Volume 13, issue 10, October 2012

30 articles in this issue

What can epigenomics do for you?

Authors
- Alexander Meissner
- Content type: Editorial
- Published: 23 October 2012
- Article: 420
The allure of the epigenome

Authors
- Naomi Attar
- Content type: Editorial
- Published: 23 October 2012
- Article: 419
Bioinformatics: living on the edge

Authors
- Evangelos Bellos
- Lachlan JM Coin
- Myrsini Kaforou
- Content type: Meeting report
- Published: 26 October 2012
- Article: 321
The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation

Authors
- Ryan Schmidt
- Kathrin Plath
- Content type: Review
- Published: 22 October 2012
- Article: 251
Surveying the epigenomic landscape, one base at a time

Authors
- Gabriel E Zentner
- Steven Henikoff
- Content type: Review
- Published: 22 October 2012
- Article: 250
Epialleles in plant evolution

Authors
- Detlef Weigel
- Vincent Colot
- Content type: Review
- Published: 11 October 2012
- Article: 249
Hypothesis-driven genomics pays off

Authors
- Gregory A Petsko
- Content type: Comment
- Published: 30 October 2012
- Article: 176
The birth of the Epitranscriptome: deciphering the function of RNA modifications

Authors (first, second and last of 6)
- Yogesh Saletore
- Kate Meyer
- Christopher E Mason
- Content type: Opinion
- Published: 31 October 2012
- Article: 175
Birds do it, bees do it, worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life

Authors
- Soojin V Yi
- Content type: Research highlight
- Published: 17 October 2012
- Article: 174
Balance of DNA methylation and demethylation in cancer development

Authors
- Chun-Xiao Song
- Chuan He
- Content type: Research highlight
- Published: 23 October 2012
- Article: 173
DNA methylation studies using twins: what are they telling us?

Authors
- Jordana T Bell
- Tim D Spector
- Content type: Opinion
- Published: 18 October 2012
- Article: 172
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

Authors (first, second and last of 7)
- Jing-Quan Lim
- Chandana Tennakoon
- Wing-Kin Sung
- Content type: Method
- Open Access
- Published: 03 October 2012
- Article: R82
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

Authors
- Kasper D Hansen
- Benjamin Langmead
- Rafael A Irizarry
- Content type: Method
- Open Access
- Published: 03 October 2012
- Article: R83
Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns

Authors (first, second and last of 8)
- Duncan Sproul
- Robert R Kitchen
- Richard R Meehan
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R84
H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

Authors (first, second and last of 8)
- Manching Ku
- Jacob D Jaffe
- Bradley E Bernstein
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R85
Enhanced top-down characterization of histone post-translational modifications

Authors (first, second and last of 10)
- Zhixin Tian
- Nikola Tolić
- Ljiljana Paša-Tolić
- Content type: Method
- Open Access
- Published: 03 October 2012
- Article: R86
methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Authors (first, second and last of 7)
- Altuna Akalin
- Matthias Kormaksson
- Christopher E Mason
- Content type: Software
- Open Access
- Published: 03 October 2012
- Article: R87
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Authors (first, second and last of 12)
- Alok K Tewari
- Galip Gürkan Yardimci
- Phillip G Febbo
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R88
Epigenetic interplay between mouse endogenous retroviruses and host genes

Authors (first, second and last of 6)
- Rita Rebollo
- Katharine Miceli-Royer
- Dixie L Mager
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R89
The landscape of DNA repeat elements in human heart failure

Authors (first, second and last of 10)
- Syed Haider
- Lina Cordeddu
- Roger Foo
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R90
Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

Authors (first, second and last of 5)
- Michael K Skinner
- Mohan Manikkam
- Marina I Savenkova
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R91
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Authors (first, second and last of 11)
- Patrick Boyle
- Kendell Clement
- Alexander Meissner
- Content type: Method
- Open Access
- Published: 03 October 2012
- Article: R92
Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome

Authors (first, second and last of 12)
- John P Thomson
- Harri Lempiäinen
- Richard R Meehan
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R93
Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis

Authors
- Lidija Berke
- Gabino F Sanchez-Perez
- Berend Snel
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R94
Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

Authors (first, second and last of 16)
- Anneleen Decock
- Maté Ongenaert
- Jo Vandesompele
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R95
Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

Authors
- John R Bracht
- David H Perlman
- Laura F Landweber
- Content type: Research
- Open Access
- Published: 17 October 2012
- Article: R99
EpiExplorer: live exploration and global analysis of large epigenomic datasets

Authors (first, second and last of 5)
- Konstantin Halachev
- Hannah Bast
- Christoph Bock
- Content type: Software
- Open Access
- Published: 03 October 2012
- Article: R96
Aging effects on DNA methylation modules in human brain and blood tissue

Authors (first, second and last of 8)
- Steve Horvath
- Yafeng Zhang
- Roel A Ophoff
- Content type: Research
- Open Access
- Published: 03 October 2012
- Article: R97
Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

Authors (first, second and last of 17)
- Fei Gao
- Xiaolei Liu
- Mingyuan Liu
- Content type: Research
- Open Access
- Published: 17 October 2012
- Article: R100
CHANCE: comprehensive software for quality control and validation of ChIP-seq data

Authors
- Aaron Diaz
- Abhinav Nellore
- Jun S Song
- Content type: Software
- Open Access
- Published: 15 October 2012
- Article: R98

Volume 13, issue 10, October 2012

What can epigenomics do for you?

The allure of the epigenome

Bioinformatics: living on the edge

The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation

Surveying the epigenomic landscape, one base at a time

Epialleles in plant evolution

Hypothesis-driven genomics pays off

The birth of the Epitranscriptome: deciphering the function of RNA modifications

Birds do it, bees do it, worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life

Balance of DNA methylation and demethylation in cancer development

DNA methylation studies using twins: what are they telling us?

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

Enhanced top-down characterization of histone post-translational modifications

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Epigenetic interplay between mouse endogenous retroviruses and host genes

The landscape of DNA repeat elements in human heart failure

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome

Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

EpiExplorer: live exploration and global analysis of large epigenomic datasets

Aging effects on DNA methylation modules in human brain and blood tissue

Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

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