Laura Eme

Publications

• Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
• Symbiosis in the microbial world: from ecology to genome evolution
• Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis
• Asgard archaea are the closest prokaryotic relatives of eukaryotes
• Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017
• Lateral gene transfer leaves lasting traces in Rhizaria
• Marine Sediments Illuminate Chlamydiae Diversity and Evolution
• A natural toroidal microswimmer with a rotary eukaryotic flagellum
• The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion
• The symbiosis that changed the world
• Archaea and the origin of eukaryotes
• Archaea
• A closed Candidatus Odinarchaeum genome exposes Asgard archaeal viruses
• Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes.
• Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids
• The eukaryotic ancestor shapes up
• Asgard archaea capable of anaerobic hydrocarbon cycling
• Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated
• Heme pathway evolution in kinetoplastid protists
• Microbial Evolution: Xenology (Apparently) Trumps Paralogy
• Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata
• Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi
• Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes
• Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes.
• A Eukaryote without a Mitochondrial Organelle
• Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria
• Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism
• Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes
• A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
• Genomics of Preaxostyla Flagellates Illuminates Evolutionary Transitions and the Path Towards Mitochondrial Loss
• Releasing uncurated datasets is essential for reproducible phylogenomics
• Lateral Gene Transfer in the Adaptation of the Anaerobic Parasite Blastocystis to the Gut
• Symbiosis in eukaryotic evolution.
• Timing the Origins of Multicellular Eukaryotes Through Phylogenomics and Relaxed Molecular Clock Analyses
• The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together
• An ancestral bacterial division system is widespread in eukaryotic mitochondria
• Archaea
• Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase
• Microbial Diversity: A Bonanza of Phyla
• A SUF Fe-S Cluster Biogenesis System in the Mitochondrion-Related Organelles of the Anaerobic Protist Pygsuia
• On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
• PhyloMagnet: Fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics
• Chlamydial contribution to anaerobic metabolism during eukaryotic evolution
• Molecular characterization of the conoid complex in Toxoplasma reveals its conservation in all apicomplexans, including Plasmodium species
• PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
• Archaea
• Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes
• Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts
• Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115)
• Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis
• Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota
• A eukaryotic-like sulfiredoxin involved in oxidative stress responses and in the reduction of the sulfinic form of 2-Cys peroxiredoxin in the cyanobacterium Anabaena PCC 7120
• The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes
• A Complex Cell Division Machinery Was Present in the Last Common Ancestor of Eukaryotes
• Phylogenomics of eukaryotic multiprotein structures involved in cell cycle and contribution to the eukaryotic phylogeny.
• Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
• Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching
• Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria
• Molecular and morphological characterization of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida
• Shaping up genomes: Prokaryotic roots and eukaryotic diversification of SMC complexes
• Create, Analyze, and Visualize Phylogenomic Datasets Using PhyloFisher
• A gene-rich mitochondrion with a unique ancestral protein transport system
• Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines
• Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta
• Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments
• GTRpmix: A linked general-time reversible model for profile mixture models
• Microbial Diversity and Open Questions about the Deep Tree of Life
• GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models
• A robustly rooted tree of eukaryotes reveals their excavate ancestry.
• A robustly rooted tree of eukaryotes reveals their excavate ancestry
• Independent Size Expansions and Intron Proliferation in Red Algal Plastid and Mitochondrial Genomes
• A eukaryote without a mitochondrial organelle
• TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets
• Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes
• Reconstructing the last common ancestor of all eukaryotes
• One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade
• CORRIGENDUM: Archaea and the origin of eukaryotes (Nature Reviews Microbiology, 2017, 15, 711–723)
• Symbiosis in eukaryotic evolution
• Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution
• The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba
• Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes
• Nephromyces represents a diverse and novel lineage of the apicomplexa that has retained apicoplasts
• New Asgard archaea capable of anaerobic hydrocarbon cycling
• Microbial diversity: A bonanza of phyla
• Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated
• A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia
• A complex cell division machinery was present in the last common ancestor of eukaryotes
• Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes
• Metagenomics of kamchatkan hot spring filaments reveal two new major (hyper) thermophilic lineages related to thaumarchaeota