Published in Proc Natl Acad Sci U S A on July 25, 2011
Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A (2012) 5.53
Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol (2012) 2.70
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res (2012) 1.93
CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol (2012) 1.84
Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLoS One (2015) 1.45
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience (2013) 1.42
Ancient DNA complements microfossil record in deep-sea subsurface sediments. Biol Lett (2013) 1.05
Targeted recovery of novel phylogenetic diversity from next-generation sequence data. ISME J (2012) 1.00
Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS One (2013) 0.93
Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy? PLoS One (2015) 0.85
High-Throughput Sequencing-The Key to Rapid Biodiversity Assessment of Marine Metazoa? PLoS One (2015) 0.85
Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case. PLoS One (2012) 0.81
Censusing marine eukaryotic diversity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci (2016) 0.81
Protistan community analysis: key findings of a large-scale molecular sampling. ISME J (2016) 0.81
Accuracy of Next Generation Sequencing Platforms. Next Gener Seq Appl (2015) 0.80
Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers? ISME J (2016) 0.77
Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life. Biol Direct (2015) 0.77
Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA. PeerJ (2016) 0.77
Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island. PLoS One (2015) 0.77
Novel benthic foraminifera are abundant and diverse in an area of the abyssal equatorial Pacific licensed for polymetallic nodule exploration. Sci Rep (2017) 0.75
Marine Nematode Taxonomy in Africa: Promising Prospects Against Scarcity of Information. J Nematol (2015) 0.75
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59
Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol (2009) 21.24
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A (2010) 19.48
First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature (2007) 4.98
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods (2009) 4.32
A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS One (2009) 2.51
Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable. PLoS One (2010) 2.42
Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science (2005) 1.78
Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. ISME J (2011) 1.76
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol (2009) 1.74
Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol (2010) 1.63
Simple foraminifera flourish at the ocean's deepest point. Science (2005) 1.54
The evolution of early Foraminifera. Proc Natl Acad Sci U S A (2003) 1.46
Global molecular phylogeography reveals persistent Arctic circumpolar isolation in a marine planktonic protist. Proc Natl Acad Sci U S A (2007) 1.45
Bipolar gene flow in deep-sea benthic foraminifera. Mol Ecol (2007) 1.36
Phylogeny of novel naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea revised. Protist (2008) 1.36
Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol Biol Evol (1997) 1.24
Short rDNA barcodes for species identification in foraminifera. J Eukaryot Microbiol (2010) 1.16
Freshwater foraminiferans revealed by analysis of environmental DNA samples. J Eukaryot Microbiol (2003) 0.92
Molecular evidence for widespread occurrence of Foraminifera in soils. Environ Microbiol (2010) 0.85
Unexpected foraminiferal diversity revealed by small-subunit rDNA analysis of Antarctic sediment. J Eukaryot Microbiol (2004) 0.82
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res (2008) 14.90
TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics (2006) 8.78
BRAF mutations in hairy-cell leukemia. N Engl J Med (2011) 7.05
Altered histone acetylation is associated with age-dependent memory impairment in mice. Science (2010) 6.38
Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics (2008) 5.00
First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature (2007) 4.98
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J Microbiol Methods (2009) 4.32
The revised classification of eukaryotes. J Eukaryot Microbiol (2012) 3.48
The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature (2011) 3.29
The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci U S A (2011) 2.74
Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype. Blood (2011) 2.71
Phylogenomics reshuffles the eukaryotic supergroups. PLoS One (2007) 2.67
microRNA-34c is a novel target to treat dementias. EMBO J (2011) 2.44
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res (2010) 2.37
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
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res (2012) 1.93
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
Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protoc (2010) 1.85
Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei. PLoS Pathog (2010) 1.85
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
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
Human endogenous retrovirus type W envelope expression in blood and brain cells provides new insights into multiple sclerosis disease. Mult Scler (2012) 1.77
Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. ISME J (2011) 1.76
The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nat Commun (2010) 1.75
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol (2009) 1.74
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
Commercially available outbred mice for genome-wide association studies. PLoS Genet (2010) 1.58
The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci U S A (2004) 1.57
A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record. Proc Biol Sci (2006) 1.53
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
Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One (2010) 1.46
The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environ Microbiol (2006) 1.46
Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One (2011) 1.44
De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. Bioinformatics (2013) 1.43
Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in rhizaria. Curr Biol (2013) 1.42
Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists. BMC Evol Biol (2010) 1.39
Composition and dynamics of bacterial communities of a drinking water supply system as assessed by RNA- and DNA-based 16S rRNA gene fingerprinting. Appl Environ Microbiol (2006) 1.28
Shewanella denitrificans sp. nov., a vigorously denitrifying bacterium isolated from the oxic-anoxic interface of the Gotland Deep in the central Baltic Sea. Int J Syst Evol Microbiol (2002) 1.28
Phylogenetic analysis and real time PCR detection of a presumbably undescribed Peronospora species on sweet basil and sage. Mycol Res (2005) 1.21
Rhinovirus genome evolution during experimental human infection. PLoS One (2010) 1.21
Highly diverse TCRα chain repertoire of pre-immune CD8⁺ T cells reveals new insights in gene recombination. EMBO J (2012) 1.21
Potential of DNA sequences to identify zoanthids (Cnidaria: Zoantharia). Zoolog Sci (2008) 1.20
Deep phylogeny and evolution of slime moulds (mycetozoa). Protist (2009) 1.16
Massive production of small RNAs from a non-coding region of Cauliflower mosaic virus in plant defense and viral counter-defense. Nucleic Acids Res (2011) 1.15
higher-order phylogeny of plasmodial slime molds (Myxogastria) based on elongation factor 1-A and small subunit rRNA gene sequences. J Eukaryot Microbiol (2005) 1.15
Rheinheimera baltica gen. nov., sp. nov., a blue-coloured bacterium isolated from the central Baltic Sea. Int J Syst Evol Microbiol (2002) 1.14
The testate lobose amoebae (order Arcellinida Kent, 1880) finally find their home within Amoebozoa. Protist (2005) 1.14
Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR. PLoS One (2011) 1.13
Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure. Microb Biotechnol (2011) 1.12
Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts. Mol Biol Evol (2006) 1.12
A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol Biol Evol (2003) 1.10
Identification of a Thiomicrospira denitrificans-like epsilonproteobacterium as a catalyst for autotrophic denitrification in the central Baltic Sea. Appl Environ Microbiol (2006) 1.08
Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol (2007) 1.08
Gain and loss of multiple functionally related, horizontally transferred genes in the reduced genomes of two microsporidian parasites. Proc Natl Acad Sci U S A (2012) 1.08
Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. BMC Genomics (2010) 1.07
Rhinovirus genome variation during chronic upper and lower respiratory tract infections. PLoS One (2011) 1.05
Ancient DNA complements microfossil record in deep-sea subsurface sediments. Biol Lett (2013) 1.05
Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol (2005) 1.05
Deep-sequencing protocols influence the results obtained in small-RNA sequencing. PLoS One (2012) 1.03
Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol Biol Evol (2003) 1.03
Evolution of dark-spored Myxomycetes (slime-molds): molecules versus morphology. Mol Phylogenet Evol (2008) 1.03
Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist (2002) 1.01
Analysis of the salivary microbiome using culture-independent techniques. J Clin Bioinforma (2012) 1.01
Profile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus. BMC Mol Biol (2011) 1.01
Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils. Int J Syst Evol Microbiol (2002) 1.01
Computational identification and analysis of novel sugarcane microRNAs. BMC Genomics (2012) 1.00
Small-subunit ribosomal RNA gene sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria. Protist (2004) 1.00
Development and application of a real-time PCR approach for quantification of uncultured bacteria in the central Baltic Sea. Appl Environ Microbiol (2004) 1.00
Molecular phylogeny and classification of the lobose amoebae. Protist (2005) 1.00
Rhizobium alamii sp. nov., an exopolysaccharide-producing species isolated from legume and non-legume rhizospheres. Int J Syst Evol Microbiol (2009) 0.99
Erwinia papayae sp. nov., a pathogen of papaya (Carica papaya). Int J Syst Evol Microbiol (2004) 0.99
Primary and secondary siRNAs in geminivirus-induced gene silencing. PLoS Pathog (2012) 0.99
Molecular identification of sequestered diatom chloroplasts and kleptoplastidy in foraminifera. Protist (2010) 0.99
Phylogenetic position of Multicilia marina and the evolution of Amoebozoa. Int J Syst Evol Microbiol (2006) 0.98
Revised small subunit rRNA analysis provides further evidence that Foraminifera are related to Cercozoa. J Mol Evol (2003) 0.96
ScripTree: scripting phylogenetic graphics. Bioinformatics (2010) 0.95
Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int J Syst Evol Microbiol (2003) 0.95
Multi-locus analysis of human infective Cryptosporidium species and subtypes using ten novel genetic loci. BMC Microbiol (2010) 0.94
Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response. Int J Cancer (2014) 0.94
Acquisition of an animal gene by microsporidian intracellular parasites. Curr Biol (2011) 0.94
Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist (2005) 0.93
Rheinheimera perlucida sp. nov., a marine bacterium of the Gammaproteobacteria isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol (2006) 0.93