Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments

An evolving view of methane metabolism in the Archaea

(2019) Paul N. Evans et al.   NATURE REVIEWS MICROBIOLOGY

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the northern South China Sea

(2019) Jiao-Mei Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

(2019) Kerrin Mendler et al.   NUCLEIC ACIDS RESEARCH

Asgard archaea capable of anaerobic hydrocarbon cycling

(2019) Kiley W. Seitz et al.   Nature Communications

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism

(2019) Anja Spang et al.   Nature Microbiology

Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’ (JS1) inferred from genomics

(2019) Yi-Fan Liu et al.   ISME Journal

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

(2019) Xiyang Dong et al.   Nature Communications

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

(2018) Cindy J. Castelle et al.   CELL

Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

(2018) Panagiotis S. Adam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi

(2018) Maliheh Mehrshad et al.   Microbiome

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

(2017) Neil D Rawlings et al.   NUCLEIC ACIDS RESEARCH

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons

(2016) Rainer U. Meckenstock et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings

(2015) D. E. LaRowe et al.   AMERICAN JOURNAL OF SCIENCE

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

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

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Formate, acetate, and propionate as substrates for sulfate reduction in sub-arctic sediments of Southwest Greenland

(2015) Clemens Glombitza et al.   Frontiers in Microbiology

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

(2014) Noha H Youssef et al.   ISME Journal

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

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

Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components

(2014) S. Pirbadian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling 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

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

(2013) Laura A Hug et al.   Microbiome

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

(2012) Y. Peng et al.   BIOINFORMATICS

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

(2012) Kyoko Kubo et al.   ISME Journal

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

A hydrothermal seep on the Costa Rica margin: middle ground in a continuum of reducing ecosystems

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

eQuilibrator--the biochemical thermodynamics calculator

(2011) A. Flamholz et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Calculation of the relative metastabilities of proteins using the CHNOSZ software package

(2008) Jeffrey M Dick   GEOCHEMICAL TRANSACTIONS

Significant contribution of Archaea to extant biomass in marine subsurface sediments

(2008) Julius S. Lipp et al.   NATURE

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment

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