LAUSR

The epigenome has been regarded as one of the most important regulators for genome on its functioning and downstream regulation, therefore, the maintenance of stable and normal functioning epigenome is quite crucial for living organisms. However, the epigenome changes over time, either naturally or triggered by various endogenous and exogenous factors like environment, disease state and infections. The alteration of the epigenome may be crucial intermediate between environments and biological phenotypes during development and pathogenesis. Therefore, developmental or pathological alterations can also be monitored using epigenome characteristics, which is exactly what epigenetics and epigenomics studies focus on. Currently, studies on epigenetics and epigenomics mainly focused on the plasticity of epigenome during twomajor biological processes: development and pathogenesis, both of which are inextricably linked to the environment through the epigenetic modifications. From the research layers, current epigenomic and epigenetic studies can be further divided into multiple layers: 1) direct methylation on DNA molecules; 2) histone protein modification; 3) chromatin structure and 4) related noncoding RNAs. Integration all layers of epigenomics and epigenetics studies, the ultimate research goal in this field is to reveal the specific role of epigenome during the development and pathogenesis of human beings and explain the related biological mechanisms using typical epigenetics/epigenomics biomarkers. Biologically, epigenetics and epigenomics describe complex interactions between environment and genomics, resulting in diverse modifications on histone and DNA molecules. With the development of detecting techniques (like microarray and Methyl-Seq), an explosive increase occurs in epigenetics and epigenomics data. To handle such massive complex data, machine learning models have been introduced in the analyses on data at this omics-level and contribute to the identification of potential disease/developmental events associated epigenetic biomarkers. However, several restrictions and challenges still remain in current epigenetics and epigenomics studies: