We report a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. Differential methylation among tumor entities relates to differences in ...
BACKGROUND: DNA N4-methylcytosine (4mC) is a critical epigenetic modification and has various roles in the restriction-modification system. Due to the high cost of experimental laboratory detection, computational methods using sequence characteristic...
Assessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise ...
Although clinical and laboratory data have long been used to guide medical practice, this information is rarely integrated with multi-omic data to identify endotypes. We present Merged Affinity Network Association Clustering (MANAclust), a coding-fre...
IEEE/ACM transactions on computational biology and bioinformatics
34043510
The availability of thousands of assays of epigenetic activity necessitates compressed representations of these data sets that summarize the epigenetic landscape of the genome. Until recently, most such representations were cell type-specific, applyi...
Methods in molecular biology (Clifton, N.J.)
36723810
Genome-wide DNA methylomes have contributed greatly to tumor detection and subclassification. However, interpreting the biological impact of the DNA methylome at the individual gene level remains a challenge. MethylationToActivity (M2A) is a pipeline...
The epigenome influences gene regulation and phenotypes in response to exposures. Epigenome assessment can determine exposure history aiding in diagnosis. Here we developed and implemented a machine learning algorithm, the exposure signature discove...
Schizophrenia is a serious mental disorder that affects millions of people worldwide. This disorder slowly disintegrates thinking ability and changes behaviours of patients. These patients will show some psychotic symptoms such as hallucinations, del...
Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational models. Existi...
Using millions of methylation segments, we developed DiffuCpG, a generative artificial intelligence (AI) diffusion model designed to solve the critical challenge of missing data in high-throughput methylation technologies. DiffuCpG goes beyond conven...