Published in Nucleic Acids Res on November 27, 2012
The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res (2013) 1.85
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res (2012) 1.66
Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLoS One (2015) 1.45
Gut microbiome and dietary patterns in different Saudi populations and monkeys. Sci Rep (2016) 1.29
Accurate multiplexing and filtering for high-throughput amplicon-sequencing. Nucleic Acids Res (2015) 1.09
454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS One (2013) 1.05
Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. ISME J (2013) 0.99
Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ (2015) 0.96
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front Microbiol (2014) 0.91
Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes. Appl Environ Microbiol (2014) 0.91
Insights into global diatom distribution and diversity in the world's ocean. Proc Natl Acad Sci U S A (2016) 0.88
High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems. Sci Rep (2015) 0.86
Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proc Biol Sci (2015) 0.86
Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system. Microb Ecol (2013) 0.86
Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat Microbiol (2016) 0.85
Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing. J Eukaryot Microbiol (2014) 0.84
Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments. BMC Microbiol (2014) 0.84
Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J (2015) 0.82
Marked seasonality and high spatial variability of protist communities in shallow freshwater systems. ISME J (2015) 0.82
Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing. PLoS One (2014) 0.82
Culturing bias in marine heterotrophic flagellates analyzed through seawater enrichment incubations. Microb Ecol (2013) 0.81
Censusing marine eukaryotic diversity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci (2016) 0.81
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nat Commun (2016) 0.81
Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll. Sci Rep (2015) 0.80
Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. Front Microbiol (2016) 0.80
Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts. Mol Biol Evol (2013) 0.79
Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites. Front Microbiol (2015) 0.79
Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases. Microb Ecol (2015) 0.79
Large variability of bathypelagic microbial eukaryotic communities across the world's oceans. ISME J (2015) 0.78
Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Sci Data (2017) 0.77
Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ (2016) 0.77
Zoosporic parasites infecting marine diatoms - A black box that needs to be opened. Fungal Ecol (2016) 0.77
Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage. Front Microbiol (2015) 0.77
Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile. Front Microbiol (2014) 0.76
Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem. PLoS One (2015) 0.76
Strong Seasonality of Marine Microbial Eukaryotes in a High-Arctic Fjord (Isfjorden, in West Spitsbergen, Norway). Appl Environ Microbiol (2016) 0.76
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database (Oxford) (2016) 0.76
Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea. Microbiologyopen (2015) 0.76
Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France. Microb Ecol (2016) 0.76
Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes. Appl Environ Microbiol (2016) 0.75
Phylogeny-aware identification and correction of taxonomically mislabeled sequences. Nucleic Acids Res (2016) 0.75
Biogeography and diversity of Collodaria (Radiolaria) in the global ocean. ISME J (2017) 0.75
High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae. J Eukaryot Microbiol (2016) 0.75
The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods. PLoS One (2017) 0.75
Resilience of Freshwater Communities of Small Microbial Eukaryotes Undergoing Severe Drought Events. Front Microbiol (2016) 0.75
Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life. Front Microbiol (2017) 0.75
Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater. PeerJ (2016) 0.75
Diversity, ecology and biogeochemistry of cyst-forming acantharia (radiolaria) in the oceans. PLoS One (2013) 0.75
Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ (2017) 0.75
An integrative approach to phylogeny reveals patterns of environmental distribution and novel evolutionary relationships in a major group of ciliates. Sci Rep (2016) 0.75
The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates. Sci Rep (2016) 0.75
Comparison of three clustering approaches for detecting novel environmental microbial diversity. PeerJ (2016) 0.75
Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins. Genomics Proteomics Bioinformatics (2016) 0.75
Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J (2016) 0.75
Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen. BMJ Open Gastroenterol (2016) 0.75
Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. ISME J (2016) 0.75
Ecological and evolutionary significance of novel protist lineages. Eur J Protistol (2016) 0.75
Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz. Sci Rep (2016) 0.75
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol (2017) 0.75
Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing. Environ Microbiol (2015) 0.75
Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach. PLoS One (2014) 0.75
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol (2017) 0.75
Phylogenetic and ecological diversity of apusomonads, a lineage of deep-branching eukaryotes. Environ Microbiol Rep (2016) 0.75
Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence. Sci Rep (2017) 0.75
Composition of heterotrophic flagellates in coastal waters of different trophic status. Curr Microbiol (2013) 0.75
Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond. Environ Microbiol (2017) 0.75
Effects of Hypoxia on the Phylogenetic Composition and Species Distribution of Protists in a Subtropical Harbor. Microb Ecol (2016) 0.75
Microbial Eukaryotes in an Arctic Under-Ice Spring Bloom North of Svalbard. Front Microbiol (2017) 0.75
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol (2006) 57.72
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res (2005) 24.85
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics (2004) 18.87
At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol (2005) 15.41
Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature (2001) 5.70
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol (2002) 5.50
Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature (2001) 5.25
Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics (2010) 4.61
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol (2003) 4.03
The revised classification of eukaryotes. J Eukaryot Microbiol (2012) 3.48
Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol (2008) 2.01
How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biol (2004) 1.89
Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ Microbiol (2010) 1.84
Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. ISME J (2011) 1.76
Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. ISME J (2012) 1.67
Multiple group II self-splicing introns in mobile DNA from Escherichia coli. C R Acad Sci III (1994) 1.59
Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One (2011) 1.44
Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proc Natl Acad Sci U S A (2011) 1.34
Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. ISME J (2012) 1.34
Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia. Mol Biol Evol (2002) 1.12
ScripTree: scripting phylogenetic graphics. Bioinformatics (2010) 0.95
Class I integron with a group II intron detected in an Escherichia coli strain from a free-range reindeer. Antimicrob Agents Chemother (2005) 0.84
Molecular detection of the oyster parasite Mikrocytos mackini, and a preliminary phylogenetic analysis. Dis Aquat Organ (2003) 0.81
TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics (2006) 8.78
The 1.2-megabase genome sequence of Mimivirus. Science (2004) 8.37
Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet (2006) 6.32
A giant virus in amoebae. Science (2003) 5.07
First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature (2007) 4.98
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res (2006) 3.76
The revised classification of eukaryotes. J Eukaryot Microbiol (2012) 3.48
Membrane lipids of symbiotic algae are diagnostic of sensitivity to thermal bleaching in corals. Proc Natl Acad Sci U S A (2004) 3.13
Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria. Appl Environ Microbiol (2004) 3.05
The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. PLoS Biol (2005) 2.88
Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol (2004) 2.88
Reductive genome evolution from the mother of Rickettsia. PLoS Genet (2007) 2.87
A holistic approach to marine eco-systems biology. PLoS Biol (2011) 2.71
Phylogenomics reshuffles the eukaryotic supergroups. PLoS One (2007) 2.67
Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes. Science (2007) 2.54
Diversification and spectral tuning in marine proteorhodopsins. EMBO J (2003) 2.53
Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environ Microbiol (2002) 2.50
The globally distributed genus Alexandrium: multifaceted roles in marine ecosystems and impacts on human health. Harmful Algae (2012) 2.46
Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Appl Environ Microbiol (2003) 2.39
Discovery of novel intermediate forms redefines the fungal tree of life. Nature (2011) 2.37
Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens. PLoS Genet (2006) 2.35
Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol (2010) 2.33
Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection. PLoS Pathog (2012) 2.30
Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol Lett (2008) 2.30
Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature (2013) 2.26
Deep carbon export from a Southern Ocean iron-fertilized diatom bloom. Nature (2012) 2.21
Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc Natl Acad Sci U S A (2008) 2.20
Diversity, nomenclature, and taxonomy of protists. Syst Biol (2007) 2.17
Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ Microbiol (2007) 2.16
Reproductive isolation among sympatric cryptic species in marine diatoms. Protist (2006) 2.12
The genome of Borrelia recurrentis, the agent of deadly louse-borne relapsing fever, is a degraded subset of tick-borne Borrelia duttonii. PLoS Genet (2008) 2.10
Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans. Proc Natl Acad Sci U S A (2009) 2.10
Pseudo-cryptic speciation in coccolithophores. Proc Natl Acad Sci U S A (2003) 2.09
Mimivirus and the emerging concept of "giant" virus. Virus Res (2006) 1.98
Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol (2009) 1.89
How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biol (2004) 1.89
Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int J Syst Evol Microbiol (2003) 1.84
CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol (2012) 1.84
Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ Microbiol (2010) 1.84
Molecular phylogeny, evolutionary rates, and divergence timing of the symbiotic dinoflagellate genus Symbiodinium. Mol Phylogenet Evol (2005) 1.82
Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science (2012) 1.80
Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. ISME J (2011) 1.76
New insights into the diversity of marine picoeukaryotes. PLoS One (2009) 1.75
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol (2009) 1.74
Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction. BMC Genomics (2009) 1.74
Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome. Genome Res (2007) 1.73
Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae). Environ Microbiol (2005) 1.70
Establishment of a real-time PCR-based approach for accurate quantification of bacterial RNA targets in water, using Salmonella as a model organism. Appl Environ Microbiol (2004) 1.70
Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. ISME J (2012) 1.67
Description of Leptopharynx bromelicola n. sp. and characterization of the genus Leptopharynx Mermod, 1914 (Protista, Ciliophora). J Eukaryot Microbiol (2011) 1.67
Novel Proteorhodopsin variants from the Mediterranean and Red Seas. Environ Microbiol (2003) 1.67
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res (2010) 1.67
Browsing repeats in genomes: Pygram and an application to non-coding region analysis. BMC Bioinformatics (2006) 1.65
Marine fungi: their ecology and molecular diversity. Ann Rev Mar Sci (2012) 1.60
Impact of experience with a retrograde-viewing device on adenoma detection rates and withdrawal times during colonoscopy: the Third Eye Retroscope study group. Gastrointest Endosc (2010) 1.59
A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel. Appl Environ Microbiol (2004) 1.57
The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci U S A (2004) 1.57
Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH. FEMS Microbiol Ecol (2007) 1.57
Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir. Environ Microbiol (2006) 1.56
Evaluating support for the current classification of eukaryotic diversity. PLoS Genet (2006) 1.55
Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin. Environ Microbiol (2008) 1.54
A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record. Proc Biol Sci (2006) 1.53
The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'. Genome Res (2009) 1.53
Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS One (2009) 1.51
The "Cheshire Cat" escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection. Proc Natl Acad Sci U S A (2008) 1.49
Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol (2004) 1.48
The evolution of early Foraminifera. Proc Natl Acad Sci U S A (2003) 1.46
The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environ Microbiol (2006) 1.46