Literature DB >> 27716489

Minute-Made Data Analysis: Tools for Rapid Interrogation of Hi-C Contacts.

M Jordan Rowley1, Victor G Corces2.   

Abstract

Juicer and Juicebox, described by Durand et al. (2016a, 2016b), are two new tools for fast and reliable processing of Hi-C data, providing approaches for read processing, multiple normalization schemes, feature annotation, and dynamic browsing of chromatin contacts, thus reducing arduous Hi-C analysis into an easy yet flexible pipeline.
Copyright © 2016 Elsevier Inc. All rights reserved.

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Year:  2016        PMID： 27716489      PMCID： PMC5289287          DOI： 10.1016/j.molcel.2016.09.029

Source DB:  PubMed          Journal:  Mol Cell        ISSN： 1097-2765            Impact factor:   17.970


  10 in total

1.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.

Authors:  Eitan Yaffe; Amos Tanay
Journal:  Nat Genet       Date:  2011-10-16       Impact factor: 38.330

2.  Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing.

Authors:  Li Li; Xiaowen Lyu; Chunhui Hou; Naomi Takenaka; Huy Q Nguyen; Chin-Tong Ong; Caelin Cubeñas-Potts; Ming Hu; Elissa P Lei; Giovanni Bosco; Zhaohui S Qin; Victor G Corces
Journal:  Mol Cell       Date:  2015-03-26       Impact factor: 17.970

3.  HiCNorm: removing biases in Hi-C data via Poisson regression.

Authors:  Ming Hu; Ke Deng; Siddarth Selvaraj; Zhaohui Qin; Bing Ren; Jun S Liu
Journal:  Bioinformatics       Date:  2012-09-27       Impact factor: 6.937

Review 4.  The three-dimensional genome: principles and roles of long-distance interactions.

Authors:  M Jordan Rowley; Victor G Corces
Journal:  Curr Opin Cell Biol       Date:  2016-02-04       Impact factor: 8.382

5.  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

6.  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

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

Authors:  Neva C Durand; James T Robinson; Muhammad S Shamim; Ido Machol; Jill P Mesirov; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell Syst       Date:  2016-07       Impact factor: 10.304

8.  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

9.  Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Authors:  Jesse R Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S Liu; Bing Ren
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

10.  Iterative correction of Hi-C data reveals hallmarks of chromosome organization.

Authors:  Maxim Imakaev; Geoffrey Fudenberg; Rachel Patton McCord; Natalia Naumova; Anton Goloborodko; Bryan R Lajoie; Job Dekker; Leonid A Mirny
Journal:  Nat Methods       Date:  2012-09-02       Impact factor: 28.547
  10 in total
  2 in total

1.  Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data.

Authors:  James T Robinson; Douglass Turner; Neva C Durand; Helga Thorvaldsdóttir; Jill P Mesirov; Erez Lieberman Aiden
Journal:  Cell Syst       Date:  2018-02-07       Impact factor: 10.304

2.  Insulator-based loops mediate the spreading of H3K27me3 over distant micro-domains repressing euchromatin genes.

Authors:  Alexandre Heurteau; Charlène Perrois; David Depierre; Olivier Fosseprez; Jonathan Humbert; Stéphane Schaak; Olivier Cuvier
Journal:  Genome Biol       Date:  2020-08-03       Impact factor: 13.583
  2 in total

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