Evidence map›Paper›PMID 27467250›Full record

ArticleCell systems2016

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.

Neva C Durand, James T Robinson, Muhammad S Shamim, Ido Machol, Jill P Mesirov, Eric S Lander, Erez Lieberman Aiden

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,641 papers.

0numbers the graph read from it
0cells of the map it votes in
1,641citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1,641 citing papers in PubMed.

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1,581 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Neva C DurandThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
James T RobinsonThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
Muhammad S ShamimThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA.
Ido MacholThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA.
Jill P MesirovBroad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
Eric S LanderBroad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Erez Lieberman AidenThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA. Electronic address: erez@erez.com.

Funding

Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6M
Center for Cell CircuitsP50HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI REGEV, AVIV · 2011 to 2015
$15.6M
Supporting Integrative Genomic Analysis Users with GenePatternR01GM074024 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2005 to 2019
$6.6M
Exploring how the genome folds through proximity ligation and sequencingDP2OD008540 · OD · BROAD INSTITUTE, INC. · PI LIEBERMAN-AIDEN, EREZ · 2011 to 2016
$3.0M
A next-generation Integrative Genomics Viewer for biomedical and cancer research.R01CA157304 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2012 to 2015
$1.9M
NCI NIH HHS R01 CA157304NHGRI NIH HHS P50 HG006193NHGRI NIH HHS U54 HG003067NIGMS NIH HHS R01 GM074024NIH HHS DP2 OD008540
6 · The paper itself

Abstract

Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.

Indexed as

GenomeHumansSoftware

Identifiers

PMID27467250
PMCPMC5596920

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.