Open Access
Integrative Genomics Viewer
James T. Robinson,Helga Thorvaldsdottir,Wendy Winckler,Mitchell Guttman,Eric S. Lander,Eric S. Lander,Gad Getz,Jill P. Mesirov +7 more
TLDR
The sheer volume and scope of data posed by this flood of data pose a significant challenge to the development of efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data.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.read more
Citations
More filters
“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal Article
The cancer cell
TL;DR: Investigations compel the view that the ratio of the vital capacity to the body length, trunk length, chest circumference, surface area or weight or any combination of these measurements, is too variable to admit of any workable standard or normal value.
Journal Article
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Nicolas Stransky,Ann Marie Egloff,Aaron D. Tward,Aleksandar Kostic,Kristian Cibulskis,Andrey Sivachenko,Gregory Kryukov,Michael S. Lawrence,Carrie Sougnez,Aaron McKenna,Erica Shefler,Alex H. Ramos,Petar Stojanov,Scott L. Carter,Douglas Voet,Maria L. Cortes,Daniel Auclair,Michael F. Berger,Gordon Saksena,Candace Guiducci,Robert C. Onofrio,Melissa Parkin,Marjorie Romkes,Joel L. Weissfeld,Raja R. Seethala,Lin Wang,Claudia Rangel-Escareño,Juan Carlos Fernández-López,Alfredo Hidalgo-Miranda,Jorge Melendez-Zajgla,Wendy Winckler,Kristin Ardlie,Stacey Gabriel,Matthew Meyerson,Eric S. Lander,Gad Getz,Todd R. Golub,Levi A. Garraway,Jennifer R. Grandis +38 more
TL;DR: The results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms and suggest the development of targeted therapies for head and neck cancer may be hindered by complex mutational profiles.
Journal ArticleDOI
Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants
Qian Wang,Sho Iketani,Zhiteng Li,Liyuan Liu,Yicheng Guo,Yiming Huang,Anthony D. Bowen,Michael Liu,Maple Wang,Jian Yu,Riccardo Valdez,Adam S. Lauring,Zizhang Sheng,Harris H. Wang,Aubree Gordon,Lihong Liu,David D. Ho +16 more
TL;DR: The BQ and XBB subvariants of SARS-CoV-2 Omicron are now rapidly expanding, possibly due to altered antibody evasion properties deriving from their additional spike mutations as discussed by the authors .
Journal ArticleDOI
Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia
Marianna Zazhytska,Albana Kodra,Daisy A. Hoagland,Justin J. Frere,John F. Fullard,Hani J. Shayya,Natalie McArthur,Rasmus Moeller,Skyler Uhl,Arina D. Omer,Max E. Gottesman,Stuart Firestein,Qizhi Gong,Peter Canoll,James E. Goldman,Panos Roussos,Benjamin R. tenOever,Jonathan B. Overdevest,Stavros Lomvardas +18 more
TL;DR: In this paper , the authors show that SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (ORs) and of their signaling components, followed by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes.
References
More filters
Journal ArticleDOI
The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data
Ethan Cerami,Jianjiong Gao,Ugur Dogrusoz,Benjamin Gross,Selcuk Onur Sumer,Bulent Arman Aksoy,Anders Jacobsen,Caitlin Byrne,Michael Heuer,Erik G. Larsson,Yevgeniy Antipin,Boris Reva,Arthur P. Goldberg,Chris Sander,Nikolaus Schultz +14 more
TL;DR: The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications.
Journal ArticleDOI
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal
Jianjiong Gao,Bulent Arman Aksoy,Ugur Dogrusoz,Gideon Dresdner,Benjamin Gross,S. Onur Sumer,Yichao Sun,Anders Jacobsen,Rileen Sinha,Erik Larsson,Ethan Cerami,Chris Sander,Nikolaus Schultz +12 more
TL;DR: A practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics, which makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries.
Journal ArticleDOI
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell,Adam Roberts,Loyal A. Goff,Loyal A. Goff,Loyal A. Goff,Geo Pertea,Daehwan Kim,Daehwan Kim,David R. Kelley,David R. Kelley,Harold Pimentel,Steven L. Salzberg,John L. Rinn,John L. Rinn,Lior Pachter +14 more
TL;DR: This protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results, which takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.
Journal ArticleDOI
A Map of Human Genome Variation From Population-Scale Sequencing
Gonçalo R. Abecasis,David Altshuler,David Altshuler,Adam Auton,Lisa D Brooks,Richard Durbin,Richard A. Gibbs,Matthew E. Hurles,Gil McVean +8 more
TL;DR: The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype as mentioned in this paper, and the results of the pilot phase of the project, designed to develop and compare different strategies for genomewide sequencing with high-throughput platforms.
Journal ArticleDOI
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
TL;DR: The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution.