Published in Bioinformatics on September 07, 2011
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Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature (2015) 4.98
Exploiting sparseness in de novo genome assembly. BMC Bioinformatics (2012) 2.88
GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics (2012) 2.72
Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature (2015) 2.41
CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med (2016) 2.40
Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science (2016) 2.29
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell (2013) 2.28
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Current challenges in de novo plant genome sequencing and assembly. Genome Biol (2012) 1.69
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods (2015) 1.53
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Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral. PLoS One (2015) 1.51
The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun (2014) 1.47
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Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome (2017) 1.46
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Ubiquitous L1 mosaicism in hippocampal neurons. Cell (2015) 1.40
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Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol Detect Quantif (2015) 1.30
Gut microbiome and dietary patterns in different Saudi populations and monkeys. Sci Rep (2016) 1.29
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Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8. PLoS Genet (2014) 1.23
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Whole-genome phylogenomic heterogeneity of Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in Canada between 1989 and 2013. J Clin Microbiol (2014) 1.19
Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism. Nat Commun (2016) 1.18
Back to Basics--The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities. PLoS One (2015) 1.17
The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl Environ Microbiol (2013) 1.16
Functional characterization of the TERRA transcriptome at damaged telomeres. Nat Commun (2014) 1.16
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R Soc Open Sci (2015) 1.14
The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling. Front Microbiol (2013) 1.12
Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol (2013) 1.10
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Extensive differences in gene expression between symbiotic and aposymbiotic cnidarians. G3 (Bethesda) (2014) 1.09
Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere. PLoS One (2013) 1.08
Differing Complex Microbiota Alter Disease Severity of the IL-10(-/-) Mouse Model of Inflammatory Bowel Disease. Front Microbiol (2017) 1.08
Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs. Retrovirology (2016) 1.07
Longitudinal study of murine microbiota activity and interactions with the host during acute inflammation and recovery. ISME J (2014) 1.06
Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science (2016) 1.06
Poly(A)-specific ribonuclease (PARN) mediates 3'-end maturation of the telomerase RNA component. Nat Genet (2015) 1.06
Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly. PLoS One (2013) 1.05
Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods (2015) 1.04
LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome (2014) 1.03
Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett (2014) 1.03
Defining the vulnerable period for re-establishment of Clostridium difficile colonization after treatment of C. difficile infection with oral vancomycin or metronidazole. PLoS One (2013) 1.03
Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions. Front Microbiol (2014) 1.03
Long-term forest soil warming alters microbial communities in temperate forest soils. Front Microbiol (2015) 1.03
Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs. BMC Genomics (2013) 1.02
MP3: a software tool for the prediction of pathogenic proteins in genomic and metagenomic data. PLoS One (2014) 1.00
Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing. PLoS One (2015) 0.98
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J (2016) 0.98
Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation. Proc Natl Acad Sci U S A (2014) 0.97
De novo transcriptome assembly of heavy metal tolerant Silene dioica. Genom Data (2017) 0.97
Integrated metagenomics and network analysis of soil microbial community of the forest timberline. Sci Rep (2015) 0.97
Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nat Genet (2016) 0.95
A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nat Genet (2016) 0.95
Genome sequence and genetic diversity of European ash trees. Nature (2016) 0.95
Characterization of VCC-1, a Novel Ambler Class A Carbapenemase from Vibrio cholerae Isolated from Imported Retail Shrimp Sold in Canada. Antimicrob Agents Chemother (2016) 0.95
Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae. Sci Rep (2016) 0.94
Noninvasive monitoring of infection and rejection after lung transplantation. Proc Natl Acad Sci U S A (2015) 0.94
Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun (2016) 0.93
Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs. Microb Ecol (2015) 0.93
Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections. J Clin Microbiol (2014) 0.93
The poultry-associated microbiome: network analysis and farm-to-fork characterizations. PLoS One (2013) 0.93
Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci U S A (2015) 0.93
Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China. Sci Rep (2015) 0.92
The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biol Evol (2015) 0.92
Small RNAs derived from tRNAs and rRNAs are highly enriched in exosomes from both old and new world Leishmania providing evidence for conserved exosomal RNA Packaging. BMC Genomics (2015) 0.92
Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome (2015) 0.92
Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME J (2015) 0.91
Limited dissemination of the wastewater treatment plant core resistome. Nat Commun (2015) 0.91
Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia. Sci Rep (2016) 0.90
Forest harvesting reduces the soil metagenomic potential for biomass decomposition. ISME J (2015) 0.90
Comparative Phylodynamics of Rabbit Hemorrhagic Disease Virus in Australia and New Zealand. J Virol (2015) 0.90
The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types. PeerJ (2014) 0.90
Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis. BMC Microbiol (2015) 0.90
Draft Genome Sequences of One Marine and One Clinical Vibrio parahaemolyticus Strain, Both Isolated in Sweden. Genome Announc (2016) 0.90
Transplanting Soil Microbiomes Leads to Lasting Effects on Willow Growth, but not on the Rhizosphere Microbiome. Front Microbiol (2015) 0.89
Amplification of RNA by an RNA polymerase ribozyme. Proc Natl Acad Sci U S A (2016) 0.89
Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession. Sci Rep (2015) 0.88
EAGER: efficient ancient genome reconstruction. Genome Biol (2016) 0.88
Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions. Sci Rep (2016) 0.88
The gene cortex controls mimicry and crypsis in butterflies and moths. Nature (2016) 0.88
Advanced Applications of RNA Sequencing and Challenges. Bioinform Biol Insights (2015) 0.88
Missense mutations in TENM4, a regulator of axon guidance and central myelination, cause essential tremor. Hum Mol Genet (2015) 0.88
Illumina amplicon sequencing of 16S rRNA tag reveals bacterial community development in the rhizosphere of apple nurseries at a replant disease site and a new planting site. PLoS One (2014) 0.88
Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD. Gut (2016) 0.87
Engineering an allosteric transcription factor to respond to new ligands. Nat Methods (2015) 0.87
Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump. Nat Commun (2015) 0.87
Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014. J Clin Microbiol (2016) 0.87
Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. Stand Genomic Sci (2014) 0.87
Mucosal-associated invariant T cell-rich congenic mouse strain allows functional evaluation. J Clin Invest (2015) 0.87
Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees. Front Microbiol (2015) 0.87
Elevated IgA Plasmablast Levels in Subjects at Risk of Developing Rheumatoid Arthritis. Arthritis Rheumatol (2016) 0.87
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
Aggressive assembly of pyrosequencing reads with mates. Bioinformatics (2008) 11.01
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76
Unlocking short read sequencing for metagenomics. PLoS One (2010) 4.88
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
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Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
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
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature (2002) 8.92
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods (2009) 8.15
Cloud computing and the DNA data race. Nat Biotechnol (2010) 7.81
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
How to map billions of short reads onto genomes. Nat Biotechnol (2009) 6.59
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol (2011) 6.23
Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature (2008) 5.96
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
Assembly of large genomes using second-generation sequencing. Genome Res (2010) 5.94
A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol (2009) 5.93
The genome of woodland strawberry (Fragaria vesca). Nat Genet (2010) 5.86
Comparative genome assembly. Brief Bioinform (2004) 5.81
Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet (2011) 5.58
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol (2005) 5.48
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biol (2006) 5.44
Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol (2014) 5.40
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37
Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci U S A (2002) 5.28
The MaSuRCA genome assembler. Bioinformatics (2013) 5.07
Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95
Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89
Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biol (2007) 4.80
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol (2007) 4.27
Beware of mis-assembled genomes. Bioinformatics (2005) 4.14
DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics (2004) 3.74
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics (2003) 3.50
Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics (2010) 3.38
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol (2004) 3.36
Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (2005) 2.71
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci U S A (2011) 2.62
Computational gene prediction using multiple sources of evidence. Genome Res (2004) 2.58
The value of complete microbial genome sequencing (you get what you pay for). J Bacteriol (2002) 2.58
Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature (2002) 2.49
JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics (2005) 2.37
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol (2004) 2.36
GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (2013) 2.24
Physiogenomic resources for rat models of heart, lung and blood disorders. Nat Genet (2006) 2.05
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biol (2006) 2.00
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol (2014) 1.90
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J Bacteriol (2011) 1.80
Automated correction of genome sequence errors. Nucleic Acids Res (2004) 1.80
Comprehensive DNA signature discovery and validation. PLoS Comput Biol (2007) 1.75
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res (2010) 1.72
Between a chicken and a grape: estimating the number of human genes. Genome Biol (2010) 1.72
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Brief Bioinform (2011) 1.70
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. Nucleic Acids Res (2003) 1.63
The complete genome sequence of Bacillus anthracis Ames "Ancestor". J Bacteriol (2008) 1.61
Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol (2010) 1.54
The age of the Arabidopsis thaliana genome duplication. Plant Mol Biol (2003) 1.52
Computational discovery of internal micro-exons. Genome Res (2003) 1.52
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res (2005) 1.48
OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res (2008) 1.47
Sequencing and assembly of the 22-gb loblolly pine genome. Genetics (2014) 1.46
What are decision trees? Nat Biotechnol (2008) 1.39
2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. PLoS One (2009) 1.32
Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics (2014) 1.32
Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol (2010) 1.29
Computational gene finding in plants. Plant Mol Biol (2002) 1.29
Clustering metagenomic sequences with interpolated Markov models. BMC Bioinformatics (2010) 1.28
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Res (2009) 1.23
Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas. PLoS One (2008) 1.22
A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biol Direct (2014) 1.20
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res (2011) 1.17
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics (2010) 1.14
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics (2007) 1.13
Do-it-yourself genetic testing. Genome Biol (2010) 1.06
Efficient decoding algorithms for generalized hidden Markov model gene finders. BMC Bioinformatics (2005) 1.05
Contamination in the draft of the human genome masquerades as lateral gene transfer. DNA Seq (2002) 1.00