Published in ISME J on August 05, 2010
Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS One (2011) 1.30
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J (2015) 1.08
Illuminating microbial dark matter in meromictic Sakinaw Lake. Appl Environ Microbiol (2014) 1.03
Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment. Biotechnol Biofuels (2013) 0.94
Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. ISME J (2015) 0.86
Community and proteomic analysis of methanogenic consortia degrading terephthalate. Appl Environ Microbiol (2012) 0.83
Total protein extraction for metaproteomics analysis of methane producing biofilm: the effects of detergents. Int J Mol Sci (2014) 0.80
Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions. PLoS One (2014) 0.79
Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. Biotechnol Biofuels (2016) 0.78
Mesophilic and thermophilic conditions select for unique but highly parallel microbial communities to perform carboxylate platform biomass conversion. PLoS One (2012) 0.78
Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing. Microb Ecol (2014) 0.76
Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system. Biotechnol Biofuels (2016) 0.75
Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion. Microb Cell Fact (2016) 0.75
A Single-Granule-Level Approach Reveals Ecological Heterogeneity in an Upflow Anaerobic Sludge Blanket Reactor. PLoS One (2016) 0.75
Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria. Front Microbiol (2016) 0.75
Dehalococcoides as a Potential Biomarker Evidence for Uncharacterized Organohalides in Environmental Samples. Front Microbiol (2017) 0.75
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93
Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev (1997) 6.71
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 5.71
Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol (2008) 4.81
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The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth. Proc Natl Acad Sci U S A (2007) 2.17
Benzoyl-coenzyme A reductase (dearomatizing), a key enzyme of anaerobic aromatic metabolism. ATP dependence of the reaction, purification and some properties of the enzyme from Thauera aromatica strain K172. Eur J Biochem (1995) 2.00
Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science (2007) 1.99
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol Mol Biol Rev (2007) 1.89
Effects of lipids on thermophilic anaerobic digestion and reduction of lipid inhibition upon addition of bentonite. Appl Microbiol Biotechnol (1990) 1.89
Methanosaeta, the forgotten methanogen? Trends Microbiol (2007) 1.61
"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol (2008) 1.60
Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens. Mol Microbiol (2005) 1.50
Characterization of microbial consortia in a terephthalate-degrading anaerobic granular sludge system. Microbiology (2001) 1.30
Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol (2008) 1.27
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics (2007) 1.18
Cyclohexa-1,5-diene-1-carbonyl-coenzyme A (CoA) hydratases of Geobacter metallireducens and Syntrophus aciditrophicus: Evidence for a common benzoyl-CoA degradation pathway in facultative and strict anaerobes. J Bacteriol (2006) 1.13
Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen. Appl Environ Microbiol (2008) 1.12
Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Arch Microbiol (2006) 1.12
Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge. Int J Syst Evol Microbiol (2008) 1.11
Anaerobic degradation of phthalate isomers by methanogenic consortia. Appl Environ Microbiol (1999) 1.09
Syntrophic growth on formate: a new microbial niche in anoxic environments. Appl Environ Microbiol (2008) 1.09
Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases. Proc Natl Acad Sci U S A (2009) 1.05
Microbial community structure in a thermophilic anaerobic hybrid reactor degrading terephthalate. Microbiology (2004) 1.00
Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases. Genomics (2005) 0.96
The Microbial Logic behind the Prevalence of Incomplete Oxidation of Organic Compounds by Acetogenic Bacteria in Methanogenic Environments. Microb Ecol (2001) 0.89
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods (2013) 31.15
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
Comparative metagenomics of microbial communities. Science (2005) 25.88
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 18.88
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics (2004) 18.87
IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics (2009) 17.90
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol (2009) 14.17
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J (2011) 13.64
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods (2010) 13.05
Prepublication data sharing. Nature (2009) 12.24
IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res (2012) 12.03
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2007) 11.24
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2009) 9.98
Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2006) 9.93
CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol (2008) 8.91
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A (2007) 7.82
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods (2007) 7.73
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
The integrated microbial genomes (IMG) system. Nucleic Acids Res (2006) 7.34
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res (2007) 7.18
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (2011) 6.93
A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol (2008) 6.82
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res (2006) 6.79
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol (2013) 6.40
IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res (2013) 6.14
The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res (2009) 6.07
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics (2007) 5.84
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2011) 5.79
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 5.71
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol (2002) 5.56
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci (2009) 5.50
Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol (2007) 5.40
Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (2006) 5.04
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science (2012) 4.93
Defining seasonal marine microbial community dynamics. ISME J (2011) 4.61
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol (2003) 4.40
A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev (2008) 4.33
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J (2010) 4.15
Assembling the marine metagenome, one cell at a time. PLoS One (2009) 4.10
Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol (2010) 4.01
Chthoniobacter flavus gen. nov., sp. nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Appl Environ Microbiol (2004) 3.81
One bacterial cell, one complete genome. PLoS One (2010) 3.69
Complete genome sequence of Kytococcus sedentarius type strain (541). Stand Genomic Sci (2009) 3.30
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J (2011) 3.24
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics (2009) 3.17
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol (2005) 3.12
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04
IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res (2013) 2.99
High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol (2008) 2.99
Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science (2009) 2.96
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci U S A (2005) 2.85
Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol (2003) 2.77
Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nat Methods (2012) 2.77
IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res (2011) 2.76
An experimental metagenome data management and analysis system. Bioinformatics (2006) 2.71
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol (2006) 2.69
Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A (2014) 2.65
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J (2012) 2.45
Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol (2007) 2.43
Microbiology: metagenomics. Nature (2008) 2.39
Taxonomic metagenome sequence assignment with structured output models. Nat Methods (2011) 2.34
The DNA sequence and biology of human chromosome 19. Nature (2004) 2.29
Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoS Comput Biol (2013) 2.28
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol (2006) 2.28
An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet (2010) 2.28
Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci U S A (2010) 2.26
The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One (2012) 2.25
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods (2010) 2.21
Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol (2003) 2.14
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol (2008) 2.12
Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Res (2012) 2.10