Published in PLoS One on January 14, 2013
Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Front Microbiol (2015) 1.30
Back to Basics--The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities. PLoS One (2015) 1.17
Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. J Clin Microbiol (2013) 1.10
Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PLoS One (2013) 1.04
Characterization of intestinal bacteria in wild and domesticated adult black tiger shrimp (Penaeus monodon). PLoS One (2014) 0.87
Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons. BMC Microbiol (2013) 0.87
Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment. Genome Med (2015) 0.87
Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity. PLoS One (2014) 0.85
Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence. PLoS Genet (2015) 0.85
The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics. PLoS One (2014) 0.84
Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection. ISME J (2014) 0.84
Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function. PLoS One (2015) 0.84
Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers. Sci Rep (2015) 0.83
The cystic fibrosis lower airways microbial metagenome. ERJ Open Res (2016) 0.82
Bacterial diversity dynamics associated with different diets and different primer pairs in the rumen of Kankrej cattle. PLoS One (2014) 0.81
A systematic search for discriminating sites in the 16S ribosomal RNA gene. Microb Inform Exp (2014) 0.81
Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators. Front Plant Sci (2016) 0.81
Metabolic characteristics of a glycogen-accumulating organism in Defluviicoccus cluster II revealed by comparative genomics. Microb Ecol (2014) 0.78
Estimating bacterial diversity for ecological studies: methods, metrics, and assumptions. PLoS One (2015) 0.78
Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. Microbiome (2016) 0.78
Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing. Sci Rep (2015) 0.77
Considerations For Optimizing Microbiome Analysis Using a Marker Gene. Front Nutr (2016) 0.77
High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes. PLoS One (2015) 0.76
Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. Front Microbiol (2016) 0.75
Changes in microbial communities, photosynthesis and calcification of the coral Acropora gemmifera in response to ocean acidification. Sci Rep (2016) 0.75
Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs. Front Microbiol (2016) 0.75
Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon. Sci Rep (2016) 0.75
Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. BMC Microbiol (2016) 0.75
Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure. Appl Environ Microbiol (2016) 0.75
First Detection of Ehrlichia canis in Cerebrospinal Fluid From a Nonthrombocytopenic Dog with Meningoencephalitis By Broad-Range PCR. J Vet Intern Med (2015) 0.75
Bacterial diversity among four healthcare-associated institutes in Taiwan. Sci Rep (2017) 0.75
Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome. Microb Ecol (2015) 0.75
Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan. Microb Ecol (2017) 0.75
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol (2007) 60.97
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res (2008) 52.43
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol (1993) 51.00
Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A (2006) 42.38
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods (2008) 32.71
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol (1997) 17.04
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol (2008) 16.57
Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods (2009) 15.25
Microbial population structures in the deep marine biosphere. Science (2007) 14.61
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol (2009) 14.17
Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J (2007) 13.95
Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol (2010) 13.19
The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A (2008) 12.99
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One (2011) 12.26
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet (2008) 10.72
Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev (2004) 10.67
Review and re-analysis of domain-specific 16S primers. J Microbiol Methods (2003) 9.49
Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res (2007) 9.15
Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol (2011) 6.03
Field guide to next-generation DNA sequencers. Mol Ecol Resour (2011) 5.93
Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A (2010) 5.02
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One (2009) 4.93
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res (2010) 4.17
Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J (2010) 4.15
Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS One (2009) 4.11
The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol (2010) 3.26
Evidence for a core gut microbiota in the zebrafish. ISME J (2011) 3.22
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol (2010) 2.41
454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J (2011) 2.32
The effects of circumcision on the penis microbiome. PLoS One (2010) 2.15
Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing. PLoS One (2011) 2.04
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J (2012) 1.86
Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends Biotechnol (2010) 1.52
Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ Microbiol (2011) 1.38
Pyrosequencing of tagged 16S rRNA gene amplicons for rapid deciphering of the microbiomes of fermented foods such as pearl millet slurries. Appl Environ Microbiol (2009) 1.33
Molecular diversity of a North Carolina wastewater treatment plant as revealed by pyrosequencing. Appl Environ Microbiol (2008) 1.32
Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis. Bioresour Technol (2012) 1.16
Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol (2012) 1.15
The genetic landscape of a cell. Science (2010) 16.52
Erlotinib in lung cancer - molecular and clinical predictors of outcome. N Engl J Med (2005) 13.01
Wnt/beta-catenin/Tcf signaling induces the transcription of Axin2, a negative regulator of the signaling pathway. Mol Cell Biol (2002) 10.95
Poly(ADP-ribosyl)ation by PARP-1: 'PAR-laying' NAD+ into a nuclear signal. Genes Dev (2005) 4.61
Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol Biol (2006) 4.45
Increased exonic de novo mutation rate in individuals with schizophrenia. Nat Genet (2011) 4.01
Role of KRAS and EGFR as biomarkers of response to erlotinib in National Cancer Institute of Canada Clinical Trials Group Study BR.21. J Clin Oncol (2008) 3.97
Local InsP3-dependent perinuclear Ca2+ signaling in cardiac myocyte excitation-transcription coupling. J Clin Invest (2006) 3.72
Ca2+/calmodulin-dependent protein kinase II regulates cardiac Na+ channels. J Clin Invest (2006) 3.33
Ca2+/Calmodulin-dependent protein kinase II phosphorylation of ryanodine receptor does affect calcium sparks in mouse ventricular myocytes. Circ Res (2006) 3.26
PALB2 links BRCA1 and BRCA2 in the DNA-damage response. Curr Biol (2009) 3.15
Linkage of beta1-adrenergic stimulation to apoptotic heart cell death through protein kinase A-independent activation of Ca2+/calmodulin kinase II. J Clin Invest (2003) 3.15
Transgenic CaMKIIdeltaC overexpression uniquely alters cardiac myocyte Ca2+ handling: reduced SR Ca2+ load and activated SR Ca2+ release. Circ Res (2003) 3.04
Complete sequencing of pNDM-HK encoding NDM-1 carbapenemase from a multidrug-resistant Escherichia coli strain isolated in Hong Kong. PLoS One (2011) 2.98
Requirement for Ca2+/calmodulin-dependent kinase II in the transition from pressure overload-induced cardiac hypertrophy to heart failure in mice. J Clin Invest (2009) 2.98
Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med (2013) 2.70
Increased sarcoplasmic reticulum calcium leak but unaltered contractility by acute CaMKII overexpression in isolated rabbit cardiac myocytes. Circ Res (2005) 2.50
Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol (2007) 2.33
454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants. ISME J (2011) 2.32
Stat3 regulates microtubules by antagonizing the depolymerization activity of stathmin. J Cell Biol (2006) 2.21
An FHL1-containing complex within the cardiomyocyte sarcomere mediates hypertrophic biomechanical stress responses in mice. J Clin Invest (2008) 2.19
Interface-induced superconductivity and strain-dependent spin density waves in FeSe/SrTiO3 thin films. Nat Mater (2013) 2.15
A computational framework for influenza antigenic cartography. PLoS Comput Biol (2010) 2.14
GRIM-19, a death-regulatory gene product, suppresses Stat3 activity via functional interaction. EMBO J (2003) 2.00
Golgi targeting of ARF-like GTPase Arl3p requires its Nalpha-acetylation and the integral membrane protein Sys1p. Nat Cell Biol (2004) 1.94
Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proc Natl Acad Sci U S A (2007) 1.85
Widespread production of extracellular superoxide by heterotrophic bacteria. Science (2013) 1.84
The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription. Mol Cell Biol (2007) 1.82
Sphingosine 1-phosphate S1P2 and S1P3 receptor-mediated Akt activation protects against in vivo myocardial ischemia-reperfusion injury. Am J Physiol Heart Circ Physiol (2007) 1.70
Cancer genomics: technology, discovery, and translation. J Clin Oncol (2012) 1.70
Regulation of Ins(3,4,5,6)P(4) signaling by a reversible kinase/phosphatase. Curr Biol (2002) 1.69
Antibiotic resistance genes in water environment. Appl Microbiol Biotechnol (2009) 1.63
Upregulation of GLUT1 expression is necessary for hypertrophy and survival of neonatal rat cardiomyocytes. J Mol Cell Cardiol (2003) 1.62
Cardiac hypertrophy and heart failure development through Gq and CaM kinase II signaling. J Cardiovasc Pharmacol (2010) 1.61
A network of multi-tasking proteins at the DNA replication fork preserves genome stability. PLoS Genet (2005) 1.61
RNF8-dependent histone modifications regulate nucleosome removal during spermatogenesis. Dev Cell (2010) 1.57
Intrabiliary RF heat-enhanced local chemotherapy of a cholangiocarcinoma cell line: monitoring with dual-modality imaging--preclinical study. Radiology (2013) 1.56
Validation of KRAS testing for anti-EGFR therapeutic decisions for patients with metastatic colorectal carcinoma. Arch Pathol Lab Med (2012) 1.56
Histone ubiquitination associates with BRCA1-dependent DNA damage response. Mol Cell Biol (2008) 1.50
Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial. Int J Cancer (2012) 1.49
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae. BMC Genet (2005) 1.47
The cold-inducible RNA-binding protein migrates from the nucleus to cytoplasmic stress granules by a methylation-dependent mechanism and acts as a translational repressor. Exp Cell Res (2007) 1.47
Interaction of radiolabeled antibodies with fungal cells and components of the immune system in vitro and during radioimmunotherapy for experimental fungal infection. J Infect Dis (2006) 1.47
Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environ Health Perspect (2013) 1.42
Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One (2011) 1.41
The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet (2009) 1.38
An adjacent pair of human NUDT genes on chromosome X are preferentially expressed in testis and encode two new isoforms of diphosphoinositol polyphosphate phosphohydrolase. J Biol Chem (2002) 1.37
Synthetic lethal analysis implicates Ste20p, a p21-activated potein kinase, in polarisome activation. Mol Biol Cell (2003) 1.37
Acquisition of adult-like TLR4 and TLR9 responses during the first year of life. PLoS One (2010) 1.37
Landau quantization of topological surface states in Bi2Se3. Phys Rev Lett (2010) 1.36
Direct observation of nodes and twofold symmetry in FeSe superconductor. Science (2011) 1.35
A novel sequence in the coiled-coil domain of Stat3 essential for its nuclear translocation. J Biol Chem (2003) 1.32
Immunotherapy with chimeric NKG2D receptors leads to long-term tumor-free survival and development of host antitumor immunity in murine ovarian cancer. J Immunol (2008) 1.32
Global analysis of transcriptional regulation by poly(ADP-ribose) polymerase-1 and poly(ADP-ribose) glycohydrolase in MCF-7 human breast cancer cells. J Biol Chem (2009) 1.32
CO(2)-driven ocean acidification alters and weakens integrity of the calcareous tubes produced by the serpulid tubeworm, Hydroides elegans. PLoS One (2012) 1.31
Ybp2 associates with the central kinetochore of Saccharomyces cerevisiae and mediates proper mitotic progression. PLoS One (2008) 1.31
Self-assembly of large-scale and ultrathin silver nanoplate films with tunable plasmon resonance properties. ACS Nano (2011) 1.30
Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing. Appl Microbiol Biotechnol (2012) 1.30
Polo-like kinase 1 is essential for early embryonic development and tumor suppression. Mol Cell Biol (2008) 1.29
Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing. Appl Microbiol Biotechnol (2012) 1.28
Plasma IP-10 is associated with rapid disease progression in early HIV-1 infection. Viral Immunol (2012) 1.28
Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge. PLoS One (2012) 1.24
Mechanisms regulating mercury bioavailability for methylating microorganisms in the aquatic environment: a critical review. Environ Sci Technol (2013) 1.23
Bioproducts from Aureobasidium pullulans, a biotechnologically important yeast. Appl Microbiol Biotechnol (2009) 1.22
Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs. Nucleic Acids Res (2009) 1.21
Analysis of the bacterial community in a laboratory-scale nitrification reactor and a wastewater treatment plant by 454-pyrosequencing. Water Res (2011) 1.21
The GTPase Arf1p and the ER to Golgi cargo receptor Erv14p cooperate to recruit the golgin Rud3p to the cis-Golgi. J Cell Biol (2004) 1.21
Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy. PLoS One (2012) 1.20
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol (2014) 1.19
Concepts and applications for influenza antigenic cartography. Influenza Other Respir Viruses (2011) 1.19
Sequential and distinct roles of the cadherin domain-containing protein Axl2p in cell polarization in yeast cell cycle. Mol Biol Cell (2007) 1.18
Ursolic acid-induced AMP-activated protein kinase (AMPK) activation contributes to growth inhibition and apoptosis in human bladder cancer T24 cells. Biochem Biophys Res Commun (2012) 1.17
Aurora A is essential for early embryonic development and tumor suppression. J Biol Chem (2008) 1.17
Tumor necrosis factor-alpha induces long-term potentiation of C-fiber evoked field potentials in spinal dorsal horn in rats with nerve injury: the role of NF-kappa B, JNK and p38 MAPK. Neuropharmacology (2006) 1.17
Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma. Gastroenterology (2012) 1.16
Interaction between a Ras and a Rho GTPase couples selection of a growth site to the development of cell polarity in yeast. Mol Biol Cell (2003) 1.16
Chimeric NKG2D receptor-bearing T cells as immunotherapy for ovarian cancer. Cancer Res (2007) 1.16
Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code. Genome Biol Evol (2014) 1.16
Evaluating total lymphocyte count as a surrogate marker for CD4 cell count in the management of HIV-infected patients in resource-limited settings: a study from China. PLoS One (2013) 1.15
Formation of a polypseudorotaxane via self-assembly of γ-cyclodextrin with poly(N-isopropylacrylamide). Macromol Rapid Commun (2012) 1.14
Suppression of terpenoid synthesis in plants by a virus promotes its mutualism with vectors. Ecol Lett (2012) 1.14
Signaling by higher inositol polyphosphates. Synthesis of bisdiphosphoinositol tetrakisphosphate ("InsP8") is selectively activated by hyperosmotic stress. J Biol Chem (2004) 1.13
The association between EGFR variant III, HPV, p16, c-MET, EGFR gene copy number and response to EGFR inhibitors in patients with recurrent or metastatic squamous cell carcinoma of the head and neck. Head Neck Oncol (2011) 1.13
Molecular characterization of the 2011 Hong Kong scarlet fever outbreak. J Infect Dis (2012) 1.13
Database and analyses of known alternatively spliced genes in plants. Genomics (2003) 1.13
Inorganic phosphate deprivation causes tRNA nuclear accumulation via retrograde transport in Saccharomyces cerevisiae. Genetics (2007) 1.12
Integrative analysis of many weighted co-expression networks using tensor computation. PLoS Comput Biol (2011) 1.12
Gold nanoparticle thin films fabricated by electrophoretic deposition method for highly sensitive SERS application. Nanoscale Res Lett (2012) 1.12
Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure. Chem Res Toxicol (2009) 1.11
Using sequence data to infer the antigenicity of influenza virus. MBio (2013) 1.10
Optimization of fixation methods for observation of bacterial cell morphology and surface ultrastructures by atomic force microscopy. Appl Microbiol Biotechnol (2011) 1.10
Rab25 is a tumor suppressor gene with antiangiogenic and anti-invasive activities in esophageal squamous cell carcinoma. Cancer Res (2012) 1.09
Effects of lovastatin on Rho isoform expression, activity, and association with guanine nucleotide dissociation inhibitors. Biochem Pharmacol (2007) 1.09
Molecular characterization of the effects of Y-27632. Cell Motil Cytoskeleton (2007) 1.09