Computational epigenetics
C Bock, T Lengauer - Bioinformatics, 2008 - academic.oup.com
Epigenetic research aims to understand heritable gene regulation that is not directly
encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and …
encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and …
[HTML][HTML] H3K4me3 breadth is linked to cell identity and transcriptional consistency
Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to
mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that …
mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that …
Model-based analysis of ChIP-Seq (MACS)
Abstract We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data
generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically …
generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically …
Histone modifications at human enhancers reflect global cell-type-specific gene expression
The human body is composed of diverse cell types with distinct functions. Although it is
known that lineage specification depends on cell-specific gene expression, which in turn is …
known that lineage specification depends on cell-specific gene expression, which in turn is …
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response
Genome-wide association studies have identified single nucleotide polymorphisms (SNPs)
in the 9p21 gene desert associated with coronary artery disease (CAD),,, and type 2 …
in the 9p21 gene desert associated with coronary artery disease (CAD),,, and type 2 …
Impact of an exercise intervention on DNA methylation in skeletal muscle from first-degree relatives of patients with type 2 diabetes
To identify epigenetic patterns, which may predispose to type 2 diabetes (T2D) due to a
family history (FH) of the disease, we analyzed DNA methylation genome-wide in skeletal …
family history (FH) of the disease, we analyzed DNA methylation genome-wide in skeletal …
PPARγ and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale
MI Lefterova, Y Zhang, DJ Steger… - Genes & …, 2008 - genesdev.cshlp.org
Peroxisome proliferator-activated receptor γ (PPARγ), a nuclear receptor and the target of
anti-diabetic thiazolinedione drugs, is known as the master regulator of adipocyte biology …
anti-diabetic thiazolinedione drugs, is known as the master regulator of adipocyte biology …
Cistrome: an integrative platform for transcriptional regulation studies
The increasing volume of ChIP-chip and ChIP-seq data being generated creates a
challenge for standard, integrative and reproducible bioinformatics data analysis platforms …
challenge for standard, integrative and reproducible bioinformatics data analysis platforms …
Differential chromatin marking of introns and expressed exons by H3K36me3
Variation in patterns of methylations of histone tails reflects and modulates chromatin
structure and function. To provide a framework for the analysis of chromatin function in …
structure and function. To provide a framework for the analysis of chromatin function in …
An integrated software system for analyzing ChIP-chip and ChIP-seq data
We present CisGenome, a software system for analyzing genome-wide chromatin
immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP …
immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP …