Published in Bioinformatics on June 20, 2010
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc (2013) 4.00
A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform (2013) 3.60
Detecting copy number variation with mated short reads. Genome Res (2010) 2.75
ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol (2012) 2.51
A survey of best practices for RNA-seq data analysis. Genome Biol (2016) 2.37
SVA: software for annotating and visualizing sequenced human genomes. Bioinformatics (2011) 2.11
GenomeView: a next-generation genome browser. Nucleic Acids Res (2011) 1.91
iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res (2012) 1.63
Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum. Mol Biol Evol (2014) 1.60
Chromatin is an ancient innovation conserved between Archaea and Eukarya. Elife (2012) 1.56
SNP Discovery through Next-Generation Sequencing and Its Applications. Int J Plant Genomics (2012) 1.46
Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res (2012) 1.32
Web-based visual analysis for high-throughput genomics. BMC Genomics (2013) 1.31
Characterizing complex structural variation in germline and somatic genomes. Trends Genet (2011) 1.25
BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform (2012) 1.08
Chromatin accessibility: a window into the genome. Epigenetics Chromatin (2014) 1.06
Newborn screening for SCID identifies patients with ataxia telangiectasia. J Clin Immunol (2012) 1.05
A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum Genet (2012) 1.05
NGS analyses by visualization with Trackster. Nat Biotechnol (2012) 1.04
Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front Plant Sci (2012) 1.02
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data. Bioinformatics (2012) 0.98
Genetic and genomic architecture of the evolution of resistance to antifungal drug combinations. PLoS Genet (2013) 0.97
Next generation sequence analysis and computational genomics using graphical pipeline workflows. Genes (Basel) (2012) 0.97
Massively parallel sequencing approaches for characterization of structural variation. Methods Mol Biol (2012) 0.96
ReadXplorer--visualization and analysis of mapped sequences. Bioinformatics (2014) 0.94
rnaSeqMap: a Bioconductor package for RNA sequencing data exploration. BMC Bioinformatics (2011) 0.92
The splicing landscape is globally reprogrammed during male meiosis. Nucleic Acids Res (2013) 0.90
PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies. Nucleic Acids Res (2011) 0.88
Variation detection based on next-generation sequencing of type Chinese 1 strains of Toxoplasma gondii with different virulence from China. BMC Genomics (2015) 0.85
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. Gigascience (2015) 0.85
Computational approaches for isoform detection and estimation: good and bad news. BMC Bioinformatics (2014) 0.85
JEnsembl: a version-aware Java API to Ensembl data systems. Bioinformatics (2012) 0.82
TASUKE: a web-based visualization program for large-scale resequencing data. Bioinformatics (2013) 0.82
Epiviz: a view inside the design of an integrated visual analysis software for genomics. BMC Bioinformatics (2015) 0.81
Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation. PLoS Pathog (2015) 0.80
Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies. Biomed Res Int (2015) 0.80
Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Front Microbiol (2015) 0.79
STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics (2013) 0.78
InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. Nucleic Acids Res (2016) 0.77
Extensive RNA editing and splicing increase immune self-representation diversity in medullary thymic epithelial cells. Genome Biol (2016) 0.76
SVGenes: a library for rendering genomic features in scalable vector graphic format. Bioinformatics (2013) 0.75
Light-RCV: a lightweight read coverage viewer for next generation sequencing data. BMC Bioinformatics (2015) 0.75
From next-generation resequencing reads to a high-quality variant data set. Heredity (Edinb) (2016) 0.75
Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges. Front Genet (2012) 0.75
Incorporating computational resources in a cancer research program. Hum Genet (2014) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
The human genome browser at UCSC. Genome Res (2002) 168.23
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Consed: a graphical tool for sequence finishing. Genome Res (1998) 59.36
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
Ensembl 2009. Nucleic Acids Res (2008) 25.38
Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Tablet--next generation sequence assembly visualization. Bioinformatics (2009) 11.75
The Staden package, 1998. Methods Mol Biol (2000) 11.30
Computational methods for discovering structural variation with next-generation sequencing. Nat Methods (2009) 7.20
Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res (2009) 6.42
Genome variation discovery with high-throughput sequencing data. Brief Bioinform (2010) 3.74
MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods (2009) 3.15
The 1000 Genomes Project: new opportunities for research and social challenges. Genome Med (2010) 2.43
The Autism Genome Project: goals and strategies. Am J Pharmacogenomics (2005) 1.37
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
The genetic landscape of a cell. Science (2010) 16.52
ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res (2005) 11.90
SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol (2009) 11.24
Computational methods for discovering structural variation with next-generation sequencing. Nat Methods (2009) 7.20
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res (2004) 4.45
SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics (2011) 3.82
Genome variation discovery with high-throughput sequencing data. Brief Bioinform (2010) 3.74
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res (2003) 3.52
MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods (2009) 3.15
A robust framework for detecting structural variations in a genome. Bioinformatics (2008) 3.03
Conservation of core gene expression in vertebrate tissues. J Biol (2009) 2.84
Detecting copy number variation with mated short reads. Genome Res (2010) 2.75
Multiple whole-genome alignments without a reference organism. Genome Res (2009) 2.31
Maximum likelihood genome assembly. J Comput Biol (2009) 2.24
Extreme genomic variation in a natural population. Proc Natl Acad Sci U S A (2007) 2.24
PhenoTips: patient phenotyping software for clinical and research use. Hum Mutat (2013) 2.04
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics (2004) 1.97
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol (2007) 1.82
PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics (2012) 1.65
iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res (2012) 1.63
Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res (2012) 1.32
Prospective, intensive study of metabolic changes associated with 48 weeks of amprenavir-based antiretroviral therapy. Clin Infect Dis (2002) 1.18
AGenDA: homology-based gene prediction. Bioinformatics (2003) 1.08
Burden among spousal and child caregivers of patients with mild cognitive impairment. Dement Geriatr Cogn Disord (2008) 1.05
SCARPA: scaffolding reads with practical algorithms. Bioinformatics (2012) 1.00
Loss of ACE2 exacerbates murine renal ischemia-reperfusion injury. PLoS One (2013) 1.00
Extensive parallelism in protein evolution. Biol Direct (2007) 1.00
Detecting Alu insertions from high-throughput sequencing data. Nucleic Acids Res (2013) 0.93
Phenotyping: targeting genotype's rich cousin for diagnosis. J Paediatr Child Health (2014) 0.89
A direct comparison of drug susceptibility to HIV type 1 from antiretroviral experienced subjects as assessed by the antivirogram and PhenoSense assays and by seven resistance algorithms. AIDS Res Hum Retroviruses (2005) 0.87
Genomic sequencing and characterization of cynomolgus macaque cytomegalovirus. J Virol (2011) 0.86
VARiD: a variation detection framework for color-space and letter-space platforms. Bioinformatics (2010) 0.86
Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi. Genetics (2008) 0.84
Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter. J Bioinform Comput Biol (2006) 0.82
Mixture model for sub-phenotyping in GWAS. Pac Symp Biocomput (2012) 0.81
Identification of deleterious synonymous variants in human genomes. Bioinformatics (2013) 0.81
Deletion of the gene for adiponectin accelerates diabetic nephropathy in the Ins2 (+/C96Y) mouse. Diabetologia (2015) 0.81
Efficacy and Safety of Abacavir/Lamivudine/Zidovudine Plus Tenofovir in HBV/HIV-1 Coinfected Adults: 48-Week Data. Open AIDS J (2010) 0.78
Neuropsychological correlates of self-reported depression and self-reported cognition among patients with mild cognitive impairment. J Geriatr Psychiatry Neurol (2008) 0.77
Further routes to psychological constructionism. Behav Brain Sci (2012) 0.77
Establishing a prognosis for functional outcome during coma recovery. Brain Inj (2006) 0.77
PhenoBlocks: Phenotype Comparison Visualizations. IEEE Trans Vis Comput Graph (2016) 0.76
PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations. IEEE Trans Vis Comput Graph (2016) 0.76
Sense of fairness: not by itself a moral sense and not a foundation of a lot of morality. Behav Brain Sci (2013) 0.75
PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models. IEEE Trans Vis Comput Graph (2017) 0.75
Identification of deleterious synonymous variants in human genomes. Bioinformatics (2014) 0.75