The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

PubWeight™: 10.30‹?› | Rank: Top 0.1%

🔗 View Article (PMC 2759552)

Published in Bioinformatics on August 04, 2009

Authors

John W Nicol1, Gregg A Helt, Steven G Blanchard, Archana Raja, Ann E Loraine

Author Affiliations

1: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA.

Articles citing this

(truncated to the top 100)

Integrative genomics viewer. Nat Biotechnol (2011) 42.83

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res (2011) 8.18

Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31

Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77

Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60

Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet (2010) 3.38

Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes. Blood (2011) 3.37

Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat Struct Mol Biol (2012) 2.65

mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol Cell (2012) 2.57

ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol (2012) 2.51

Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res (2011) 2.48

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A (2012) 2.39

H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J (2011) 2.38

Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res (2010) 2.36

Genomic variation in natural populations of Drosophila melanogaster. Genetics (2012) 2.33

Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature (2014) 2.33

A snapshot of the expression signature of androgen receptor splicing variants and their distinctive transcriptional activities. Prostate (2011) 2.21

An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO J (2012) 2.10

Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol (2010) 2.06

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. BMC Bioinformatics (2009) 1.91

GenomeView: a next-generation genome browser. Nucleic Acids Res (2011) 1.91

Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci U S A (2011) 1.89

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. Elife (2012) 1.82

Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genet (2011) 1.82

Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol (2013) 1.81

ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics (2011) 1.80

A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS Genet (2013) 1.73

Alternative splicing of CD44 mRNA by ESRP1 enhances lung colonization of metastatic cancer cell. Nat Commun (2012) 1.71

Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69

CloudMap: a cloud-based pipeline for analysis of mutant genome sequences. Genetics (2012) 1.64

Using MACS to identify peaks from ChIP-Seq data. Curr Protoc Bioinformatics (2011) 1.64

A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PLoS Pathog (2011) 1.63

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife (2013) 1.63

Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli. Immunity (2015) 1.61

dNTP pools determine fork progression and origin usage under replication stress. EMBO J (2012) 1.58

Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinformatics (2010) 1.56

The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiol (2013) 1.56

RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol (2013) 1.55

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A (2010) 1.53

H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet (2010) 1.51

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics (2010) 1.40

Supervillin Is a Component of the Hair Cell's Cuticular Plate and the Head Plates of Organ of Corti Supporting Cells. PLoS One (2016) 1.39

Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence. Proc Natl Acad Sci U S A (2011) 1.38

An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep (2016) 1.36

Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Mol Cell Biol (2010) 1.35

High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology. PLoS One (2011) 1.35

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat Struct Mol Biol (2012) 1.34

AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol (2009) 1.33

Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res (2010) 1.32

Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing. Nucleic Acids Res (2010) 1.30

Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol (2013) 1.30

Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell (2012) 1.27

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. Plant Physiol (2013) 1.25

Analysis of replication profiles reveals key role of RFC-Ctf18 in yeast replication stress response. Nat Struct Mol Biol (2010) 1.23

The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity. J Exp Med (2014) 1.21

Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol (2011) 1.19

Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression. PLoS Genet (2012) 1.17

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States. Plant Cell (2014) 1.16

Prevalence of alternative splicing choices in Arabidopsis thaliana. BMC Plant Biol (2010) 1.13

CisGenome Browser: a flexible tool for genomic data visualization. Bioinformatics (2010) 1.10

JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol (2016) 1.09

Analysis methods for studying the 3D architecture of the genome. Genome Biol (2015) 1.09

MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Bioinformatics (2012) 1.09

NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature (2014) 1.08

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions. Plant Methods (2011) 1.08

BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform (2012) 1.08

TFIIH phosphorylation of the Pol II CTD stimulates mediator dissociation from the preinitiation complex and promoter escape. Mol Cell (2014) 1.07

Taking the next step: building an Arabidopsis information portal. Plant Cell (2012) 1.06

Chromosome visualization tool: a whole genome viewer. Int J Plant Genomics (2011) 1.04

RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proc Natl Acad Sci U S A (2013) 1.04

A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS Genet (2013) 1.04

A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni. PLoS Pathog (2014) 1.03

Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front Plant Sci (2012) 1.02

Integration and visualization of systems biology data in context of the genome. BMC Bioinformatics (2010) 1.02

Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments. Nucleic Acids Res (2015) 1.02

Genometa--a fast and accurate classifier for short metagenomic shotgun reads. PLoS One (2012) 1.02

Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method. Genome Res (2012) 1.01

Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins. BMC Dev Biol (2013) 1.00

A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. Plant Cell (2013) 1.00

Analysis and visualization of RNA-Seq expression data using RStudio, Bioconductor, and Integrated Genome Browser. Methods Mol Biol (2015) 0.99

Transcriptional landscape and essential genes of Neisseria gonorrhoeae. Nucleic Acids Res (2014) 0.98

Identification and characterization of an epi-allele of FIE1 reveals a regulatory linkage between two epigenetic marks in rice. Plant Cell (2012) 0.98

Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host-pathogen transcriptomes. Proc Natl Acad Sci U S A (2017) 0.98

Genes required for aerial growth, cell division, and chromosome segregation are targets of WhiA before sporulation in Streptomyces venezuelae. MBio (2013) 0.97

Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci U S A (2015) 0.97

Genome stability of Propionibacterium acnes: a comprehensive study of indels and homopolymeric tracts. Sci Rep (2016) 0.97

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Comput Biol (2015) 0.97

A global view of the oncogenic landscape in nasopharyngeal carcinoma: an integrated analysis at the genetic and expression levels. PLoS One (2012) 0.97

Rif1 binds to G quadruplexes and suppresses replication over long distances. Nat Struct Mol Biol (2015) 0.96

Potential role for snoRNAs in PKR activation during metabolic stress. Proc Natl Acad Sci U S A (2015) 0.96

Genome-wide analysis of the binding of the Hox protein Ultrabithorax and the Hox cofactor Homothorax in Drosophila. PLoS One (2011) 0.96

Farnesoid X receptor induces murine scavenger receptor Class B type I via intron binding. PLoS One (2012) 0.96

RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium. PLoS Pathog (2015) 0.96

A Phase I Trial of BKM120 (Buparlisib) in Combination with Fulvestrant in Postmenopausal Women with Estrogen Receptor-Positive Metastatic Breast Cancer. Clin Cancer Res (2015) 0.96

Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis. PLoS Comput Biol (2011) 0.95

Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia. J Bacteriol (2012) 0.95

Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq. Nucleic Acids Res (2015) 0.94

Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics (2013) 0.94

The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis. BMC Microbiol (2010) 0.94

Articles cited by this

An extended transcriptional network for pluripotency of embryonic stem cells. Cell (2008) 14.64

A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21

Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62

Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol (2007) 9.45

Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells. Nature (2007) 7.04

Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56

Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS One (2006) 3.03

DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res (2008) 2.48

The cost of gene expression underlies a fitness trade-off in yeast. Proc Natl Acad Sci U S A (2009) 2.28

Comparing whole genomes using DNA microarrays. Nat Rev Genet (2008) 2.27

A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors. PLoS Genet (2009) 2.07

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. BMC Bioinformatics (2009) 1.91

BioViews: Java-based tools for genomic data visualization. Genome Res (1998) 1.87

Visualizing the genome: techniques for presenting human genome data and annotations. BMC Bioinformatics (2002) 1.57

Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoS One (2009) 1.45

Global correlation analysis between redundant probe sets using a large collection of Arabidopsis ath1 expression profiling data. Comput Syst Bioinformatics Conf (2006) 1.41

Dispersed mutations in histone H3 that affect transcriptional repression and chromatin structure of the CHA1 promoter in Saccharomyces cerevisiae. Eukaryot Cell (2008) 1.31

Articles by these authors

NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res (2003) 14.37

Functional consequences of cysteine modification in the ligand binding sites of peroxisome proliferator activated receptors by GW9662. Biochemistry (2002) 2.97

Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol (2008) 2.08

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. BMC Bioinformatics (2009) 1.91

Web Apollo: a web-based genomic annotation editing platform. Genome Biol (2013) 1.69

CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiol (2008) 1.60

Visualizing the genome: techniques for presenting human genome data and annotations. BMC Bioinformatics (2002) 1.57

Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing. PLoS One (2009) 1.45

Genome of Mycoplasma arthritidis. Infect Immun (2008) 1.25

Prevalence of alternative splicing choices in Arabidopsis thaliana. BMC Plant Biol (2010) 1.13

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies. Nucleic Acids Res (2008) 1.07

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a. Am J Bot (2012) 0.94

Subtype specific effects of peroxisome proliferator-activated receptor ligands on corepressor affinity. Biochemistry (2003) 0.88

Protein-based analysis of alternative splicing in the human genome. Proc IEEE Comput Soc Bioinform Conf (2002) 0.88

Exploring alternative transcript structure in the human genome using blocks and InterPro. J Bioinform Comput Biol (2003) 0.86

Visualization techniques for genomic data. Proc IEEE Comput Soc Bioinform Conf (2002) 0.81

Energy Transfer from Quantum Dots to Graphene and MoS2: The Role of Absorption and Screening in Two-Dimensional Materials. Nano Lett (2016) 0.78

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature (2016) 0.77

A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser. Methods Mol Biol (2014) 0.77

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. Plant Genome (2016) 0.76

Structure-based comparison of four eukaryotic genomes. Pac Symp Biocomput (2002) 0.75

Dynamic optical tuning of interlayer interactions in the transition metal dichalcogenides. Nano Lett (2017) 0.75