Published in Nucleic Acids Res on April 19, 2010
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Arixanthomycins A-C: Phylogeny-guided discovery of biologically active eDNA-derived pentangular polyphenols. ACS Chem Biol (2014) 0.89
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. ISME J (2014) 0.88
Impacts of the Three Gorges Dam on microbial structure and potential function. Sci Rep (2015) 0.88
Metagenomic profiling of microbial composition and antibiotic resistance determinants in Puget Sound. PLoS One (2012) 0.88
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Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw. Sci Rep (2015) 0.87
Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. Proc Natl Acad Sci U S A (2016) 0.87
Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants. Front Microbiol (2015) 0.87
Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Res (2015) 0.87
Intestinal Microbiota Distinguish Gout Patients from Healthy Humans. Sci Rep (2016) 0.87
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Identification of protein coding regions in RNA transcripts. Nucleic Acids Res (2015) 0.86
Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue. PLoS Comput Biol (2014) 0.86
Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach. BMC Gastroenterol (2013) 0.86
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Sci Rep (2016) 0.86
Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes. J Ind Microbiol Biotechnol (2014) 0.85
SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles. Bioinformatics (2013) 0.85
Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. Proc Natl Acad Sci U S A (2015) 0.85
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinformatics (2012) 0.84
Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. Sci Rep (2016) 0.84
Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean. mSphere (2017) 0.84
Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections. Appl Environ Microbiol (2016) 0.84
Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers. Sci Rep (2015) 0.83
Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. Biotechnol Biofuels (2015) 0.83
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics. Front Genet (2015) 0.82
Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). BMC Genomics (2012) 0.82
Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau. BMC Genomics (2013) 0.82
Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis. Sci Rep (2014) 0.82
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. Front Microbiol (2017) 0.81
Mining soil metagenomes to better understand the evolution of natural product structural diversity: pentangular polyphenols as a case study. J Am Chem Soc (2014) 0.81
A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves. AMB Express (2013) 0.81
Integrative workflows for metagenomic analysis. Front Cell Dev Biol (2014) 0.81
Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Front Microbiol (2016) 0.80
Gene prediction in metagenomic fragments based on the SVM algorithm. BMC Bioinformatics (2013) 0.80
Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling. Sci Rep (2015) 0.80
Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness. Sci Rep (2016) 0.80
MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota. Microbiome (2016) 0.79
Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes. Front Microbiol (2014) 0.79
MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. Bioinformatics (2012) 0.79
Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes. Front Microbiol (2015) 0.79
Cold shock induction of recombinant Arctic environmental genes. BMC Biotechnol (2015) 0.79
Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics. Antimicrob Agents Chemother (2015) 0.79
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. Nucleic Acids Res (2012) 0.79
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput Biol (2015) 0.79
Marine Metagenome as A Resource for Novel Enzymes. Genomics Proteomics Bioinformatics (2015) 0.79
The perinatal microbiome and pregnancy: moving beyond the vaginal microbiome. Cold Spring Harb Perspect Med (2015) 0.78
New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. PLoS One (2014) 0.78
Selective enrichment of environmental DNA libraries for genes encoding nonribosomal peptides and polyketides by phosphopantetheine transferase-dependent complementation of siderophore biosynthesis. ACS Chem Biol (2012) 0.78
Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
Environmental genome shotgun sequencing of the Sargasso Sea. Science (2004) 45.23
An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 44.35
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Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
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GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res (2001) 24.24
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MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res (2008) 6.82
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res (2006) 6.64
EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinformatics (2003) 6.63
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A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol (2001) 3.15
YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol (2003) 2.67
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. BMC Bioinformatics (2008) 2.67
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Finding novel genes in bacterial communities isolated from the environment. Bioinformatics (2006) 2.55
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Improving gene annotation of complete viral genomes. Nucleic Acids Res (2003) 1.80
Identification of proteins associated with murine cytomegalovirus virions. J Virol (2004) 1.72
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Orphelia: predicting genes in metagenomic sequencing reads. Nucleic Acids Res (2009) 1.43
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Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis. J Biomol Struct Dyn (2004) 0.96
Effects of choice of DNA sequence model structure on gene identification accuracy. Bioinformatics (2004) 0.95
The mystery of two straight lines in bacterial genome statistics. Bull Math Biol (2007) 0.86
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The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell (2010) 2.47
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Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J Bioinform Comput Biol (2010) 1.26
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Evaluating the protein coding potential of exonized transposable element sequences. Biol Direct (2007) 1.05
In silico identification of genes in bacteriophage DNA. Methods Mol Biol (2009) 1.04
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinformatics (2006) 1.04
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Exonization of the LTR transposable elements in human genome. BMC Genomics (2007) 0.99
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Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi. BMC Genomics (2011) 0.97
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Control of Streptococcus pyogenes virulence: modeling of the CovR/S signal transduction system. J Theor Biol (2006) 0.95
Identification of new human cadherin genes using a combination of protein motif search and gene finding methods. J Mol Biol (2004) 0.89
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Probabilistic models for biological sequences: selection and Maximum Likelihood estimation. Int J Bioinform Res Appl (2006) 0.83
MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. Bioinformatics (2012) 0.79
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. Nucleic Acids Res (2012) 0.79
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Protein secondary structure prediction with semi Markov HMMs. Conf Proc IEEE Eng Med Biol Soc (2004) 0.76
UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing. Nucleic Acids Res (2013) 0.75
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Convergence rate estimation for the TKF91 model of biological sequence length evolution. Math Biosci (2007) 0.75