Laura Eme

Publications

Article dans une revue (39)

Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors Brittany Baker,Charley Mccarthy,Purificación López-García,Romain Leroy,Edward Suskoet al. Nature Microbiology, 2025, 10 (7), pp.1593-1604. ⟨10.1038/s41564-025-02024-5⟩ Article dans une revue hal-05391319v1
Repeated duplications and losses shaped SMC complex evolution from archaeal ancestors to modern eukaryotes Jolien J.E. van Hooff,Maximilian W.D. Raas,Eelco Tromer,Laura Eme Cell Reports, 2025, 44 (7), pp.115855. ⟨10.1016/j.celrep.2025.115855⟩ Article dans une revue hal-05404770v1
Protist genomics: key to understanding eukaryotic evolution Alexandra Schoenle,Ore Francis,John M Archibald,Fabien Burki,Jan de Vrieset al. Trends in Genetics, 2025, 41 (10), pp.868-882. ⟨10.1016/j.tig.2025.05.004⟩ Article dans une revue hal-05404906v1
Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments Brittany Baker,Ana Gutiérrez-Preciado,Álvaro Rodríguez del Río,Charley Mccarthy,Purificación López-Garcíaet al. Nature Microbiology, 2024, 9 (4), pp.964-975. ⟨10.1038/s41564-024-01647-4⟩ Article dans une revue hal-04782651v1
Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines Ana Gutiérrez-Preciado,Bledina Dede,Brittany Baker,Laura Eme,David Moreiraet al. Nature Ecology & Evolution, 2024, 8 (10), pp.1856-1869. ⟨10.1038/s41559-024-02505-6⟩ Article dans une revue hal-04782858v1
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution Tom Williams,Adrian Davin,Lénárd Szánthó,Alexandros Stamatakis,Noah Wahlet al. The International Society of Microbiologial Ecology Journal, 2024, 18 (1), ⟨10.1093/ismejo/wrae129⟩ Article dans une revue hal-04796828v1
Microbial Diversity and Open Questions about the Deep Tree of Life Laura Eme,Daniel Tamarit Genome Biology and Evolution, 2024, 16 (4), ⟨10.1093/gbe/evae053⟩ Article dans une revue hal-04796832v1
Reconstructing the last common ancestor of all eukaryotes Thomas A Richards,Laura Eme,John M Archibald,Guy Leonard,Susana M Coelhoet al. PLoS Biology, 2024, 22 (11), pp.e3002917. ⟨10.1371/journal.pbio.3002917⟩ Article dans une revue hal-05391266v1
Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher Robert Jones,Alexander Tice,Marek Eliáš,Laura Eme,Martin Kolískoet al. Current Protocols, 2024, 4 (1), ⟨10.1002/cpz1.969⟩ Article dans une revue hal-04796821v1
One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade Jazmin Blaz,Luis Javier Galindo,Aaron Heiss,Harpreet Kaur,Guifré Torruellaet al. Scientific Data , 2023, 10 (1), pp.603. ⟨10.1038/s41597-023-02488-2⟩ Article dans une revue hal-04384869v1
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes Laura Eme,Daniel Tamarit,Eva F Caceres,Courtney W Stairs,Valerie de Andaet al. Nature, 2023, 618 (7967), pp.992-999. ⟨10.1038/s41586-023-06186-2⟩ Article dans une revue hal-04289789v1
Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria Lukáš V F Novák,Sebastian C Treitli,Jan Pyrih,Paweł Hałakuc,Shweta V Pipaliyaet al. PLoS Genetics, 2023, 19 (12), ⟨10.1371/journal.pgen.1011050⟩ Article dans une revue hal-04385954v2
Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida Naoji Yubuki,Guifré Torruella,Luis Javier Galindo,Aaron A Heiss,Maria Cristina Ciobanuet al. Journal of Eukaryotic Microbiology, 2023, 70 (6), pp.e12997. ⟨10.1111/jeu.12997⟩ Article dans une revue hal-04272301v1
Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria Sergio A Muñoz-Gómez,Edward Susko,Kelsey Williamson,Laura Eme,Claudio H. Slamovitset al. Nature Ecology & Evolution, 2022, 6, pp.253-262. ⟨10.1038/s41559-021-01638-2⟩ Article dans une revue hal-03847570v1
TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets Xi Zhang,Yining Hu,Laura Eme,Shinichiro Maruyama,Robert J.M. Eveleighet al. STAR Protocols, 2022, 3 (1), pp.101175. ⟨10.1016/j.xpro.2022.101175⟩ Article dans une revue hal-03800384v1
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses Daniel Tamarit,Eva F. Caceres,Mart Krupovic,Reindert Nijland,Laura Emeet al. Nature Microbiology, 2022, 7, pp.948-952. ⟨10.1038/s41564-022-01122-y⟩ Article dans une revue pasteur-03711310v1
Independent Size Expansions and Intron Proliferation in Red Algal Plastid and Mitochondrial Genomes Fabian van Beveren,Laura Eme,Purificación López-García,Maria Ciobanu,David Moreira Genome Biology and Evolution, 2022, 14 (4), ⟨10.1093/gbe/evac037⟩ Article dans une revue hal-03800403v1
Molecular characterization of the conoid complex in Toxoplasma reveals its conservation in all apicomplexans, including Plasmodium species Ludek Koreny,Mohammad Zeeshan,Konstantin Barylyuk,Eelco C Tromer,Jolien J E van Hooffet al. PLoS Biology, 2021, ⟨10.1371/journal.pbio.3001081⟩ Article dans une revue hal-03368636v1
The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba Vojtěch Žárský,Vladimír Klimeš,Jan Pačes,Čestmír Vlček,Miluše Hradilováet al. Molecular Biology and Evolution, 2021, 38 (6), pp.20. ⟨10.1093/molbev/msab020⟩ Article dans une revue hal-03368460v1
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships Alexander K. Tice,David Zihala,Tomáš Pánek,Robert E Jones,Eric D Salomakiet al. PLoS Biology, 2021, ⟨10.1371/journal.pbio.3001365⟩ Article dans une revue hal-03368434v2
Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes Courtney W Stairs,Petr Táborský,Eric D Salomaki,Martin Kolisko,Tomáš Páneket al. Current Biology, 2021, ⟨10.1016/j.cub.2021.10.010⟩ Article dans une revue hal-03461937v1
Releasing uncurated datasets is essential for reproducible phylogenomics Eric Salomaki,Laura Eme,Matthew Brown,Martin Kolisko Nature Ecology & Evolution, 2020, 4 (11), pp.1435-1437. ⟨10.1038/s41559-020-01296-w⟩ Article dans une revue hal-03368653v1
Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes Shannon Sibbald,Laura Eme,John Archibald,Andrew Roger Trends in Parasitology, 2020, 36 (11), pp.927-941. ⟨10.1016/j.pt.2020.07.014⟩ Article dans une revue hal-03368658v1
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution Courtney Stairs,Jennah Dharamshi,Daniel Tamarit,Laura Eme,Steffen Jørgensenet al. Science Advances , 2020, 6 (35), ⟨10.1126/sciadv.abb7258⟩ Article dans une revue hal-04384939v1
Marine Sediments Illuminate Chlamydiae Diversity and Evolution Jennah Dharamshi,Daniel Tamarit,Laura Eme,Courtney Stairs,Joran Martijnet al. Current Biology, 2020, 30 (6), pp.1032-+. ⟨10.1016/j.cub.2020.02.016⟩ Article dans une revue hal-03368662v1
Asgard archaea capable of anaerobic hydrocarbon cycling Kiley Seitz,Nina Dombrowski,Laura Eme,Anja Spang,Jonathan Lombardet al. Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-09364-x⟩ Article dans une revue hal-03368676v1
Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism Anja Spang,Courtney Stairs,Nina Dombrowski,Laura Eme,Jonathan Lombardet al. Nature Microbiology, 2019, 4 (7), pp.1138-1148. ⟨10.1038/s41564-019-0406-9⟩ Article dans une revue hal-03368673v1
A natural toroidal microswimmer with a rotary eukaryotic flagellum Sebastian Hess,Laura Eme,Andrew Roger,Alastair Simpson Nature Microbiology, 2019, 4 (10), pp.1620-1626. ⟨10.1038/s41564-019-0478-6⟩ Article dans une revue hal-03368670v1
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics Max E Schön,Laura Eme,Thijs J G Ettema Bioinformatics, 2019, ⟨10.1093/bioinformatics/btz799⟩ Article dans une revue hal-03368665v1
Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts Sergio Muñoz-Gómez,Keira Durnin,Laura Eme,Christopher Paight,Christopher Laneet al. Genome Biology and Evolution, 2019, ⟨10.1093/gbe/evz155⟩ Article dans une revue hal-03368668v1
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion Anna Karnkowska,Sebastian Treitli,Ondřej Brzoň,Lukáš Novák,Vojtěch Vaceket al. Molecular Biology and Evolution, 2019, 36 (10), pp.2292-2312. ⟨10.1093/molbev/msz147⟩ Article dans une revue hal-03368666v1
Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115) Michelle Leger,Laura Eme,Courtney Stairs,Andrew Roger BioEssays, 2018, 40 (5), pp.1700242. ⟨10.1002/bies.201700242⟩ Article dans une revue hal-03368697v1
Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids Ugo Cenci,Shannon Sibbald,Bruce Curtis,Ryoma Kamikawa,Laura Emeet al. BMC Biology, 2018, 16 (1), pp.137. ⟨10.1186/s12915-018-0593-5⟩ Article dans une revue hal-02046523v1
Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes Gordon Lax,Yana Eglit,Laura Eme,Erin Bertrand,Andrew Rogeret al. Nature, 2018, 564 (7736), pp.410-414. ⟨10.1038/s41586-018-0708-8⟩ Article dans une revue hal-03368693v1
The eukaryotic ancestor shapes up Laura Eme,Thijs Ettema Nature, 2018, 562 (7727), pp.352-353. ⟨10.1038/d41586-018-06868-2⟩ Article dans une revue hal-03368695v1
Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis Courtney Stairs,Laura Eme,Sergio Muñoz-Gómez,Alejandro Cohen,Graham Dellaireet al. eLife, 2018, 7, ⟨10.7554/eLife.34292⟩ Article dans une revue hal-03368699v1
Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis Eleni Gentekaki,Bruce Curtis,Courtney Stairs,Vladimír Klimeš,Marek Eliášet al. PLoS Biology, 2017, 15 (9), pp.e2003769. ⟨10.1371/journal.pbio.2003769⟩ Article dans une revue hal-01802863v1
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated Mathieu Groussin,Bastien Boussau,Gergely J Szollosi,Laura Eme,Manolo Gouyet al. Molecular Biology and Evolution, 2016, 33 (2), pp.305 - 310. ⟨10.1093/molbev/msv249⟩ Article dans une revue hal-01913926v1
A Complex Cell Division Machinery Was Present in the Last Common Ancestor of Eukaryotes Laura Eme,David Moreira,Emmanuel Talla,Céline Brochier-Armanet PLoS ONE, 2009, 4 (4), pp.e5021. ⟨10.1371/journal.pone.0005021⟩ Article dans une revue hal-03368340v1

Chapitre d'ouvrage (1)

Archaea Nina Dombrowski,Tara Mahendrarajah,Sarah T Gross,Laura Eme,Anja Spang Lorrence H Green, Emanuel Goldman. Practical Handbook of Microbiology, CRC Press, 2021, 9780367567644. ⟨10.1201/9781003099277⟩ Chapitre d'ouvrage hal-03368633v1

Pré-publication, Document de travail (10)

A robustly rooted tree of eukaryotes reveals their excavate ancestry Kelsey Williamson,Laura Eme,Hector Baños,Charley Mccarthy,Edward Suskoet al. 2024 Pré-publication, Document de travail hal-04796810v1
Shaping up genomes: Prokaryotic roots and eukaryotic diversification of SMC complexes Jolien J.E. van Hooff,Maximilian W.D. Raas,Eelco Tromer,Laura Eme 2024 Pré-publication, Document de travail hal-04796815v1
Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta Lukas Novak,Sergio Muñoz-Gómez,Fabian van Beveren,Maria Ciobanu,Laura Emeet al. 2024 Pré-publication, Document de travail hal-04796817v1
Molecular and morphological characterisation of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida Naoji Yubuki,Guifré Torruella,Luis Javier Galindo,Aaron A Heiss,Maria Cristina Ciobanuet al. 2023 Pré-publication, Document de travail hal-04289805v1
Several independent adaptations of archaea to hypersaline environments Brittany A Baker,Ana Gutiérrez-Preciado,Álvaro Rodríguez del Río,Charley G P Mccarthy,Purificación López-Garcíaet al. 2023 Pré-publication, Document de travail hal-04289833v1
Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching Guillaume Tahon,Stephan Köstlbacher,Erik Pelve,Brett Baker,Jimmy Sawet al. 2024 Pré-publication, Document de travail hal-04796819v1
High quality genome and transcriptome data for two new species of Mantamonas, a deep-branching eukaryote clade Jazmin Blaz,Luis Javier Galindo,Aaron A Heiss,Harpreet Kaur,Guifré Torruellaet al. 2023 Pré-publication, Document de travail hal-04289757v1
Lateral gene transfer leaves lasting traces in Rhizaria Jolien J.E. van Hooff,Laura Eme 2023 Pré-publication, Document de travail hal-04289849v1
A site-and-branch-heterogeneous model on an expanded dataset favor mitochondria as sister to known Alphaproteobacteria Sergio A Muñoz-Gómez,Edward Susko,Kelsey Williamson,Laura Eme,Claudio Slamovitset al. 2021 Pré-publication, Document de travail hal-03368518v1
A closed Candidatus Odinarchaeum genome exposes Asgard archaeal viruses Daniel Tamarit,Eva F Caceres,Mart Krupovic,Reindert Nijland,Laura Emeet al. 2021 Pré-publication, Document de travail hal-03368645v1

Thèse (1)

Phylogénomique des structures multiprotéiques eucaryotes impliquées dans le cycle cellulaire et contribution à la phylogénie des eucaryotes. Laura Eme Evolution [q-bio.PE]. Université de la Méditerranée, 2011. Français. ⟨NNT : ⟩ Thèse tel-03368378v1