Literature DB >> 26437592

Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool.

Viviana I Risca1, William J Greenleaf2.   

Abstract

Paired-end sequencing has enabled a variety of new methods for high-throughput interrogation of both genome structure and chromatin architecture. Here, we discuss how the paired-end paradigm can be used to interpret sequencing data as biophysical measurements of in vivo chromatin structure that report on single molecules in single cells.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  chromatin; chromosome structure; in vivo measurements; paired-end sequencing

Mesh：

Year:  2015        PMID： 26437592      PMCID： PMC5540433          DOI： 10.1016/j.tcb.2015.08.004

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN： 0962-8924            Impact factor:   20.808


  13 in total

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2.  Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.

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Journal:  Nat Genet       Date:  2014-10-19       Impact factor: 38.330

3.  Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.

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Journal:  Cell       Date:  2014-05-08       Impact factor: 41.582

4.  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

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Journal:  Nature       Date:  2009-11-05       Impact factor: 49.962

Review 6.  Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.

Authors:  Clifford A Meyer; X Shirley Liu
Journal:  Nat Rev Genet       Date:  2014-09-16       Impact factor: 53.242

7.  Controls of nucleosome positioning in the human genome.

Authors:  Daniel J Gaffney; Graham McVicker; Athma A Pai; Yvonne N Fondufe-Mittendorf; Noah Lewellen; Katelyn Michelini; Jonathan Widom; Yoav Gilad; Jonathan K Pritchard
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Authors:  Andrew Adey; Jacob O Kitzman; Joshua N Burton; Riza Daza; Akash Kumar; Lena Christiansen; Mostafa Ronaghi; Sasan Amini; Kevin L Gunderson; Frank J Steemers; Jay Shendure
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9.  Single-cell paired-end genome sequencing reveals structural variation per cell cycle.

Authors:  Thierry Voet; Parveen Kumar; Peter Van Loo; Susanna L Cooke; John Marshall; Meng-Lay Lin; Masoud Zamani Esteki; Niels Van der Aa; Ligia Mateiu; David J McBride; Graham R Bignell; Stuart McLaren; Jon Teague; Adam Butler; Keiran Raine; Lucy A Stebbings; Michael A Quail; Thomas D'Hooghe; Yves Moreau; P Andrew Futreal; Michael R Stratton; Joris R Vermeesch; Peter J Campbell
Journal:  Nucleic Acids Res       Date:  2013-04-29       Impact factor: 16.971

Review 10.  RNA sequencing: from tag-based profiling to resolving complete transcript structure.

Authors:  Eleonora de Klerk; Johan T den Dunnen; Peter A C 't Hoen
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  1 in total

1.  Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.

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  1 in total

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