Integrative genomics viewer

Published on Jan 1, 2011in Nature Biotechnology 35.72
· DOI :10.1038/nbt.1754
James Robinson84
Estimated H-index: 84
(Massachusetts Institute of Technology),
Helga Thorvaldsdottir10
Estimated H-index: 10
(Massachusetts Institute of Technology)
+ 4 AuthorsJill P. Mesirov70
Estimated H-index: 70
(Massachusetts Institute of Technology)
Abstract
Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.
  • References (13)
  • Citations (3777)
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References13
Published on Mar 1, 2010in Nature Methods 26.92
Cydney B. Nielsen17
Estimated H-index: 17
,
Michael N. Cantor6
Estimated H-index: 6
+ 2 AuthorsTing Wang35
Estimated H-index: 35
(Washington University in St. Louis)
As our ability to generate sequencing data continues to increase, data analysis is replacing data generation as the rate-limiting step in genomics studies. Here we provide a guide to genomic data visualization tools that facilitate analysis tasks by enabling researchers to explore, interpret and manipulate their data, and in some cases perform on-the-fly computations. We will discuss graphical methods designed for the analysis of de novo sequencing assemblies and read alignments, genome browsing...
114 Citations Source Cite
Published on Mar 1, 2009in Nature 41.58
Mitchell Guttman35
Estimated H-index: 35
(Broad Institute),
Ido Amit50
Estimated H-index: 50
(Broad Institute)
+ 17 AuthorsJohn P. Cassady15
Estimated H-index: 15
(Massachusetts Institute of Technology)
There is growing recognition that mammalian cells produce many thousands of large intergenic transcripts. However, the functional significance of these transcripts has been particularly controversial. Although there are some well-characterized examples, most (>95%) show little evidence of evolutionary conservation and have been suggested to represent transcriptional noise. Here we report a new approach to identifying large non-coding RNAs using chromatin-state maps to discover discrete transcrip...
2,329 Citations Source Cite
Published on Oct 23, 2008in Nature 41.58
Roger E. McLendon87
Estimated H-index: 87
(Duke University),
Allan H. Friedman86
Estimated H-index: 86
(Duke University)
+ 228 AuthorsKenneth D. Aldape84
Estimated H-index: 84
(University of Texas MD Anderson Cancer Center)
Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberratio...
4,281 Citations Source Cite
Published on Feb 1, 2010in Bioinformatics 5.48
Iain Milne14
Estimated H-index: 14
(Scottish Crop Research Institute),
Micha Bayer18
Estimated H-index: 18
(Scottish Crop Research Institute)
+ 4 AuthorsDavid Marshall23
Estimated H-index: 23
(Scottish Crop Research Institute)
Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bi...
416 Citations Source Cite
Published on Jul 30, 2008in Genome Research 10.10
Weichun Huang7
Estimated H-index: 7
(Boston College),
Gabor T. Marth35
Estimated H-index: 35
(Boston College)
The emergence of high-throughput next-generation sequencing technologies (e.g., 454 Life Sciences [Roche], Illumina sequencing [formerly Solexa sequencing]) has dramatically sped up whole-genome de novo sequencing and resequencing. While the low cost of these sequencing technologies provides an unparalleled opportunity for genome-wide polymorphism discovery, the analysis of the new data types and huge data volume poses formidable informatics challenges for base calling, read alignment and genome...
110 Citations Source Cite
Published on Jun 15, 2009in Bioinformatics 5.48
Hua Bao11
Estimated H-index: 11
(Sun Yat-sen University),
Hui Guo18
Estimated H-index: 18
(Sun Yat-sen University)
+ 3 AuthorsSuhua Shi29
Estimated H-index: 29
(Sun Yat-sen University)
Summary: We introduce a new visual analytics tool named MapView to facilitate the representation of large-scale short reads alignment data and genetic variation analysis. MapView can handle hundreds of millions of short reads on a desktop computer with limited memory. It supports a compact alignment view for both single-end and paired end short reads, multiple navigation and zoom modes and multithread processing. Moreover, MapView offers automated genetic variation detection. MapView has been us...
70 Citations Source Cite
Published on Aug 15, 2010in Bioinformatics 5.48
Marc Fiume9
Estimated H-index: 9
(University of Toronto),
Vanessa Williams5
Estimated H-index: 5
(University of Toronto)
+ 1 AuthorsMichael Brudno44
Estimated H-index: 44
(University of Toronto)
Motivation: The advent of high-throughput sequencing (HTS) technologies has made it affordable to sequence many individuals’ genomes. Simultaneously the computational analysis of the large volumes of data generated by the new sequencing machines remains a challenge. While a plethora of tools are available to map the resulting reads to a reference genome, and to conduct primary analysis of the mappings, it is often necessary to visually examine the results and underlying data to confirm predictio...
91 Citations Source Cite
Published on Oct 1, 2009in Bioinformatics 5.48
John W. Nicol2
Estimated H-index: 2
(University of North Carolina at Charlotte),
Gregg A. Helt1
Estimated H-index: 1
(University of North Carolina at Charlotte)
+ 2 AuthorsAnn E. Loraine24
Estimated H-index: 24
(University of North Carolina at Charlotte)
Summary: Experimental techniques that survey an entire genome demand flexible, highly interactive visualization tools that can display new data alongside foundation datasets, such as reference gene annotations. The Integrated Genome Browser (IGB) aims to meet this need. IGB is an open source, desktop graphical display tool implemented in Java that supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-...
435 Citations Source Cite
Published on Jan 1, 2010in Cancer Cell 22.84
Roel G.W. Verhaak4
Estimated H-index: 4
(Harvard University),
Katherine A. Hoadley53
Estimated H-index: 53
(University of North Carolina at Chapel Hill)
+ 30 AuthorsJill P. Mesirov70
Estimated H-index: 70
(Harvard University)
Summary The Cancer Genome Atlas Network recently cataloged recurrent genomic abnormalities in glioblastoma multiforme (GBM). We describe a robust gene expression-based molecular classification of GBM into Proneural, Neural, Classical, and Mesenchymal subtypes and integrate multidimensional genomic data to establish patterns of somatic mutations and DNA copy number. Aberrations and gene expression of EGFR , NF1 , and PDGFRA/IDH1 each define the Classical, Mesenchymal, and Proneural subtypes, resp...
3,186 Citations Source Cite
Published on Jan 1, 2002in Genome Biology 13.21
Se Lewis2
Estimated H-index: 2
(University of California),
Smj Searle2
Estimated H-index: 2
(Wellcome Trust Sanger Institute)
+ 16 AuthorsMadeline A. Crosby17
Estimated H-index: 17
(Harvard University)
The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used...
337 Citations Source Cite
  • References (13)
  • Citations (3777)
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Cited By3777
Published on Jan 1, 2013in Methods of Molecular Biology
Rachelly Normand2
Estimated H-index: 2
(Technion – Israel Institute of Technology),
Itai Yanai28
Estimated H-index: 28
(Technion – Israel Institute of Technology)
Abstract The dramatic fall in the cost of DNA sequencing has revolutionized the experiments within reach in the life sciences. Here we provide an introduction for the domains of analyses possible using high-throughput sequencing, distinguishing between "counting" and "reading" applications. We discuss the steps in designing a high-throughput sequencing experiment, introduce the most widely used applications, and describe basic sequencing concepts. We review the various software programs availabl...
6 Citations Source Cite
Published on Jun 1, 2014in Medizinische Genetik 0.21
R. Weißmann , C. Gilissen (Radboud University Nijmegen)
Next Generation Sequencing (NGS) wird immer haufiger in der Humangenetik eingesetzt. Die Analyse der anfallenden Datenmengen birgt allerdings andere und grosere Herausforderungen als bisher eingesetzte Verfahren. In diesem Artikel werden einige Grundlagen, die dem Verstandnis der anfallenden Daten und Analyseschritte beim NGS dienen sollen, beschrieben. Ein besonderer Schwerpunkt ist dabei die Qualitatskontrolle.
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Published on Jan 1, 2012in Methods in Cell Biology 1.59
Christopher S. Poultney7
Estimated H-index: 7
(New York University),
Alex Greenfield9
Estimated H-index: 9
(New York University),
Richard Bonneau50
Estimated H-index: 50
(Courant Institute of Mathematical Sciences)
Abstract Regulatory and signaling networks coordinate the enormously complex interactions and processes that control cellular processes (such as metabolism and cell division), coordinate response to the environment, and carry out multiple cell decisions (such as development and quorum sensing). Regulatory network inference is the process of inferring these networks, traditionally from microarray data but increasingly incorporating other measurement types such as proteomics, ChIP-seq, metabolomic...
16 Citations Source Cite
Published on Nov 1, 2012in The Journal of Molecular Diagnostics 4.88
Maurice Chan2
Estimated H-index: 2
,
Shen Mo Ji1
Estimated H-index: 1
+ 7 AuthorsAnn Siew Gek Lee4
Estimated H-index: 4
In a clinical setting, next-generation sequencing (NGS) approaches for the enrichment and resequencing of DNA targets may have limitations in throughput, cost, or accuracy. We evaluated an NGS workflow for targeted DNA sequencing for mutation detection. Targeted sequence data of the BRCA1 and BRCA2 genes, generated using a PCR-based, multiplexed NGS approach using the SOLiD 4 (n = 24) and Ion Torrent PGM (n = 20) next-generation sequencers, were evaluated against sequence data obtained by Sanger...
55 Citations Source Cite
Published on Jul 28, 2014in PLOS ONE 2.77
Rohan G. T. Lowe12
Estimated H-index: 12
(University of Melbourne),
Andrew Cassin11
Estimated H-index: 11
(University of Melbourne)
+ 4 AuthorsBarbara J. Howlett41
Estimated H-index: 41
(University of Melbourne)
Leptosphaeria maculans ‘brassicae’ is a damaging fungal pathogen of canola (Brassica napus), causing lesions on cotyledons and leaves, and cankers on the lower stem. A related species, L. biglobosa ‘canadensis’, colonises cotyledons but causes few stem cankers. We describe the complement of genes encoding carbohydrate-active enzymes (CAZys) and peptidases of these fungi, as well as of four related plant pathogens. We also report dual-organism RNA-seq transcriptomes of these two Leptosphaeria spe...
31 Citations Source Cite
Published on Jan 1, 2014in The Journal of Molecular Diagnostics 4.88
Somak Roy13
Estimated H-index: 13
(University of Pittsburgh),
Mary Beth Durso8
Estimated H-index: 8
(University of Pittsburgh)
+ 2 AuthorsMarina N. Nikiforova46
Estimated H-index: 46
(University of Pittsburgh)
A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was d...
23 Citations Source Cite
Published on Jan 1, 2013in Methods of Molecular Biology
Wenming Xiao20
Estimated H-index: 20
(National Institutes of Health),
Bao Tran2
Estimated H-index: 2
+ 1 AuthorsRoland Schmitz22
Estimated H-index: 22
5 Citations Source Cite
Published on Jan 1, 2012in Methods of Molecular Biology
Rinki Ratna Priya3
Estimated H-index: 3
(National Institutes of Health),
Harsha Rajasimha6
Estimated H-index: 6
(National Institutes of Health)
+ 1 AuthorsAnand Swaroop35
Estimated H-index: 35
(National Institutes of Health)
8 Citations Source Cite
Published on Jan 1, 2012in Current Topics in Developmental Biology 3.11
Stein Aerts33
Estimated H-index: 33
(Katholieke Universiteit Leuven)
Abstract Transcription factors (TFs) are key proteins that decode the information in our genome to express a precise and unique set of proteins and RNA molecules in each cell type in our body. These factors play a pivotal role in all biological processes, including the determination of a cell's fate during development and the maintenance of a cell's physiological function. To achieve this, a TF binds to specific DNA sequences in the noncoding part of the genome, recruits chromatin modifiers and ...
28 Citations Source Cite
Published on Jan 1, 2015in Methods of Molecular Biology
Mariette F. Ducatez5
Estimated H-index: 5
(University of Toulouse),
Jean-Luc Guérin16
Estimated H-index: 16
(University of Toulouse)
1 Citations Source Cite