Literature DB >> 21653521

nucleR: a package for non-parametric nucleosome positioning.

Oscar Flores1, Modesto Orozco.   

Abstract

SUMMARY: nucleR is an R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats. AVAILABILITY: Additional information and methodological details can be found at http://mmb.pcb.ub.es/nucleR

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Year:  2011        PMID： 21653521     DOI： 10.1093/bioinformatics/btr345

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  41 in total

1.  PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.

Authors:  Sangsoon Woo; Xuekui Zhang; Renan Sauteraud; François Robert; Raphael Gottardo
Journal:  Bioinformatics       Date:  2013-06-20       Impact factor: 6.937

Review 2.  Nucleosome positioning in yeasts: methods, maps, and mechanisms.

Authors:  Corinna Lieleg; Nils Krietenstein; Maria Walker; Philipp Korber
Journal:  Chromosoma       Date:  2014-12-23       Impact factor: 4.316

3.  Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin.

Authors:  Young Sam Shim; Yoonjung Choi; Keunsoo Kang; Kun Cho; Seunghee Oh; Junwoo Lee; Shiv I S Grewal; Daeyoup Lee
Journal:  EMBO J       Date:  2012-09-18       Impact factor: 11.598

4.  Interacting Genomic Landscapes of REC8-Cohesin, Chromatin, and Meiotic Recombination in Arabidopsis.

Authors:  Christophe Lambing; Andrew J Tock; Stephanie D Topp; Kyuha Choi; Pallas C Kuo; Xiaohui Zhao; Kim Osman; James D Higgins; F Chris H Franklin; Ian R Henderson
Journal:  Plant Cell       Date:  2020-02-05       Impact factor: 11.277

5.  Q-Nuc: a bioinformatics pipeline for the quantitative analysis of nucleosomal profiles.

Authors:  Yuan Wang; Qiu Sun; Jie Liang; Hua Li; Daniel M Czajkowsky; Zhifeng Shao
Journal:  Interdiscip Sci       Date:  2019-12-16       Impact factor: 2.233

6.  Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants.

Authors:  Tao Zhang; Wenli Zhang; Jiming Jiang
Journal:  Plant Physiol       Date:  2015-07-04       Impact factor: 8.340

7.  Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes.

Authors:  Handong Su; Yalin Liu; Chang Liu; Qinghua Shi; Yuhong Huang; Fangpu Han
Journal:  Plant Cell       Date:  2019-07-16       Impact factor: 11.277

8.  The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres.

Authors:  Tao Zhang; Paul B Talbert; Wenli Zhang; Yufeng Wu; Zujun Yang; Jorja G Henikoff; Steven Henikoff; Jiming Jiang
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-04       Impact factor: 11.205

9.  Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.

Authors:  Diana Buitrago; Laia Codó; Ricard Illa; Pau de Jorge; Federica Battistini; Oscar Flores; Genis Bayarri; Romina Royo; Marc Del Pino; Simon Heath; Adam Hospital; Josep Lluís Gelpí; Isabelle Brun Heath; Modesto Orozco
Journal:  Nucleic Acids Res       Date:  2019-10-10       Impact factor: 16.971

10.  H3K36ac Is an Evolutionary Conserved Plant Histone Modification That Marks Active Genes.

Authors:  Walid Mahrez; Minerva Susana Trejo Arellano; Jordi Moreno-Romero; Miyuki Nakamura; Huan Shu; Paolo Nanni; Claudia Köhler; Wilhelm Gruissem; Lars Hennig
Journal:  Plant Physiol       Date:  2016-01-13       Impact factor: 8.340
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