AIMC Topic: Epigenomics

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TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data.

Nature communications
It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of diseases. The use of large-scale mult...

Pathogenomic fingerprinting to identify associations between tumor morphology and epigenetic states.

European journal of cancer (Oxford, England : 1990)
INTRODUCTION: Measuring the chromatin state of a tumor provides a powerful map of its epigenetic commitments; however, as these are generally bulk measurements, it has not yet been possible to connect changes in chromatin accessibility to the patholo...

Genome-wide methylome modeling via generative AI incorporating long- and short-range interactions.

Science advances
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...

Integration of epigenomic and genomic data to predict residual feed intake and the feed conversion ratio in dairy sheep via machine learning algorithms.

BMC genomics
BACKGROUND: Feed efficiency (FE) is an essential trait in livestock species because of the constant demand to increase the productivity and sustainability of livestock production systems. A better understanding of the biological mechanisms associated...

Spatial recognition and semi-quantification of epigenetic events in pancreatic cancer subtypes with multiplexed molecular imaging and machine learning.

Scientific reports
Genomic alterations are the driving force behind pancreatic cancer (PC) tumorigenesis, but they do not fully account for its diverse phenotypes. Investigating the epigenetic landscapes of PC offers a more comprehensive understanding and could identif...

Identification of 17 novel epigenetic biomarkers associated with anxiety disorders using differential methylation analysis followed by machine learning-based validation.

Clinical epigenetics
BACKGROUND: The changes in DNA methylation patterns may reflect both physical and mental well-being, the latter being a relatively unexplored avenue in terms of clinical utility for psychiatric disorders. In this study, our objective was to identify ...

Interpretable deep learning of single-cell and epigenetic data reveals novel molecular insights in aging.

Scientific reports
Deep learning (DL) and explainable artificial intelligence (XAI) have emerged as powerful machine-learning tools to identify complex predictive data patterns in a spatial or temporal domain. Here, we consider the application of DL and XAI to large om...

Epigenetic profiling for prognostic stratification and personalized therapy in breast cancer.

Frontiers in immunology
BACKGROUND: The rising incidence of breast cancer and its heterogeneity necessitate precise tools for predicting patient prognosis and tailoring personalized treatments. Epigenetic changes play a critical role in breast cancer progression and therapy...

EpiBrCan-Lite: A lightweight deep learning model for breast cancer subtype classification using epigenomic data.

Computer methods and programs in biomedicine
BACKGROUND AND OBJECTIVES: Early breast cancer subtypes classification improves the survival rate as it facilitates prognosis of the patient. In literature this problem was prominently solved by various Machine Learning and Deep Learning techniques. ...