Literature DB >> 27467250

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

Neva C Durand1, James T Robinson2, Muhammad S Shamim3, Ido Machol3, Jill P Mesirov4, Eric S Lander5, Erez Lieberman Aiden6.   

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.
Copyright © 2016 Elsevier Inc. All rights reserved.

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Year:  2016        PMID： 27467250      PMCID： PMC5596920          DOI： 10.1016/j.cels.2015.07.012

Source DB:  PubMed          Journal:  Cell Syst        ISSN： 2405-4712            Impact factor:   10.304


  7 in total

1.  HiTC: exploration of high-throughput 'C' experiments.

Authors:  Nicolas Servant; Bryan R Lajoie; Elphège P Nora; Luca Giorgetti; Chong-Jian Chen; Edith Heard; Job Dekker; Emmanuel Barillot
Journal:  Bioinformatics       Date:  2012-08-24       Impact factor: 6.937

2.  Exploring long-range genome interactions using the WashU Epigenome Browser.

Authors:  Xin Zhou; Rebecca F Lowdon; Daofeng Li; Heather A Lawson; Pamela A F Madden; Joseph F Costello; Ting Wang
Journal:  Nat Methods       Date:  2013-05       Impact factor: 28.547

3.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

4.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.

Authors:  Neva C Durand; Muhammad S Shamim; Ido Machol; Suhas S P Rao; Miriam H Huntley; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell Syst       Date:  2016-07       Impact factor: 10.304

5.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

6.  Integrative genomics viewer.

Authors:  James T Robinson; Helga Thorvaldsdóttir; Wendy Winckler; Mitchell Guttman; Eric S Lander; Gad Getz; Jill P Mesirov
Journal:  Nat Biotechnol       Date:  2011-01       Impact factor: 54.908

7.  HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.

Authors:  Jonas Paulsen; Geir Kjetil Sandve; Sveinung Gundersen; Tonje G Lien; Kai Trengereid; Eivind Hovig
Journal:  Bioinformatics       Date:  2014-02-07       Impact factor: 6.937
  7 in total
  371 in total

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Authors:  Atsushi Okabe; Kie Kyon Huang; Keisuke Matsusaka; Masaki Fukuyo; Manjie Xing; Xuewen Ong; Takayuki Hoshii; Genki Usui; Motoaki Seki; Yasunobu Mano; Bahityar Rahmutulla; Teru Kanda; Takayoshi Suzuki; Sun Young Rha; Tetsuo Ushiku; Masashi Fukayama; Patrick Tan; Atsushi Kaneda
Journal:  Nat Genet       Date:  2020-07-27       Impact factor: 38.330

2.  Producing genome structure populations with the dynamic and automated PGS software.

Authors:  Nan Hua; Harianto Tjong; Hanjun Shin; Ke Gong; Xianghong Jasmine Zhou; Frank Alber
Journal:  Nat Protoc       Date:  2018-04-05       Impact factor: 13.491

3.  Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans.

Authors:  Chen-Yu Wang; Harrison Brand; Natalie D Shaw; Michael E Talkowski; Jeannie T Lee
Journal:  Genetics       Date:  2019-08-16       Impact factor: 4.562

4.  The chromosome-scale genome reveals the evolution and diversification after the recent tetraploidization event in tea plant.

Authors:  Jie-Dan Chen; Chao Zheng; Jian-Qiang Ma; Chen-Kai Jiang; Sezai Ercisli; Ming-Zhe Yao; Liang Chen
Journal:  Hortic Res       Date:  2020-05-01       Impact factor: 6.793

5.  Cooler: scalable storage for Hi-C data and other genomically labeled arrays.

Authors:  Nezar Abdennur; Leonid A Mirny
Journal:  Bioinformatics       Date:  2020-01-01       Impact factor: 6.937

6.  Broadening our understanding of the genetics of Juvenile Idiopathic Arthritis (JIA): Interrogation of three dimensional chromatin structures and genetic regulatory elements within JIA-associated risk loci.

Authors:  Kaiyu Jiang; Haeja Kessler; Yungki Park; Marc Sudman; Susan D Thompson; James N Jarvis
Journal:  PLoS One       Date:  2020-07-30       Impact factor: 3.240

7.  HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples.

Authors:  Fritz Lekschas; Benjamin Bach; Peter Kerpedjiev; Nils Gehlenborg; Hanspeter Pfister
Journal:  IEEE Trans Vis Comput Graph       Date:  2017-08-29       Impact factor: 4.579

8.  Maintenance of CTCF- and Transcription Factor-Mediated Interactions from the Gametes to the Early Mouse Embryo.

Authors:  Yoon Hee Jung; Isaac Kremsky; Hannah B Gold; M Jordan Rowley; Kanchana Punyawai; Alyx Buonanotte; Xiaowen Lyu; Brianna J Bixler; Anthony W S Chan; Victor G Corces
Journal:  Mol Cell       Date:  2019-05-02       Impact factor: 17.970

9.  Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment.

Authors:  Celeste D Rosencrance; Haneen N Ammouri; Qi Yu; Tiffany Ge; Emily J Rendleman; Stacy A Marshall; Kyle P Eagen
Journal:  Mol Cell       Date:  2020-04-02       Impact factor: 17.970

10.  A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells.

Authors:  Frédéric Van Gool; Michelle L T Nguyen; Maxwell R Mumbach; Ansuman T Satpathy; Wendy L Rosenthal; Simone Giacometti; Duy T Le; Weihong Liu; Todd M Brusko; Mark S Anderson; Alexander Y Rudensky; Alexander Marson; Howard Y Chang; Jeffrey A Bluestone
Journal:  Immunity       Date:  2019-01-29       Impact factor: 31.745
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