Published in PLoS One on June 22, 2012
Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition. Biotechnol Biofuels (2016) 0.84
Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. Biotechnol Biofuels (2015) 0.83
Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis. Sci Rep (2014) 0.82
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res (2008) 27.83
Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev (2002) 12.84
DNA sequence quality trimming and vector removal. Bioinformatics (2001) 10.04
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (2011) 6.93
The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res (2009) 6.07
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Stand Genomic Sci (2009) 5.50
Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A (2009) 4.03
Cellulase, clostridia, and ethanol. Microbiol Mol Biol Rev (2005) 3.81
Genomics of cellulosic biofuels. Nature (2008) 3.43
Energy conservation via electron-transferring flavoprotein in anaerobic bacteria. J Bacteriol (2007) 2.17
Growth of syntrophic propionate-oxidizing bacteria with fumarate in the absence of methanogenic bacteria. Appl Environ Microbiol (1993) 2.12
Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05
Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One (2010) 2.02
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A (2010) 1.89
Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J (2010) 1.78
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol (2009) 1.63
Waste to bioproduct conversion with undefined mixed cultures: the carboxylate platform. Trends Biotechnol (2010) 1.52
Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose. Appl Environ Microbiol (2000) 1.44
Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J (2009) 1.40
The effects of operational and environmental variations on anaerobic wastewater treatment systems: a review. Bioresour Technol (2005) 1.11
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J (2010) 1.05
Caproate formation in mixed-culture fermentative hydrogen production. Bioresour Technol (2010) 0.90
Microbial community composition and dynamics in a semi-industrial-scale facility operating under the MixAlco™ bioconversion platform. J Appl Microbiol (2011) 0.83
Biomass conversion to mixed alcohol fuels using the MixAlco process. Appl Biochem Biotechnol (1999) 0.82
Conversion of sugarcane bagasse to carboxylic acids using a mixed culture of mesophilic microorganisms. Appl Biochem Biotechnol (2003) 0.82
Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Appl Microbiol Biotechnol (2010) 0.82
Carboxylate platform: the MixAlco process part 2: process economics. Appl Biochem Biotechnol (2009) 0.79
Investigation of intermittent air exposure on four-stage and one-stage anaerobic semi-continuous mixed-acid fermentations. Bioresour Technol (2011) 0.78
Techno-economic analysis of biomass to fuel conversion via the MixAlco process. J Ind Microbiol Biotechnol (2010) 0.78
Conversion of municipal solid wastes to carboxylic acids by thermophilic fermentation. Appl Biochem Biotechnol (2003) 0.78
Fermentation of sugarcane bagasse and chicken manure to calcium carboxylates under thermophilic conditions. Appl Biochem Biotechnol (2009) 0.78
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
The genome sequence of the rice blast fungus Magnaporthe grisea. Nature (2005) 6.95
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (2011) 6.93
Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev (2004) 3.67
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J (2007) 3.15
Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci U S A (2006) 3.07
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
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
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol (2006) 2.43
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
GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J (2010) 2.21
Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nat Methods (2010) 2.21
Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol (2011) 2.17
Whole-genome analyses of speciation events in pathogenic Brucellae. Infect Immun (2005) 2.11
Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol (2006) 2.08
Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets. Open Microbiol J (2010) 1.94
The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PLoS One (2011) 1.90
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Appl Environ Microbiol (2007) 1.82
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun (2013) 1.80
Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J (2010) 1.78
Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J (2010) 1.71
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome (2013) 1.69
Global distribution of a wild alga revealed by targeted metagenomics. Curr Biol (2012) 1.64
Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol (2012) 1.58
A call for standardized classification of metagenome projects. Environ Microbiol (2010) 1.58
Process and technoeconomic analysis of leading pretreatment technologies for lignocellulosic ethanol production using switchgrass. Bioresour Technol (2011) 1.51
Microarray-based analysis of microbial community RNAs by whole-community RNA amplification. Appl Environ Microbiol (2006) 1.49
Identification of peptaibols from Trichoderma virens and cloning of a peptaibol synthetase. J Biol Chem (2002) 1.47
Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun (2013) 1.42
The Neurospora crassa pheromone precursor genes are regulated by the mating type locus and the circadian clock. Mol Microbiol (2002) 1.40
Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae. BMC Microbiol (2009) 1.39
A mitogen-activated protein kinase pathway essential for mating and contributing to vegetative growth in Neurospora crassa. Genetics (2005) 1.37
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J (2013) 1.28
Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts. J Bacteriol (2011) 1.27
Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One (2013) 1.24
Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genet Biol (2004) 1.23
Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Appl Environ Microbiol (2006) 1.21
Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J (2008) 1.21
Gene clusters for insecticidal loline alkaloids in the grass-endophytic fungus Neotyphodium uncinatum. Genetics (2005) 1.19
Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation. ISME J (2010) 1.19
Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PLoS Genet (2012) 1.19
Hydrazine synthase, a unique phylomarker with which to study the presence and biodiversity of anammox bacteria. Appl Environ Microbiol (2011) 1.18
Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol (2006) 1.16
High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci U S A (2013) 1.16
Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens. ISME J (2012) 1.15
Expressed sequence tags and genes associated with loline alkaloid expression by the fungal endophyte Neotyphodium uncinatum. Fungal Genet Biol (2002) 1.15
Structural features affecting biomass enzymatic digestibility. Bioresour Technol (2007) 1.14
Microbial iron cycling in acidic geothermal springs of yellowstone national park: integrating molecular surveys, geochemical processes, and isolation of novel fe-active microorganisms. Front Microbiol (2012) 1.14
Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J (2011) 1.12
The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. Front Microbiol (2013) 1.12
The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Front Microbiol (2013) 1.12
Lime pretreatment and enzymatic hydrolysis of corn stover. Bioresour Technol (2005) 1.11
Relationship between abundance and specific activity of bacterioplankton in open ocean surface waters. Appl Environ Microbiol (2012) 1.10
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One (2013) 1.08
A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ (2013) 1.08
Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park. ISME J (2012) 1.07
The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS One (2012) 1.05
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J (2010) 1.05
Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol (2011) 1.05
Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. Front Microbiol (2013) 1.05
Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. Front Microbiol (2013) 1.05
Effect of structural features on enzyme digestibility of corn stover. Bioresour Technol (2005) 1.04
Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett (2014) 1.03
Comparative data on effects of leading pretreatments and enzyme loadings and formulations on sugar yields from different switchgrass sources. Bioresour Technol (2011) 1.03
FSR1 is essential for virulence and female fertility in Fusarium verticillioides and F. graminearum. Mol Plant Microbe Interact (2006) 1.02
Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl Environ Microbiol (2013) 1.01
The fluffy gene of Neurospora crassa is necessary and sufficient to induce conidiophore development. Genetics (2004) 1.00
Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol (2013) 0.97
Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J (2012) 0.97
Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle. PLoS One (2013) 0.95
Identification and quantification of methanogenic Archaea in adult chicken ceca. Appl Environ Microbiol (2006) 0.95
Comparative study on enzymatic digestibility of switchgrass varieties and harvests processed by leading pretreatment technologies. Bioresour Technol (2011) 0.95
Comparison of loline alkaloid gene clusters across fungal endophytes: predicting the co-regulatory sequence motifs and the evolutionary history. Fungal Genet Biol (2007) 0.94
Water management impacts on arsenic speciation and iron-reducing bacteria in contrasting rice-rhizosphere compartments. Environ Sci Technol (2011) 0.93
The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biol Evol (2009) 0.93
Surface and ultrastructural characterization of raw and pretreated switchgrass. Bioresour Technol (2011) 0.92
Influence of carbon-to-nitrogen ratio on the mixed-acid fermentation of wastewater sludge and pretreated bagasse. Bioresour Technol (2012) 0.92
Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer. Appl Environ Microbiol (2011) 0.92
Temporal and spatial regulation of gene expression during asexual development of Neurospora crassa. Genetics (2010) 0.92
Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions. MBio (2015) 0.90
Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases. Biotechnol Biofuels (2011) 0.90
Application of cellulase and hemicellulase to pure xylan, pure cellulose, and switchgrass solids from leading pretreatments. Bioresour Technol (2011) 0.90
Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. ISME J (2012) 0.90