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Helga Thorvaldsdottir
Broad Institute
31Publications
12H-index
19.6kCitations
Publications 31
Newest
#1James Robinson (UCSD: University of California, San Diego)H-Index: 91
#2Douglass Turner (UCSD: University of California, San Diego)H-Index: 3
Last.Erez Lieberman AidenH-Index: 12
view all 6 authors...
Summary Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL...
#1James Robinson (UCSD: University of California, San Diego)H-Index: 91
#2Helga Thorvaldsdottir (Broad Institute)H-Index: 12
Last.Jill P. Mesirov (UCSD: University of California, San Diego)H-Index: 71
view all 5 authors...
Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly increase the confidence in calls, reduce the risk of false positives, and help characterize complex events. The Integrative Genomics Viewer (IGV) was one of the first tools to provide NGS data visualization, and it currently provides a rich set of tools for inspection, validation, and in...
#1Michael M. Reich (UCSD: University of California, San Diego)H-Index: 2
#2Thorin Tabor (UCSD: University of California, San Diego)H-Index: 2
Last.Jill P. Mesirov (UCSD: University of California, San Diego)H-Index: 71
view all 7 authors...
Summary Interactive analysis notebook environments promise to streamline genomics research through interleaving text, multimedia, and executable code into unified, sharable, reproducible "research narratives." However, current notebook systems require programming knowledge, limiting their wider adoption by the research community. We have developed the GenePattern Notebook environment (http://www.genepattern-notebook.org), to our knowledge the first system to integrate the dynamic capabilities of...
#1Daniel E. Carlin (UCSD: University of California, San Diego)H-Index: 11
#2Kassi Kosnicki (UCSD: University of California, San Diego)
Last.Jill P. Mesirov (UCSD: University of California, San Diego)H-Index: 71
view all 7 authors...
One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor. However, until now, this this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identifying protein occupancies along the g...
#1Michael M. Reich (UCSD: University of California, San Diego)H-Index: 2
#2Thorin Tabor (Broad Institute)H-Index: 1
Last.Jill P. Mesirov (UCSD: University of California, San Diego)H-Index: 71
view all 10 authors...
As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, the need has become more urgent for a software environment that supports the entire “idea to dissemination” cycle of an integrative cancer genomics analysis. Such a system would need to provide access to a large number of analysis tools without the need for programming, be sufficiently flexible to accommodate the practices of non-programming biologists as well as experien...
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