Asgard archaea illuminate the origin of eukaryotic cellular complexity

Energy for two: New archaeal lineages and the origin of mitochondria

(2016) William F. Martin et al.   BIOESSAYS

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

(2016) Kiley W Seitz et al.   ISME Journal

LokiarchaeotaMarks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems

(2016) Marco Mariotti et al.   MOLECULAR BIOLOGY AND EVOLUTION

Are There Rab GTPases in Archaea?

(2016) Jaroslaw Surkont et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks

(2016) Christen M. Klinger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mitochondria in the second act

(2016) Thijs J. G. Ettema   NATURE

On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype

(2016) Gautam Dey et al.   TRENDS IN CELL BIOLOGY

Bacterial Vesicle Secretion and the Evolutionary Origin of the Eukaryotic Endomembrane System

(2016) Sven B. Gould et al.   TRENDS IN MICROBIOLOGY

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

(2016) Brett J. Baker et al.   Nature Microbiology

Lokiarchaeon is hydrogen dependent

(2016) Filipa L. Sousa et al.   Nature Microbiology

Archaeal ancestors of eukaryotes: not so elusive any more

(2015) Eugene V. Koonin   BMC BIOLOGY

Endosymbiosis and Eukaryotic Cell Evolution

(2015) John M. Archibald   CURRENT BIOLOGY

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

Unexpected Ancient Paralogs and an Evolutionary Model for the COPII Coat Complex

(2015) Alexander Schlacht et al.   Genome Biology and Evolution

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Endosymbiotic origin and differential loss of eukaryotic genes

(2015) Chuan Ku et al.   NATURE

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Endosymbiotic theories for eukaryote origin

(2015) William F. Martin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2015) Jimmy H. Saw et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?

(2015) Eugene V. Koonin   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The two-domain tree of life is linked to a new root for the Archaea

(2015) Kasie Raymann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Open Questions on the Origin of Eukaryotes

(2015) Purificación López-García et al.   TRENDS IN ECOLOGY & EVOLUTION

A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

(2015) Mark A. Lever et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The hybrid nature of the Eukaryota and a consilient view of life on Earth

(2014) James O. McInerney et al.   NATURE REVIEWS MICROBIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic Origins: How and When Was the Mitochondrion Acquired?

(2014) A. M. Poole et al.   Cold Spring Harbor Perspectives in Biology

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

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery

(2014) Kira S. Makarova et al.   Frontiers in Microbiology

S-layer and cytoplasmic membrane – exceptions from the typical archaeal cell wall with a focus on double membranes

(2014) Andreas Klingl   Frontiers in Microbiology

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

(2013) Joran Martijn et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2013) Tom A. Williams et al.   NATURE

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Functional and Genomic Analyses of Alpha-Solenoid Proteins

(2013) David Fournier et al.   PLoS One

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Archaeal origin of tubulin

(2012) Natalya Yutin et al.   Biology Direct

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Phylogenomics of Prokaryotic Ribosomal Proteins

(2012) Natalya Yutin 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

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

On a bender—BARs, ESCRTs, COPs, and finally getting your coat

(2011) Mark C. Field et al.   JOURNAL OF CELL BIOLOGY

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

(2011) Lionel Guy et al.   TRENDS IN MICROBIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

The energetics of genome complexity

(2010) Nick Lane et al.   NATURE

Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis

(2010) U. Kuper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The origins of phagocytosis and eukaryogenesis

(2009) Natalya Yutin et al.   Biology Direct

Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors

(2009) Tahir H Tahirov et al.   Biology Direct

The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins

(2009) Camilla Raiborg et al.   NATURE

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system

(2008) Mircea Podar et al.   Biology Direct

The archaebacterial origin of eukaryotes

(2008) C. J. Cox et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The TRAPP Complex: Insights into its Architecture and Function

(2008) Michael Sacher et al.   TRAFFIC