Published in Environ Microbiol on February 24, 2012
Genomic insights into the marine sponge microbiome. Nat Rev Microbiol (2012) 1.83
Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun (2013) 1.40
Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. ISME J (2012) 1.28
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J (2013) 1.18
A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. Nat Commun (2013) 1.12
Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea. ISME J (2014) 1.00
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One (2012) 0.99
Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota. ISME J (2016) 0.94
Evidence of a putative deep sea specific microbiome in marine sponges. PLoS One (2014) 0.93
Reconstruction of ribosomal RNA genes from metagenomic data. PLoS One (2012) 0.93
Metatranscriptomic census of active protists in soils. ISME J (2015) 0.92
Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS One (2013) 0.92
Transcriptional response of the archaeal ammonia oxidizer Nitrosopumilus maritimus to low and environmentally relevant ammonia concentrations. Appl Environ Microbiol (2013) 0.89
The Sponge Hologenome. MBio (2016) 0.88
Archaea in symbioses. Archaea (2012) 0.87
Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts. MBio (2013) 0.86
A straightforward DOPE (double labeling of oligonucleotide probes)-FISH (fluorescence in situ hybridization) method for simultaneous multicolor detection of six microbial populations. Appl Environ Microbiol (2012) 0.86
Unraveling the stratification of an iron-oxidizing microbial mat by metatranscriptomics. PLoS One (2014) 0.86
Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges. Front Microbiol (2014) 0.83
Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras. PeerJ (2014) 0.83
Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics. Sci Rep (2014) 0.83
Transcriptome analyses to investigate symbiotic relationships between marine protists. Front Microbiol (2015) 0.82
How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans. Bioessays (2014) 0.82
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Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange. Front Microbiol (2015) 0.80
Meta-omic characterization of prokaryotic gene clusters for natural product biosynthesis. Curr Opin Biotechnol (2013) 0.79
Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei. Sci Rep (2016) 0.77
Composition of Archaea in seawater, sediment, and sponges in the Kepulauan Seribu reef system, Indonesia. Microb Ecol (2014) 0.77
Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome. Front Microbiol (2016) 0.76
Comparative sequence analysis of bacterial symbionts from the marine sponges Geodia cydonium and Ircinia muscarum. Bioinformation (2014) 0.76
Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation. BMC Genomics (2014) 0.76
Environmental heterogeneity and microbial inheritance influence sponge-associated bacterial composition of Spongia lamella. Microb Ecol (2014) 0.76
Emerging Sponge Models of Animal-Microbe Symbioses. Front Microbiol (2016) 0.75
Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling. Sci Rep (2016) 0.75
Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria. Front Microbiol (2016) 0.75
Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges. Mar Biotechnol (NY) (2016) 0.75
Predicting the HMA-LMA Status in Marine Sponges by Machine Learning. Front Microbiol (2017) 0.75
The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle. Microb Ecol (2016) 0.75
Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45
Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol (2006) 5.77
Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol (2005) 5.32
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS One (2008) 4.54
Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics (2007) 4.45
Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06
The dynamic genome of Hydra. Nature (2010) 4.00
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A (2006) 3.85
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
Illuminating the evolutionary history of chlamydiae. Science (2004) 3.39
The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol (2008) 3.34
Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A (2011) 3.25
Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR. Environ Microbiol (2003) 3.08
Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol (2010) 2.84
Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol (2009) 2.68
Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol Microbiol (2003) 2.65
Sequence-based prediction of type III secreted proteins. PLoS Pathog (2009) 2.58
In vivo activity of CRISPR-mediated virus defence in a hyperthermophilic archaeon. Mol Microbiol (2011) 2.35
A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci U S A (2010) 2.25
The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr Opin Microbiol (2011) 2.14
Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environ Microbiol (2004) 2.02
amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol (2011) 2.02
probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity. Environ Microbiol (2008) 1.85
Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates. J Bacteriol (2010) 1.83
Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ Microbiol (2009) 1.78
PEDANT covers all complete RefSeq genomes. Nucleic Acids Res (2008) 1.78
UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Mol Microbiol (2011) 1.71
Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends Microbiol (2006) 1.69
SIMAP--the similarity matrix of proteins. Bioinformatics (2005) 1.62
Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol (2013) 1.62
Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol (2009) 1.61
B2G-FAR, a species-centered GO annotation repository. Bioinformatics (2011) 1.53
A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttle vector. Mol Microbiol (2003) 1.48
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics (2011) 1.48
Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol (2011) 1.47
Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage. J Bacteriol (2007) 1.46
Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol (2004) 1.45
Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol Ecol (2008) 1.44
Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis. ISME J (2012) 1.43
The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol (2012) 1.42
Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun (2013) 1.40
Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies. Extremophiles (2002) 1.40
Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc Natl Acad Sci U S A (2012) 1.37
Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea. J Bioenerg Biomembr (2004) 1.37
The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria. J Bacteriol (2009) 1.36
UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol (2008) 1.35
The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res (2009) 1.32
Archaea in biogeochemical cycles. Annu Rev Microbiol (2013) 1.31
Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environ Microbiol (2010) 1.30
CREST--classification resources for environmental sequence tags. PLoS One (2012) 1.28
Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. ISME J (2012) 1.28
Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism. Environ Microbiol (2009) 1.27
Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge. Nat Commun (2010) 1.25
Regulation of expression of the arabinose and glucose transporter genes in the thermophilic archaeon Sulfolobus solfataricus. Extremophiles (2006) 1.24
Effective--a database of predicted secreted bacterial proteins. Nucleic Acids Res (2010) 1.23
Independent evolution of the core domain and its flanking sequences in small heat shock proteins. FASEB J (2010) 1.20
First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol (2002) 1.20
Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 1.20
MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res (2010) 1.19
Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology (2007) 1.18
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PLoS Pathog (2012) 1.16
Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiol Lett (2006) 1.15
Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses. PLoS One (2012) 1.14
The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer. Front Microbiol (2013) 1.14
Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environ Microbiol (2012) 1.13
Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiol Ecol (2012) 1.11
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PLoS One (2013) 1.11
Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA. FEMS Microbiol Ecol (2011) 1.10
Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture. Environ Microbiol (2010) 1.09
Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges. Environ Microbiol (2011) 1.06
Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. ISME J (2013) 1.06
Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics. Environ Microbiol (2006) 1.04
Responses of the terrestrial ammonia-oxidizing archaeon Ca. Nitrososphaera viennensis and the ammonia-oxidizing bacterium Nitrosospira multiformis to nitrification inhibitors. FEMS Microbiol Lett (2013) 1.02
Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland. Soil Biol Biochem (2013) 1.02
CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus. Nucleic Acids Res (2014) 1.02
Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases. Mol Microbiol (2010) 1.00
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res (2006) 0.99
Distribution of Crenarchaeota representatives in terrestrial hot springs of Russia and Iceland. Appl Environ Microbiol (2008) 0.99
Molecular phylogeny of the Astrophorida (Porifera, Demospongiae(p)) reveals an unexpected high level of spicule homoplasy. PLoS One (2011) 0.98
Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon Sulfolobus solfataricus. Nucleic Acids Res (2013) 0.98
NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira. Environ Microbiol (2013) 0.97
Targeting effectors: the molecular recognition of Type III secreted proteins. Microbes Infect (2010) 0.97
Molecular characterization of the symbionts associated with marine nematodes of the genus Robbea. Environ Microbiol Rep (2009) 0.96
Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals. BMC Genomics (2011) 0.95
The legacy of Carl Woese and Wolfram Zillig: from phylogeny to landmark discoveries. Nat Rev Microbiol (2013) 0.94
Inter- and intra-habitat bacterial diversity associated with cold-water corals. ISME J (2009) 0.94
Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environ Microbiol (2013) 0.93