Literature DB >> 27019695

Chromas from chromatin: sonification of the epigenome.

Davide Cittaro1, Dejan Lazarevic1, Paolo Provero2.   

Abstract

The epigenetic modifications are organized in patterns determining the functional properties of the underlying genome. Such patterns, typically measured by ChIP-seq assays of histone modifications, can be combined and translated into musical scores, summarizing multiple signals into a single waveform. As music is recognized as a universal way to convey meaningful information, we wanted to investigate properties of music obtained by sonification of ChIP-seq data. We show that the music produced by such quantitative signals is perceived by human listeners as more pleasant than that produced from randomized signals. Moreover, the waveform can be analyzed to predict phenotypic properties, such as differential gene expression.

Entities:  

Keywords:  Chromatin; Epigenomics; Information; Music; Sonification

Year:  2016        PMID: 27019695      PMCID: PMC4805159          DOI: 10.12688/f1000research.8001.1

Source DB:  PubMed          Journal:  F1000Res        ISSN: 2046-1402


  26 in total

1.  ChromHMM: automating chromatin-state discovery and characterization.

Authors:  Jason Ernst; Manolis Kellis
Journal:  Nat Methods       Date:  2012-02-28       Impact factor: 28.547

Review 2.  Chromatin modifications and their function.

Authors:  Tony Kouzarides
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

3.  Chromas from chromatin: sonification of the epigenome.

Authors:  Davide Cittaro; Dejan Lazarevic; Paolo Provero
Journal:  F1000Res       Date:  2016-03-03

4.  limma powers differential expression analyses for RNA-sequencing and microarray studies.

Authors:  Matthew E Ritchie; Belinda Phipson; Di Wu; Yifang Hu; Charity W Law; Wei Shi; Gordon K Smyth
Journal:  Nucleic Acids Res       Date:  2015-01-20       Impact factor: 16.971

5.  Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns.

Authors:  Rie Takahashi; Jeffrey H Miller
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

6.  A scaling normalization method for differential expression analysis of RNA-seq data.

Authors:  Mark D Robinson; Alicia Oshlack
Journal:  Genome Biol       Date:  2010-03-02       Impact factor: 13.583

7.  Spectacle: fast chromatin state annotation using spectral learning.

Authors:  Jimin Song; Kevin C Chen
Journal:  Genome Biol       Date:  2015-02-12       Impact factor: 13.583

8.  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.

Authors: 
Journal:  Nat Biotechnol       Date:  2014-08-24       Impact factor: 54.908

9.  An integrated encyclopedia of DNA elements in the human genome.

Authors: 
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

10.  Integrative annotation of chromatin elements from ENCODE data.

Authors:  Michael M Hoffman; Jason Ernst; Steven P Wilder; Anshul Kundaje; Robert S Harris; Max Libbrecht; Belinda Giardine; Paul M Ellenbogen; Jeffrey A Bilmes; Ewan Birney; Ross C Hardison; Ian Dunham; Manolis Kellis; William Stafford Noble
Journal:  Nucleic Acids Res       Date:  2012-12-05       Impact factor: 16.971

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  3 in total

1.  Chromas from chromatin: sonification of the epigenome.

Authors:  Davide Cittaro; Dejan Lazarevic; Paolo Provero
Journal:  F1000Res       Date:  2016-03-03

2.  An auditory display tool for DNA sequence analysis.

Authors:  Mark D Temple
Journal:  BMC Bioinformatics       Date:  2017-04-24       Impact factor: 3.169

3.  Real-time audio and visual display of the Coronavirus genome.

Authors:  Mark D Temple
Journal:  BMC Bioinformatics       Date:  2020-10-02       Impact factor: 3.169

  3 in total

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