EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes [PDF]
, 2017 Existence of some extra-genetic (epigenetic) codes has been postulated since the discovery of the primary genetic code. Evident effects of histone post-translational modifications or DNA methylation over the efficiency and the regulation of DNA processes
Santoni, Federico Andrea
core
A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy [PDF]
, 2013 During hematopoiesis, lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. We explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor
Barde, I. +10 more
core +1 more source
RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection
Molecular Ecology Resources, Volume 25, Issue 7, October 2025.ABSTRACT Tandem repeats play an important role in centromere structure, subtelomeric regions, DNA methylation, recombination and the regulation of gene activity. Analysis of their distribution in genomes offers a potential means for predicting putative centromere locations, which continues to be a challenge for genome annotation.
Cassandra Elphinstone +3 more
wiley +1 more source
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression
Computational and Structural Biotechnology Journal, 2023 Glucocorticoids are potent immunosuppressive drugs, but long-term treatment leads to severe side-effects. While there is a commonly accepted model for GR-mediated gene activation, the mechanism behind repression remains elusive.
Barbara Höllbacher +4 more
doaj +1 more source
A reversible infinite HMM using normalised random measures [PDF]
, 2014 We present a nonparametric prior over reversible Markov chains. We use completely random measures, specifically gamma processes, to construct a countably infinite graph with weighted edges.
Ghahramani, Zoubin +2 more
core +1 more source
Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis [PDF]
, 2016 BACKGROUND: There has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized ...
Mark Bieda +2 more
core +1 more source
Advanced Science, Volume 12, Issue 33, September 4, 2025.The SNP rs2863002 at the 11p11.2 locus, identified through GWAS, is associated with an increased risk of neuroblastoma. The rs2863002‐C allele impairs the binding of the transcription factor GATA3, resulting in upregulation of the HSD17B12 gene.
Teresa Maiorino +20 more
wiley +1 more source
ChIPulate: A comprehensive ChIP-seq simulation pipeline.
PLoS Computational Biology, 2019 ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) is a high-throughput technique to identify genomic regions that are bound in vivo by a particular protein, e.g., a transcription factor (TF).
Vishaka Datta +2 more
doaj +1 more source
BayesPeak: Bayesian analysis of ChIP-seq data
BMC Bioinformatics, 2009 Background High-throughput sequencing technology has become popular and widely used to study protein and DNA interactions. Chromatin immunoprecipitation, followed by sequencing of the resulting samples, produces large amounts of data that can be used to ...
Stark Rory +3 more
doaj +1 more source
Software for Computing and Annotating Genomic Ranges [PDF]
, 2013 We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges,
Aboyoun, Patrick +7 more
core +3 more sources