Aging is a process of gradual decline in the functional capacity of the human body that leads to a significant increase in the risk of death over time. Although it is a process universal to all animals, its rate is not the same. Biomarkers of aging a...
The multi-omics molecular characterization of cancer opened a new horizon for our understanding of cancer biology and therapeutic strategies. However, a tumor biopsy comprises diverse types of cells limited not only to cancerous cells but also to tum...
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 ...
Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function, not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mec...
MOTIVATION: Predictive models of DNA chromatin profile (i.e. epigenetic state), such as transcription factor binding, are essential for understanding regulatory processes and developing gene therapies. It is known that the 3D genome, or spatial struc...
BACKGROUND: Gene expression plays a key intermediate role in linking molecular features at the DNA level and phenotype. However, owing to various limitations in experiments, the RNA-seq data are missing in many samples while there exist high-quality ...
MOTIVATION: Interactions among cis-regulatory elements such as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expres...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2019
C.H. Waddington introduced the epigenetic landscape as a metaphor to represent cellular decision-making during development. Like a population of balls rolling down a rough hillside, developing cells follow specific trajectories (valleys) and eventual...
BACKGROUND: On a tide of big data, machine learning is coming to its day. Referring to huge amounts of epigenetic data coming from biological experiments and clinic, machine learning can help in detecting epigenetic features in genome, finding correl...
MOTIVATION: One of the goals of functional genomics is to understand the regulatory implications of experimentally obtained genomic regions of interest (ROIs). Most sequencing technologies now generate ROIs distributed across the whole genome. The in...
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