Published in Bioinformatics on December 04, 2009
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods (2013) 31.15
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform (2010) 18.05
Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet (2010) 9.53
Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol (2012) 8.99
Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88
Savant: genome browser for high-throughput sequencing data. Bioinformatics (2010) 6.51
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol (2011) 4.98
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol (2012) 3.94
Comparing de novo assemblers for 454 transcriptome data. BMC Genomics (2010) 3.49
Gap5--editing the billion fragment sequence assembly. Bioinformatics (2010) 2.84
Novel bacterial taxa in the human microbiome. PLoS One (2012) 2.35
Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol (2010) 2.32
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach. Nucleic Acids Res (2013) 2.08
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics (2011) 2.02
GenomeView: a next-generation genome browser. Nucleic Acids Res (2011) 1.91
High-resolution human cytomegalovirus transcriptome. Proc Natl Acad Sci U S A (2011) 1.67
Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection. MBio (2013) 1.66
MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. Nucleic Acids Res (2010) 1.49
Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. PLoS One (2012) 1.47
SNP Discovery through Next-Generation Sequencing and Its Applications. Int J Plant Genomics (2012) 1.46
Evolution and diversity in human herpes simplex virus genomes. J Virol (2013) 1.35
Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res (2010) 1.34
Complete genome sequences of elephant endotheliotropic herpesviruses 1A and 1B determined directly from fatal cases. J Virol (2013) 1.31
Multiple mitochondrial introgression events and heteroplasmy in trypanosoma cruzi revealed by maxicircle MLST and next generation sequencing. PLoS Negl Trop Dis (2012) 1.28
A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics (2014) 1.27
Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics (2011) 1.26
Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate. BMC Genomics (2010) 1.24
Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. Mol Biol Evol (2012) 1.23
Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia. Planta (2014) 1.19
Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell (2014) 1.15
Molecular definition of vaginal microbiota in East African commercial sex workers. Appl Environ Microbiol (2011) 1.13
Deep sequencing analysis of defective genomes of parainfluenza virus 5 and their role in interferon induction. J Virol (2013) 1.12
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics (2011) 1.10
A novel approach for mining polymorphic microsatellite markers in silico. PLoS One (2011) 1.09
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Bioinformatics (2012) 1.09
An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6. BMC Genomics (2010) 1.08
BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform (2012) 1.08
Whole-exome sequencing identifies MYO15A mutations as a cause of autosomal recessive nonsyndromic hearing loss in Korean families. BMC Med Genet (2013) 1.07
Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Appl Environ Microbiol (2012) 1.06
Chromatin accessibility: a window into the genome. Epigenetics Chromatin (2014) 1.06
Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate Pseudomonas aeruginosa 96. Antimicrob Agents Chemother (2013) 1.05
First fatality associated with elephant endotheliotropic herpesvirus 5 in an Asian elephant: pathological findings and complete viral genome sequence. Sci Rep (2014) 1.03
Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One (2013) 1.03
Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions. Microb Inform Exp (2014) 1.02
Stimulation of gross chromosomal rearrangements by the human CEB1 and CEB25 minisatellites in Saccharomyces cerevisiae depends on G-quadruplexes or Cdc13. PLoS Genet (2012) 1.00
Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PLoS One (2012) 1.00
Fast skeletal muscle transcriptome of the gilthead sea bream (Sparus aurata) determined by next generation sequencing. BMC Genomics (2012) 0.99
Novel bacteriophages containing a genome of another bacteriophage within their genomes. PLoS One (2012) 0.99
Identification of the porcine XIST gene and its differential CpG methylation status in male and female pig cells. PLoS One (2013) 0.99
Next generation sequencing in predicting gene function in podophyllotoxin biosynthesis. J Biol Chem (2012) 0.98
Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. PLoS One (2012) 0.98
Ongoing phenotypic and genomic changes in experimental coevolution of RNA bacteriophage Qβ and Escherichia coli. PLoS Genet (2011) 0.97
Origin and spread of Bos taurus: new clues from mitochondrial genomes belonging to haplogroup T1. PLoS One (2012) 0.97
Reductive evolution in Streptococcus agalactiae and the emergence of a host adapted lineage. BMC Genomics (2013) 0.97
Chemical and transcriptional responses of Norway spruce genotypes with different susceptibility to Heterobasidion spp. infection. BMC Plant Biol (2011) 0.96
CancerDR: cancer drug resistance database. Sci Rep (2013) 0.96
Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective. BMC Genomics (2012) 0.95
RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter. PLoS One (2012) 0.95
A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species. Plant Physiol (2013) 0.95
Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts. Microb Cell Fact (2011) 0.95
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PLoS One (2012) 0.95
Mitochondrial genome sequence analysis: a custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy. BMC Bioinformatics (2011) 0.95
MinION nanopore sequencing of an influenza genome. Front Microbiol (2015) 0.93
The mitochondrial genome of soybean reveals complex genome structures and gene evolution at intercellular and phylogenetic levels. PLoS One (2013) 0.92
Identification of putative candidate genes involved in cuticle formation in Prunus avium (sweet cherry) fruit. Ann Bot (2012) 0.92
Buying in to bioinformatics: an introduction to commercial sequence analysis software. Brief Bioinform (2014) 0.92
ZOOM Lite: next-generation sequencing data mapping and visualization software. Nucleic Acids Res (2010) 0.92
Genome Sequences of Two Pseudorabies Virus Strains Isolated in Greece. Genome Announc (2016) 0.91
Bioinformatics for next generation sequencing data. Genes (Basel) (2010) 0.91
Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNP. Biology (Basel) (2012) 0.90
Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryot Cell (2013) 0.90
Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode. PLoS Genet (2014) 0.90
Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing. J Mol Biol (2012) 0.89
Genome Sequencing of Ralstonia solanacearum FQY_4, Isolated from a Bacterial Wilt Nursery Used for Breeding Crop Resistance. Genome Announc (2013) 0.89
A method enabling high-throughput sequencing of human cytomegalovirus complete genomes from clinical isolates. PLoS One (2014) 0.89
Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti. Genome Biol Evol (2013) 0.89
Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol (2012) 0.89
PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies. Nucleic Acids Res (2011) 0.88
Phylogenomic Analysis Reveals an Asian Origin for African Burkholderia pseudomallei and Further Supports Melioidosis Endemicity in Africa. mSphere (2016) 0.88
Anguillid herpesvirus 1 transcriptome. J Virol (2012) 0.88
Comparative genome sequencing identifies a prophage-associated genomic island linked to host adaptation of Lawsonia intracellularis infections. Vet Res (2013) 0.88
Mutational dynamics of aroid chloroplast genomes. Genome Biol Evol (2012) 0.88
Origin and domestication of papaya Yh chromosome. Genome Res (2015) 0.88
Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer. BMC Plant Biol (2014) 0.87
Next-generation sequence analysis of the genome of RFHVMn, the macaque homolog of Kaposi's sarcoma (KS)-associated herpesvirus, from a KS-like tumor of a pig-tailed macaque. J Virol (2013) 0.87
Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns. PLoS One (2011) 0.86
Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex. G3 (Bethesda) (2013) 0.86
Two novel toxin variants revealed by whole-genome sequencing of 175 Clostridium botulinum type E strains. Appl Environ Microbiol (2014) 0.86
Widespread genome reorganization of an obligate virus mutualist. PLoS Genet (2014) 0.85
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience (2015) 0.85
Genomic Sequence of a Ranavirus Isolated from Short-Finned Eel (Anguilla australis). Genome Announc (2016) 0.85
The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression. Genome Biol Evol (2014) 0.85
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data. BMC Genomics (2012) 0.85
A simple sequence repeat- and single-nucleotide polymorphism-based genetic linkage map of the brown planthopper, Nilaparvata lugens. DNA Res (2012) 0.85
A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium. PLoS Genet (2014) 0.85
LayerCake: a tool for the visual comparison of viral deep sequencing data. Bioinformatics (2015) 0.85
Identification of microRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis. PLoS One (2012) 0.85
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
Consed: a graphical tool for sequence finishing. Genome Res (1998) 59.36
EagleView: a genome assembly viewer for next-generation sequencing technologies. Genome Res (2008) 7.50
MapView: visualization of short reads alignment on a desktop computer. Bioinformatics (2009) 6.77
Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biol (2007) 4.80
Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform (2012) 4.36
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics (2008) 3.21
Plant snoRNA database. Nucleic Acids Res (2003) 3.15
Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci U S A (2006) 2.90
A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J (2004) 2.77
TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics (2004) 2.44
Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet (2012) 2.34
Simplified COPD screening: validation of the PiKo-6® in primary care. Prim Care Respir J (2011) 2.28
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res (2011) 2.26
Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis. Opt Express (2010) 2.18
Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics (2005) 2.16
Single-feature polymorphism discovery in the barley transcriptome. Genome Biol (2005) 2.15
Phylogenetic Relationships Among Xiphinema and Xiphidorus Nematode Species from Brazil Inferred from 18S rDNA Sequences. J Nematol (2004) 1.80
An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics (2006) 1.79
Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics (2012) 1.75
The assessment of facial variation in 4747 British school children. Eur J Orthod (2011) 1.70
Molecular characterization of pigmented and nonpigmented isolates of Mycobacterium avium subsp. paratuberculosis. J Clin Microbiol (2002) 1.67
Adrenocortical carcinoma: clinical, morphologic, and molecular characterization. J Clin Oncol (2002) 1.62
Highly parallel gene-to-BAC addressing using microarrays. Biotechniques (2011) 1.52
Flapjack--graphical genotype visualization. Bioinformatics (2010) 1.52
Nebulized hypertonic saline attenuates acute lung injury following trauma and hemorrhagic shock via inhibition of matrix metalloproteinase-13. Crit Care Med (2012) 1.51
Co-ordinated gene expression during phases of dormancy release in raspberry (Rubus idaeus L.) buds. J Exp Bot (2007) 1.47
Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3 (Bethesda) (2013) 1.42
An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics (2014) 1.37
The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol (2010) 1.35
Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans. Mol Biol Evol (2004) 1.33
Neighbourhood food environment and area deprivation: spatial accessibility to grocery stores selling fresh fruit and vegetables in urban and rural settings. Int J Epidemiol (2009) 1.32
Correlates of medication knowledge and adherence: findings from the residency research network of South Texas. Fam Med (2005) 1.28
Variations in fresh fruit and vegetable quality by store type, urban-rural setting and neighbourhood deprivation in Scotland. Public Health Nutr (2009) 1.28
Automated choroidal segmentation of 1060 nm OCT in healthy and pathologic eyes using a statistical model. Biomed Opt Express (2011) 1.22
Suicide trends and geographical variations in the United Kingdom, 1991-2004. Health Stat Q (2006) 1.19
Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor Appl Genet (2011) 1.17
New developments in sleep research: molecular genetics, gene expression, and systems neurobiology. J Neurosci (2008) 1.14
Trends and geographical variations in alcohol-related deaths in the United Kingdom, 1991-2004. Health Stat Q (2007) 1.12
A practical method for monitoring general practice mortality in the UK: findings from a pilot study in a health board of Northern Ireland. Br J Gen Pract (2005) 1.11
Changes in gene expression during meristem activation processes in Solanum tuberosum with a focus on the regulation of an auxin response factor gene. J Exp Bot (2004) 1.10
Arabidopsis nucleolar protein database (AtNoPDB). Nucleic Acids Res (2005) 1.05
Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.). BMC Plant Biol (2010) 1.03
Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One (2013) 1.03
ANCA-associated renal vasculitis following anti-tumor necrosis factor alpha therapy. Am J Kidney Dis (2008) 1.03
Comparative visualization of genetic and physical maps with Strudel. Bioinformatics (2011) 1.01
An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana. Nucleic Acids Res (2012) 1.00
Sample sequencing of a selected region of the genome of Erwinia carotovora subsp. atroseptica reveals candidate phytopathogenicity genes and allows comparison with Escherichia coli. Microbiology (2002) 1.00
GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections. Plant Physiol (2005) 1.00
Iterative high-throughput polymorphism studies on acetaminophen and an experimentally derived structure for form III. J Am Chem Soc (2002) 0.99
Use of genome sequence data in the design and testing of SSR markers for Phytophthora species. BMC Genomics (2008) 0.99
Relocalization of nuclear ALY proteins to the cytoplasm by the tomato bushy stunt virus P19 pathogenicity protein. Plant Physiol (2004) 0.97
High diversity of arbuscular mycorrhizal fungi in a boreal herb-rich coniferous forest. New Phytol (2008) 0.97
An eQTL analysis of partial resistance to Puccinia hordei in barley. PLoS One (2010) 0.96
Multi-organ failure in adult onset Still's disease: a septic disguise. Clin Rheumatol (2008) 0.96
Expression profiling of potato germplasm differentiated in quality traits leads to the identification of candidate flavour and texture genes. J Exp Bot (2008) 0.95
Potato oxysterol binding protein and cathepsin B are rapidly up-regulated in independent defence pathways that distinguish R gene-mediated and field resistances to Phytophthora infestans. Mol Plant Pathol (2004) 0.95
Registration of 3D point clouds and meshes: a survey from rigid to nonrigid. IEEE Trans Vis Comput Graph (2013) 0.95
A systematic review and mixed treatment comparison of the efficacy of pharmacological treatments for fibromyalgia. Semin Arthritis Rheum (2011) 0.94
A comparative analysis of transcript abundance using SAGE and Affymetrix arrays. Funct Integr Genomics (2005) 0.93
Paediatric benign cystic monodermal testicular teratoma. BMJ Case Rep (2014) 0.93
Combined use of crystalline salt forms and precipitation inhibitors to improve oral absorption of celecoxib from solid oral formulations. J Pharm Sci (2007) 0.92
Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana. Plant Signal Behav (2013) 0.92
A hAT superfamily transposase recruited by the cereal grass genome. Mol Genet Genomics (2006) 0.91
Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome. Mol Genet Genomics (2008) 0.91
Development and mapping of DArT markers within the Festuca - Lolium complex. BMC Genomics (2009) 0.90
Purpose-in-life and breast health behavior in Hispanic and Anglo women. J Holist Nurs (2002) 0.88
The generation challenge programme platform: semantic standards and workbench for crop science. Int J Plant Genomics (2008) 0.87
Why small males have big sperm: dimorphic squid sperm linked to alternative mating behaviours. BMC Evol Biol (2011) 0.85
The effect of contaminated surgical margins revisited. Clin Orthop Relat Res (2002) 0.84
Exploiting induced variation to dissect quantitative traits in barley. Biochem Soc Trans (2010) 0.84
Trans-species polymorphism and selection in the MHC class II DRA genes of domestic sheep. PLoS One (2010) 0.84
The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression. Plant J (2014) 0.84
Processing of Chlamydia abortus polymorphic membrane protein 18D during the chlamydial developmental cycle. PLoS One (2012) 0.83
Characterizing the financial burden of pulmonary arterial hypertension within an integrated healthcare delivery system. J Med Econ (2013) 0.83
Detecting interspecific recombination with a pruned probabilistic divergence measure. Bioinformatics (2004) 0.83
Syringyl lignin is unaltered by severe sinapyl alcohol dehydrogenase suppression in tobacco. Plant Cell (2011) 0.82
Characterisation and functional analysis of two barley caleosins expressed during barley caryopsis development. Planta (2005) 0.82
Novel chlamydia-like organisms as cause of bovine abortions, UK. Emerg Infect Dis (2010) 0.82
Amiodarone-induced thyroid dysfunction. S Afr Med J (2005) 0.82
Self-regulation and inhibition in comorbid ADHD children: an evaluation of executive functions. J Atten Disord (2005) 0.82