BACKGROUND: The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERα) for proliferation, but little is known about its transcriptional regulation in these tumors.
We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genome...
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
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Drawing inspiration from convolutional neural networks, graph convolutional networks (GCNs) have been implemented in various applications. Yet, the integration of GCNs into clinical settings, particularly in the context of complex health conditions l...
MOTIVATION: For more than 25 years, learning-based eukaryotic gene predictors were driven by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently, Holst et al. demonstrated with their program Helixer that the accuracy of...
BACKGROUND: Disease Ontology (DO) has been widely studied in biomedical research and clinical practice to describe the roles of genes. DO enrichment analysis is an effective means to discover associations between genes and diseases. Compared to hundr...
Sequence-based deep learning models have emerged as powerful tools for deciphering the cis-regulatory grammar of the human genome but cannot generalize to unobserved cellular contexts. Here, we present EpiBERT, a multi-modal transformer that learns g...
The Homo sapiens Chromosomal Location Ontology (HSCLO) is designed to facilitate the integration of human genomic features into biomedical knowledge graphs from releases GRCh37 and GRCh38 at multiple resolutions. HSCLO comprises two distinct versions...
A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this g...
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range of human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here,...
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...