Samuel C. Forster,Gregory B. Gloor,Aleksandra Tarkowska,Trevor D. Lawley,Robert D. Finn +7 more
TL;DR: The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.
Journal ArticleDOI
A unified catalog of 204,938 reference genomes from the human gut microbiome.
Alexandre Almeida,Alexandre Almeida,Stephen Nayfach,Stephen Nayfach,Miguel Boland,Francesco Strozzi,Martin Beracochea,Zhou Jason Shi,Katherine S. Pollard,Ekaterina A. Sakharova,Donovan H. Parks,Philip Hugenholtz,Nicola Segata,Nikos C. Kyrpides,Nikos C. Kyrpides,Robert D. Finn +15 more
TL;DR: The Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes, is presented, providing comprehensive resources for microbiome researchers.
Journal ArticleDOI
A human gut bacterial genome and culture collection for improved metagenomic analyses.
Samuel C. Forster,Samuel C. Forster,Samuel C. Forster,Nitin Kumar,Blessing O. Anonye,Blessing O. Anonye,Alexandre Almeida,Alexandre Almeida,Elisa Viciani,Mark D. Stares,Matthew Dunn,Tapoka T. Mkandawire,Ana Zhu,Yan Shao,Lindsay J. Pike,Thomas J. Louie,Hilary P. Browne,Alex L. Mitchell,B. Anne Neville,Robert D. Finn,Trevor D. Lawley +20 more
TL;DR: The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.
Journal ArticleDOI
MGnify: the microbiome analysis resource in 2020
Alex L. Mitchell,Alexandre Almeida,Alexandre Almeida,Martin Beracochea,Miguel Boland,Josephine Burgin,Guy Cochrane,Michael R. Crusoe,Varsha Kale,Simon C. Potter,Lorna Richardson,Ekaterina A. Sakharova,Maxim Scheremetjew,Anton Korobeynikov,Alexander Shlemov,Olga Kunyavskaya,Alla Lapidus,Robert D. Finn +17 more
TL;DR: An updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility.
Journal ArticleDOI
Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese,Daniel R. Mende,Lucas Paoli,Guillem Salazar,Hans-Joachim Ruscheweyh,Miguelangel Cuenca,Pascal Hingamp,Renato J. Alves,Paul I. Costea,Luis Pedro Coelho,Thomas Schmidt,Alexandre Almeida,Alex L. Mitchell,Robert D. Finn,Jaime Huerta-Cepas,Peer Bork,Georg Zeller,Shinichi Sunagawa +17 more
TL;DR: mOTUs2, an updated and functionally extended profiling tool for microbial abundance, activity and population profiling, shows that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members.