Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Microfluidics Expanding the Frontiers of Microbial Ecology

(2014) Roberto Rusconi et al.   Annual Review of Biophysics

Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes

(2014) Nicolas C. Rochette et al.   MOLECULAR BIOLOGY AND EVOLUTION

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Recent advances in genomic DNA sequencing of microbial species from single cells

(2014) Roger S. Lasken et al.   NATURE REVIEWS GENETICS

The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective

(2014) L. Guy et al.   Cold Spring Harbor Perspectives in Biology

The Dispersed Archaeal Eukaryome and the Complex Archaeal Ancestor of Eukaryotes

(2014) E. V. Koonin et al.   Cold Spring Harbor Perspectives in Biology

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell

(2013) Joran Martijn et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses

(2013) Jun Meng et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

An archaeal origin of eukaryotes supports only two primary domains of life

(2013) Tom A. Williams et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Genomes from Metagenomics

(2013) I. Sharon et al.   SCIENCE

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

(2013) Jeremy A. Dodsworth et al.   Nature Communications

The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

(2013) Patrick Forterre   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Archaeal origin of tubulin

(2012) Natalya Yutin et al.   Biology Direct

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin

(2012) Thorsten Thiergart et al.   Genome Biology and Evolution

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

(2012) Kyoko Kubo et al.   ISME Journal

MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species

(2012) Yi Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

(2012) Kaustubh Raosaheb Patil et al.   PLoS One

Korarchaeota Diversity, Biogeography, and Abundance in Yellowstone and Great Basin Hot Springs and Ecological Niche Modeling Based on Machine Learning

(2012) Robin L. Miller-Coleman et al.   PLoS One

A congruent phylogenomic signal places eukaryotes within the Archaea

(2012) T. A. Williams et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

(2012) Alan M. Durbin et al.   Frontiers in Microbiology

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Genomic Analysis at the Single-Cell Level

(2011) Tomer Kalisky et al.   Annual Review of Genetics

Transcript amplification from single bacterium for transcriptome analysis

(2011) Y. Kang et al.   GENOME RESEARCH

An actin-based cytoskeleton in archaea

(2011) Thijs J. G. Ettema et al.   MOLECULAR MICROBIOLOGY

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

(2011) Lionel Guy et al.   TRENDS IN MICROBIOLOGY

ClaMS: A Classifier for Metagenomic Sequences

(2011) Amrita Pati et al.   Standards in Genomic Sciences

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

(2010) Simonetta Gribaldo et al.   NATURE REVIEWS MICROBIOLOGY

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis

(2010) Anthony M. Poole et al.   RESEARCH IN MICROBIOLOGY

Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge

(2010) Rolf B. Pedersen et al.   Nature Communications

The origin and early evolution of eukaryotes in the light of phylogenomics

(2010) Eugene V Koonin   GENOME BIOLOGY

The origins of phagocytosis and eukaryogenesis

(2009) Natalya Yutin et al.   Biology Direct

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

A DNA topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya

(2008) Céline Brochier-Armanet et al.   Biology Direct

Phylogenetic classification of short environmental DNA fragments

(2008) Lutz Krause et al.   NUCLEIC ACIDS RESEARCH

A unique cell division machinery in the Archaea

(2008) A.-C. Lindas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for the ESCRT System in Cell Division in Archaea

(2008) R. Y. Samson et al.   SCIENCE