Literature DB >> 34928367

HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries.

Claire Marchal1,2, Nivedita Singh1, Ximena Corso-Díaz1, Anand Swaroop1.   

Abstract

Three-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. Hi-C is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any Hi-C experimental design. Here, we present the mathematical concepts to estimate the resolution of a dataset and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to several Hi-C libraries. Published by Oxford University Press on behalf of Nucleic Acids Research 2021.

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Year:  2022        PMID： 34928367      PMCID： PMC8990515          DOI： 10.1093/nar/gkab1235

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  41 in total

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Authors:  Apolinar Maya-Mendoza; Dean A Jackson
Journal:  Curr Protoc Cell Biol       Date:  2017-06-19

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Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

Review 5.  Control of DNA replication timing in the 3D genome.

Authors:  Claire Marchal; Jiao Sima; David M Gilbert
Journal:  Nat Rev Mol Cell Biol       Date:  2019-09-02       Impact factor: 94.444

6.  HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

Authors:  Tao Yang; Feipeng Zhang; Galip Gürkan Yardımcı; Fan Song; Ross C Hardison; William Stafford Noble; Feng Yue; Qunhua Li
Journal:  Genome Res       Date:  2017-08-30       Impact factor: 9.043

7.  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

8.  Multiscale 3D Genome Rewiring during Mouse Neural Development.

Authors:  Boyan Bonev; Netta Mendelson Cohen; Quentin Szabo; Lauriane Fritsch; Giorgio L Papadopoulos; Yaniv Lubling; Xiaole Xu; Xiaodan Lv; Jean-Philippe Hugnot; Amos Tanay; Giacomo Cavalli
Journal:  Cell       Date:  2017-10-19       Impact factor: 41.582

9.  Measuring the reproducibility and quality of Hi-C data.

Authors:  Galip Gürkan Yardımcı; Hakan Ozadam; Michael E G Sauria; Oana Ursu; Koon-Kiu Yan; Tao Yang; Abhijit Chakraborty; Arya Kaul; Bryan R Lajoie; Fan Song; Ye Zhan; Ferhat Ay; Mark Gerstein; Anshul Kundaje; Qunhua Li; James Taylor; Feng Yue; Job Dekker; William S Noble
Journal:  Genome Biol       Date:  2019-03-19       Impact factor: 13.583

10.  4D Genome Rewiring during Oncogene-Induced and Replicative Senescence.

Authors:  Satish Sati; Boyan Bonev; Quentin Szabo; Daniel Jost; Paul Bensadoun; Francois Serra; Vincent Loubiere; Giorgio Lucio Papadopoulos; Juan-Carlos Rivera-Mulia; Lauriane Fritsch; Pauline Bouret; David Castillo; Josep Ll Gelpi; Modesto Orozco; Cedric Vaillant; Franck Pellestor; Frederic Bantignies; Marc A Marti-Renom; David M Gilbert; Jean-Marc Lemaitre; Giacomo Cavalli
Journal:  Mol Cell       Date:  2020-03-26       Impact factor: 17.970
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  2 in total

1.  Nucleome programming is required for the foundation of totipotency in mammalian germline development.

Authors:  Masahiro Nagano; Bo Hu; Shihori Yokobayashi; Akitoshi Yamamura; Fumiya Umemura; Mariel Coradin; Hiroshi Ohta; Yukihiro Yabuta; Yukiko Ishikura; Ikuhiro Okamoto; Hiroki Ikeda; Naofumi Kawahira; Yoshiaki Nosaka; Sakura Shimizu; Yoji Kojima; Ken Mizuta; Tomoko Kasahara; Yusuke Imoto; Killian Meehan; Roman Stocsits; Gordana Wutz; Yasuaki Hiraoka; Yasuhiro Murakawa; Takuya Yamamoto; Kikue Tachibana; Jan-Michel Peters; Leonid A Mirny; Benjamin A Garcia; Jacek Majewski; Mitinori Saitou
Journal:  EMBO J       Date:  2022-06-15       Impact factor: 14.012

2.  High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci.

Authors:  Claire Marchal; Nivedita Singh; Zachary Batz; Jayshree Advani; Catherine Jaeger; Ximena Corso-Díaz; Anand Swaroop
Journal:  Nat Commun       Date:  2022-10-07       Impact factor: 17.694
  2 in total

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