[HTML][HTML] Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer
Endocrine therapy resistance frequently develops in estrogen receptor positive (ER+) breast
cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that …
cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that …
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data
Motivation DNA methylation is important for gene silencing and imprinting in both plants and
animals. Recent advances in bisulfite sequencing allow detection of single nucleotide …
animals. Recent advances in bisulfite sequencing allow detection of single nucleotide …
[HTML][HTML] DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
Background DNA methylation at promoters is largely correlated with inhibition of gene
expression. However, the role of DNA methylation at enhancers is not fully understood …
expression. However, the role of DNA methylation at enhancers is not fully understood …
DNA sequencing technologies: sequencing data protocols and bioinformatics tools
The recent advances in DNA sequencing technology, from first-generation sequencing
(FGS) to third-generation sequencing (TGS), have constantly transformed the genome …
(FGS) to third-generation sequencing (TGS), have constantly transformed the genome …
[HTML][HTML] Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten
Background Comprehensive genome-wide DNA methylation profiling is critical to gain
insights into epigenetic reprogramming during development and disease processes. Among …
insights into epigenetic reprogramming during development and disease processes. Among …
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data
As reference genome assemblies are updated there is a need to convert epigenome
sequence data from older genome assemblies to newer versions, to facilitate data …
sequence data from older genome assemblies to newer versions, to facilitate data …
Rules governing the mechanism of epigenetic reprogramming memory
Aim: Disclosing the mechanisms that regulate reprogramming memory. Materials &
methods: We established computational procedure to find DNA methylation somatic memory …
methods: We established computational procedure to find DNA methylation somatic memory …
BigMPI4py: python module for parallelization of big data objects discloses germ layer specific DNA demethylation motifs
AM Ascensión, MJ Araúzo-Bravo - IEEE/ACM Transactions on …, 2020 - ieeexplore.ieee.org
Parallelization in Python integrates Message Passing Interface via the mpi4py module.
Since mpi4py does not support parallelization of objects greater than bytes, we developed …
Since mpi4py does not support parallelization of objects greater than bytes, we developed …
[HTML][HTML] ARPEGGIO: automated reproducible polyploid EpiGenetic GuIdance workflOw
Background Whole genome duplication (WGD) events are common in the evolutionary
history of many living organisms. For decades, researchers have been trying to understand …
history of many living organisms. For decades, researchers have been trying to understand …
[HTML][HTML] NaviSE: superenhancer navigator integrating epigenomics signal algebra
AM Ascensión, M Arrospide-Elgarresta, A Izeta… - BMC …, 2017 - Springer
Background Superenhancers are crucial structural genomic elements determining cell fate,
and they are also involved in the determination of several diseases, such as cancer or …
and they are also involved in the determination of several diseases, such as cancer or …