Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

Research trends and hotspots related to ammonia oxidation based on bibliometric analysis

(2017) Maosheng Zheng et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Impact of Recombination on the Base Composition of Bacteria and Archaea

(2017) Louis-Marie Bobay et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Global patterns and substrate-based mechanisms of the terrestrial nitrogen cycle

(2016) Shuli Niu et al.   ECOLOGY LETTERS

Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters

(2016) Bradley B Tolar et al.   ISME Journal

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment

(2015) Erin R. Reichenberger et al.   Genome Biology and Evolution

Influence of temperature, pH, and salinity on membrane lipid composition and TEX 86 of marine planktonic thaumarchaeal isolates

(2015) Felix J. Elling et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation

(2015) Barbara Bayer et al.   ISME Journal

Complete nitrification by a single microorganism

(2015) Maartje A. H. J. van Kessel et al.   NATURE

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Genomic and proteomic characterization of “CandidatusNitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

(2015) Alyson E. Santoro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

(2015) Takuro Nunoura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

(2015) Cécile Gubry-Rangin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins

(2014) Alexander Goncearenco et al.   Biology Direct

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

(2014) Jennifer D Rocca et al.   ISME Journal

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models

(2014) Simon Whelan et al.   SYSTEMATIC BIOLOGY

Targeting spatiotemporal dynamics of planktonic SAGMGC-1 and segregation of ammonia-oxidizing thaumarchaeota ecotypes by newly designed primers and quantitative polymerase chain reaction

(2013) Claudia X. Restrepo-Ortiz et al.   ENVIRONMENTAL MICROBIOLOGY

Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey

(2013) Huaiying Yao et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell genomics shedding light on marine Thaumarchaeota diversification

(2013) Haiwei Luo et al.   ISME Journal

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

(2013) Ricardo J Eloy Alves et al.   ISME Journal

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

(2013) A. Goncearenco et al.   NUCLEIC ACIDS RESEARCH

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The global nitrogen cycle in the twenty-first century

(2013) D. Fowler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global Ecological Pattern of Ammonia-Oxidizing Archaea

(2013) Huiluo Cao et al.   PLoS One

Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations

(2012) Jörg Simon et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments

(2012) Peter W Collingridge et al.   BMC BIOINFORMATICS

ArchaealamoA gene diversity points to distinct biogeography of ammonia-oxidizingCrenarchaeotain the ocean

(2012) Eva Sintes et al.   ENVIRONMENTAL MICROBIOLOGY

Habitat-Associated Phylogenetic Community Patterns of Microbial Ammonia Oxidizers

(2012) Antoni Fernàndez-Guerra et al.   PLoS One

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

A selective force favoring increased G+C content in bacterial genes

(2012) R. Raghavan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthesis of Methylphosphonic Acid by Marine Microbes: A Source for Methane in the Aerobic Ocean

(2012) W. W. Metcalf et al.   SCIENCE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Global Biodiversity of Aquatic Ammonia-Oxidizing Archaea is Partitioned by Habitat

(2012) Steven J. Biller et al.   Frontiers in Microbiology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

(2011) Michael Pester et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

(2011) Alyson E Santoro et al.   ISME Journal

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

(2011) M. Mussmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Niche specialization of terrestrial archaeal ammonia oxidizers

(2011) C. Gubry-Rangin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

The archaeal ‘TACK’ superphylum and the origin of eukaryotes

(2011) Lionel Guy et al.   TRENDS IN MICROBIOLOGY

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

(2011) Maya Botzman et al.   GENOME BIOLOGY

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

(2010) Y. Liu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Sediment-associated microdiversity within the Marine Group I Crenarchaeota

(2010) Alan M. Durbin et al.   Environmental Microbiology Reports

A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs

(2010) Patricia L. Tavormina et al.   Environmental Microbiology Reports

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

(2009) Carsten Kemena et al.   BIOINFORMATICS

Bacteriarather thanArchaeadominate microbial ammonia oxidation in an agricultural soil

(2009) Zhongjun Jia et al.   ENVIRONMENTAL MICROBIOLOGY

The radiocarbon signature of microorganisms in the mesopelagic ocean

(2009) R. L. Hansman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

(2008) Amarendran R Subramanian et al.   Algorithms for Molecular Biology

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

(2008) Annika C. Mosier et al.   ENVIRONMENTAL MICROBIOLOGY

Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment

(2008) James I. Prosser et al.   ENVIRONMENTAL MICROBIOLOGY

Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms

(2008) Maria Tourna et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California

(2008) J Michael Beman et al.   ISME Journal

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY