Published in BMC Genomics on December 13, 2014
Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS One (2015) 0.85
Whole-Genome Sequence of the Cheese Isolate Streptococcus macedonicus 679. Genome Announc (2016) 0.75
Diversity and Control of Spoilage Fungi in Dairy Products: An Update. Microorganisms (2017) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
CAP3: A DNA sequence assembly program. Genome Res (1999) 50.04
FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One (2010) 26.15
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res (1989) 19.85
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res (2011) 10.82
Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A (2006) 10.24
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
Integrative analysis of environmental sequences using MEGAN4. Genome Res (2011) 8.60
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Genomics. Genome project standards in a new era of sequencing. Science (2009) 7.72
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
Accurate and universal delineation of prokaryotic species. Nat Methods (2013) 3.14
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol (2014) 2.85
The rpoB gene as a tool for clinical microbiologists. Trends Microbiol (2008) 2.12
Use of the DNA sequence of variable regions of the 16S rRNA gene for rapid and accurate identification of bacteria in the Lactobacillus acidophilus complex. J Appl Microbiol (2000) 1.72
High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl Environ Microbiol (2013) 1.52
Comparative bacterial proteomics: analysis of the core genome concept. PLoS One (2008) 1.49
Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell (2014) 1.42
Surface microflora of four smear-ripened cheeses. Appl Environ Microbiol (2005) 1.33
Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences. Res Microbiol (2007) 1.32
The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PLoS One (2010) 1.28
"Remake" by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl Environ Microbiol (2012) 1.23
High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl Environ Microbiol (2012) 1.23
Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation. BMC Genomics (2011) 1.23
Temporal stability and biodiversity of two complex antilisterial cheese-ripening microbial consortia. Appl Environ Microbiol (2003) 1.19
Assessment of the rind microbial diversity in a farmhouse-produced vs a pasteurized industrially produced soft red-smear cheese using both cultivation and rDNA-based methods. J Appl Microbiol (2004) 1.19
Does smearing inoculum reflect the bacterial composition of the smear at the end of the ripening of a French soft, red-smear cheese? J Dairy Sci (2004) 1.17
Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl Environ Microbiol (2007) 1.15
Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus. Food Microbiol (2012) 1.15
Molecular fingerprinting of dairy microbial ecosystems by use of temporal temperature and denaturing gradient gel electrophoresis. Appl Environ Microbiol (2004) 1.13
Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments. Microbiology (2000) 1.12
Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol (2011) 1.12
Facility-specific "house" microbiome drives microbial landscapes of artisan cheesemaking plants. Appl Environ Microbiol (2013) 1.10
Characteristics of microbial biofilm on wooden vats ('gerles') in PDO Salers cheese. Int J Food Microbiol (2012) 1.10
Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov., novel coryneform species isolated from the surfaces of cheeses. Int J Syst Evol Microbiol (2005) 1.10
The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese. PLoS One (2010) 1.08
Traditional cheeses: rich and diverse microbiota with associated benefits. Int J Food Microbiol (2014) 1.08
Genome sequence of Leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture. J Bacteriol (2012) 1.03
Stability of the biodiversity of the surface consortia of Gubbeen, a red-smear cheese. J Dairy Sci (2007) 0.98
Microbacterium gubbeenense sp. nov., from the surface of a smear-ripened cheese. Int J Syst Evol Microbiol (2001) 0.98
Commercial ripening starter microorganisms inoculated into cheese milk do not successfully establish themselves in the resident microbial ripening consortia of a South german red smear cheese. Appl Environ Microbiol (2008) 0.93
The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR. Int J Food Microbiol (2011) 0.91
Cow teat skin, a potential source of diverse microbial populations for cheese production. Appl Environ Microbiol (2011) 0.90
Assessment of the microbial diversity at the surface of Livarot cheese using culture-dependent and independent approaches. Int J Food Microbiol (2009) 0.90
Agrococcus casei sp. nov., isolated from the surfaces of smear-ripened cheeses. Int J Syst Evol Microbiol (2007) 0.88
Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment. BMC Genomics (2013) 0.87
Characterization of microflora in Latin-style cheeses by next-generation sequencing technology. BMC Microbiol (2012) 0.86
Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses. Int J Syst Evol Microbiol (2009) 0.86
Pooled Genomic Indexing (PGI): analysis and design of experiments. J Comput Biol (2004) 0.85
Surface microbial consortia from Livarot, a French smear-ripened cheese. Can J Microbiol (2011) 0.85
Presence of halophilic and alkaliphilic lactic acid bacteria in various cheeses. Lett Appl Microbiol (2007) 0.81
Surface microbiota analysis of Taleggio, Gorgonzola, Casera, Scimudin and Formaggio di Fossa Italian cheeses. Int J Food Microbiol (2010) 0.81
Hard ewe's milk cheese manufactured from milk of three different groups of somatic cell counts. J Dairy Sci (2003) 0.77
Microbial and sensory changes throughout the ripening of Prato cheese made from milk with different levels of somatic cells. J Dairy Sci (2008) 0.77
Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis. BMC Microbiol (2010) 0.76
Biodiversity and growth dynamics of lactic acid bacteria in artisanal PDO Ossau-Iraty cheeses made from raw ewe's milk with different starters. Food Microbiol (2011) 0.76
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother (2012) 13.77
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res (2012) 11.33
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol (2012) 8.15
Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol (2009) 8.06
ARDB--Antibiotic Resistance Genes Database. Nucleic Acids Res (2008) 7.82
Minimus: a fast, lightweight genome assembler. BMC Bioinformatics (2007) 7.65
The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (2005) 7.61
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
The genome of the protist parasite Entamoeba histolytica. Nature (2005) 5.33
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Genome assembly forensics: finding the elusive mis-assembly. Genome Biol (2008) 4.91
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Differential abundance analysis for microbial marker-gene surveys. Nat Methods (2013) 4.49
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol (2005) 4.42
Next generation sequence assembly with AMOS. Curr Protoc Bioinformatics (2011) 3.60
Dietary intervention impact on gut microbial gene richness. Nature (2013) 3.56
The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23K. Nat Biotechnol (2005) 3.48
Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics (2010) 3.45
Exploiting sparseness in de novo genome assembly. BMC Bioinformatics (2012) 2.88
Figaro: a novel statistical method for vector sequence removal. Bioinformatics (2008) 2.81
Enzyme replacement therapy for murine hypophosphatasia. J Bone Miner Res (2008) 2.64
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A (2011) 2.62
Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics (2008) 2.61
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics (2011) 2.55
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science (2012) 2.38
Bambus 2: scaffolding metagenomes. Bioinformatics (2011) 2.24
Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J Comput Biol (2009) 2.10
Sequence assembly demystified. Nat Rev Genet (2013) 2.09
Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nat Biotechnol (2007) 2.06
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC Bioinformatics (2010) 2.01
Complete genome sequence of the probiotic Lactobacillus casei strain BL23. J Bacteriol (2010) 1.98
An optimized system for expression and purification of secreted bacterial proteins. Protein Expr Purif (2005) 1.96
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One (2012) 1.96
snpTree--a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics (2012) 1.88
Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes. Microbiology (2005) 1.79
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol (2013) 1.74
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform (2011) 1.70
Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev (2009) 1.67
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics (2011) 1.66
Genomic characterization of the Yersinia genus. Genome Biol (2010) 1.63
Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria. Proteomics (2009) 1.58
Benchmarking of methods for genomic taxonomy. J Clin Microbiol (2014) 1.51
Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour. Mol Microbiol (2009) 1.48
Burden of illness in Parkinson's disease. Mov Disord (2005) 1.48
Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci U S A (2013) 1.40
Simultaneous delivery of tenofovir and acyclovir via an intravaginal ring. Antimicrob Agents Chemother (2011) 1.38
Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics (2014) 1.33
Characterization of Ehp, a secreted complement inhibitory protein from Staphylococcus aureus. J Biol Chem (2007) 1.32
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC Genomics (2010) 1.31
Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries. J Clin Microbiol (2013) 1.30
The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PLoS One (2010) 1.28
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biol (2014) 1.24
Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene. ISME J (2011) 1.22
Fructose utilization in Lactococcus lactis as a model for low-GC gram-positive bacteria: its regulator, signal, and DNA-binding site. J Bacteriol (2005) 1.18
An intravaginal ring for the simultaneous delivery of multiple drugs. J Pharm Sci (2012) 1.17
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res (2011) 1.17
Severity of premenstrual symptoms in a health maintenance organization population. Obstet Gynecol (2002) 1.17
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol (2005) 1.16
Microbial interactions within a cheese microbial community. Appl Environ Microbiol (2007) 1.16
Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. J Comput Biol (2010) 1.15
Bacterial natural transformation by highly fragmented and damaged DNA. Proc Natl Acad Sci U S A (2013) 1.15
Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl Environ Microbiol (2007) 1.15
Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism. Immunology (2010) 1.15
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics (2011) 1.13
Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl Environ Microbiol (2011) 1.12
Safety and pharmacokinetics of intravaginal rings delivering tenofovir in pig-tailed macaques. Antimicrob Agents Chemother (2012) 1.11
Low-pass sequencing for microbial comparative genomics. BMC Genomics (2004) 1.11
Tenofovir and tenofovir disoproxil fumarate pharmacokinetics from intravaginal rings. AIDS (2012) 1.10
Characteristics of microbial biofilm on wooden vats ('gerles') in PDO Salers cheese. Int J Food Microbiol (2012) 1.10
Bacterial community dynamics during production of registered designation of origin Salers cheese as evaluated by 16S rRNA gene single-strand conformation polymorphism analysis. Appl Environ Microbiol (2003) 1.10
Stability of microbial communities in goat milk during a lactation year: molecular approaches. Syst Appl Microbiol (2007) 1.09
The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese. PLoS One (2010) 1.08
De novo likelihood-based measures for comparing genome assemblies. BMC Res Notes (2013) 1.07