AIMC Topic: Epigenesis, Genetic

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Kinetics of -induced gene silencing can be predicted from combinations of epigenetic and genomic features.

Genome research
To initiate X-Chromosome inactivation (XCI), the long noncoding RNA mediates chromosome-wide gene silencing of one X Chromosome in female mammals to equalize gene dosage between the sexes. The efficiency of gene silencing is highly variable across g...

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.

Nature communications
DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifica...

Deep Learning/Artificial Intelligence and Blood-Based DNA Epigenomic Prediction of Cerebral Palsy.

International journal of molecular sciences
The etiology of cerebral palsy (CP) is complex and remains inadequately understood. Early detection of CP is an important clinical objective as this improves long term outcomes. We performed genome-wide DNA methylation analysis to identify epigenomic...

MRCNN: a deep learning model for regression of genome-wide DNA methylation.

BMC genomics
BACKGROUND: Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence the cell differentiation which ...

CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features.

BMC medical genomics
BACKGROUND: Long noncoding RNAs (lncRNAs) are widely involved in the initiation and development of cancer. Although some computational methods have been proposed to identify cancer-related lncRNAs, there is still a demanding to improve the prediction...

RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes.

BMC genomics
BACKGROUND: Although different quality controls have been applied at different stages of the sample preparation and data analysis to ensure both reproducibility and reliability of RNA-seq results, there are still limitations and bias on the detectabi...

Advances in the computational and molecular understanding of the prostate cancer cell nucleus.

Journal of cellular biochemistry
Nuclear alterations are a hallmark of many types of cancers, including prostate cancer (PCa). Recent evidence shows that subvisual changes, ones that may not be visually perceptible to a pathologist, to the nucleus and its ultrastructural components ...

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.

Proceedings of the National Academy of Sciences of the United States of America
Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell type. Here, we show that this chromatin architecture can be predicted de novo using epigenetic data derived from chromatin immunoprecipitation-sequencing ...