Helga Thorvaldsdottir
Broad Institute
31Publications
10H-index
18.7kCitations
Publications 31
Newest
Published on Jul 1, 2018in Cancer Research 9.13
Michael Reich2
Estimated H-index: 2
,
Thorin Tabor2
Estimated H-index: 2
+ 3 AuthorsJill P. Mesirov70
Estimated H-index: 70
Source Cite
Published on Feb 1, 2018in Cell systems 8.98
James T. Robinson6
Estimated H-index: 6
(University of California, San Diego),
Douglass Turner3
Estimated H-index: 3
(University of California, San Diego)
+ 3 AuthorsErez Lieberman Aiden18
Estimated H-index: 18
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...
8 Citations Source Cite
Published on Jul 1, 2017in Cancer Research 9.13
Michael Reich2
Estimated H-index: 2
,
Thorin Tabor2
Estimated H-index: 2
+ 3 AuthorsJill P. Mesirov70
Estimated H-index: 70
Source Cite
Published on Aug 1, 2017in Cell systems 8.98
Michael Reich2
Estimated H-index: 2
(University of California, San Diego),
Thorin Tabor2
Estimated H-index: 2
(University of California, San Diego)
+ 4 AuthorsJill P. Mesirov70
Estimated H-index: 70
(University of California, San Diego)
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...
4 Citations Source Cite
Published on Nov 1, 2017in Cancer Research 9.13
James T. Robinson6
Estimated H-index: 6
(University of California, San Diego),
Helga Thorvaldsdottir10
Estimated H-index: 10
(Broad Institute)
+ 2 AuthorsJill P. Mesirov70
Estimated H-index: 70
(University of California, San Diego)
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...
8 Citations Source Cite
Published on Jun 6, 2017in F1000Research
Daniel E. Carlin10
Estimated H-index: 10
(University of California, San Diego),
Kassi Kosnicki (University of California, San Diego)+ 4 AuthorsJill P. Mesirov70
Estimated H-index: 70
(University of California, San Diego)
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...
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Published on Aug 8, 2017in F1000Research
Ted Liefeld15
Estimated H-index: 15
,
Marco Ocana2
Estimated H-index: 2
+ 2 AuthorsJill P. Mesirov70
Estimated H-index: 70
Source Cite
Published on Jul 15, 2016in Cancer Research 9.13
Michael Reich2
Estimated H-index: 2
(University of California, San Diego),
Thorin Tabor1
Estimated H-index: 1
(Broad Institute)
+ 7 AuthorsJill P. Mesirov70
Estimated H-index: 70
(University of California, San Diego)
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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Published on Aug 1, 2016in F1000Research
Michael Reich47
Estimated H-index: 47
,
Thorin Tabor2
Estimated H-index: 2
+ 6 AuthorsJill P. Mesirov70
Estimated H-index: 70
Source Cite
Published on Mar 1, 2016in Nature Methods 26.92
Kun Qu28
Estimated H-index: 28
(Stanford University),
Sara Garamszegi1
Estimated H-index: 1
(Broad Institute)
+ 20 AuthorsBarry Demchak12
Estimated H-index: 12
(University of California, San Diego)
Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes', short workflows to guide investigators through high-uti...
18 Citations Source Cite
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