DNA methylation-based predictors of health: applications and statistical considerations
DNA methylation data have become a valuable source of information for biomarker
development, because, unlike static genetic risk estimates, DNA methylation varies …
development, because, unlike static genetic risk estimates, DNA methylation varies …
DNA methylation-based biomarkers and the epigenetic clock theory of ageing
S Horvath, K Raj - Nature reviews genetics, 2018 - nature.com
Identifying and validating molecular targets of interventions that extend the human health
span and lifespan has been difficult, as most clinical biomarkers are not sufficiently …
span and lifespan has been difficult, as most clinical biomarkers are not sufficiently …
Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …
generated from genome-scale (omics) experiments. This method identifies biological …
Inflammation and cancer
M Murata - Environmental health and preventive medicine, 2018 - Springer
Infection and inflammation account for approximately 25% of cancer-causing factors.
Inflammation-related cancers are characterized by mutagenic DNA lesions, such as 8-oxo-7 …
Inflammation-related cancers are characterized by mutagenic DNA lesions, such as 8-oxo-7 …
Clinical epigenetics: seizing opportunities for translation
M Berdasco, M Esteller - Nature Reviews Genetics, 2019 - nature.com
Biomarker discovery and validation are necessary for improving the prediction of clinical
outcomes and patient monitoring. Despite considerable interest in biomarker discovery and …
outcomes and patient monitoring. Despite considerable interest in biomarker discovery and …
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
Abstract The Cancer Genome Atlas (TCGA) research network has made public a large
collection of clinical and molecular phenotypes of more than 10 000 tumor patients across …
collection of clinical and molecular phenotypes of more than 10 000 tumor patients across …
Droplet Cas12a assay enables DNA quantification from unamplified samples at the single-molecule level
DNA quantification is important for biomedical research, but the routinely used techniques
rely on nucleic acid amplification which have inherent issues like cross-contamination risk …
rely on nucleic acid amplification which have inherent issues like cross-contamination risk …
SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
We report a new class of artifacts in DNA methylation measurements from Illumina
HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed …
HumanMethylation450 and MethylationEPIC arrays. These artifacts reflect failed …
Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge
K Tomczak, P Czerwińska… - Contemporary Oncology …, 2015 - termedia.pl
The Cancer Genome Atlas (TCGA) is a public funded project that aims to catalogue and
discover major cancer-causing genomic alterations to create a comprehensive “atlas” of …
discover major cancer-causing genomic alterations to create a comprehensive “atlas” of …
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning
Recent technological advances have enabled DNA methylation to be assayed at single-cell
resolution. However, current protocols are limited by incomplete CpG coverage and hence …
resolution. However, current protocols are limited by incomplete CpG coverage and hence …