Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

(2016) Cassandre Sara Lazar et al.   ENVIRONMENTAL MICROBIOLOGY

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

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

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

A new view of the tree of life

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

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

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

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

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

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence

(2015) Alexandra K. Perras et al.   Frontiers in Microbiology

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

(2015) Brett J Baker et al.   Microbiome

In Vitro Assembly of the Outer Core of the Lipopolysaccharide from Escherichia coli K-12 and Salmonella typhimurium

(2014) Jinghua Qian et al.   BIOCHEMISTRY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

ITEP: An integrated toolkit for exploration of microbial pan-genomes

(2014) Matthew N Benedict et al.   BMC GENOMICS

Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea

(2014) Kasie Raymann et al.   Genome Biology and Evolution

Single Cell Genomics of Uncultured, Health-Associated Tannerella BU063 (Oral Taxon 286) and Comparison to the Closely Related Pathogen Tannerella forsythia

(2014) Clifford J. Beall et al.   PLoS One

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

(2014) Brandon K. Swan et al.   PLoS One

Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface

(2014) Alexander J. Probst et al.   Nature Communications

Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm

(2014) Alexandra K. Perras et al.   Frontiers in Microbiology

Structure and Substrate Specificity of the Pyrococcal Coenzyme A Disulfide Reductases/Polysulfide Reductases (CoADR/Psr): Implications for S0-Based Respiration and a Sulfur-Dependent Antioxidant System in Pyrococcus

(2013) Sanna Herwald et al.   BIOCHEMISTRY

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

(2013) Mircea Podar et al.   Biology Direct

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Y. Peng et al.   BIOINFORMATICS

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

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

Galactose Metabolism Plays a Crucial Role in Biofilm Formation by Bacillus subtilis

(2012) Y. Chai et al.   mBio

Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea

(2011) Karen G. Lloyd et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation of Genes Involved in Biofilm Formation of a Klebsiella pneumoniae Strain Causing Pyogenic Liver Abscess

(2011) Meng-Chuan Wu et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

The characterization of functions involved in the establishment and maturation of Klebsiella pneumoniae in vitro biofilm reveals dual roles for surface exopolysaccharides

(2008) Damien Balestrino et al.   ENVIRONMENTAL MICROBIOLOGY