AIMC Topic: Genome, Human
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Deep learning deciphers the related role of master regulators and G-quadruplexes in tissue specification.
Scientific reports
Jul 2, 2025
G-quadruplexes (GQs) are non-canonical DNA structures encoded by G-flipons with potential roles in gene regulation and chromatin structure. Here, we explore the role of G-flipons in tissue specification. We present a deep learning-based framework for...
Genome-wide methylome modeling via generative AI incorporating long- and short-range interactions.
Science advances
Apr 11, 2025
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...
SVLearn: a dual-reference machine learning approach enables accurate cross-species genotyping of structural variants.
Nature communications
Mar 11, 2025
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,...
A compendium of human gene functions derived from evolutionary modelling.
Nature
Feb 26, 2025
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...
A multi-modal transformer for cell type-agnostic regulatory predictions.
Cell genomics
Jan 29, 2025
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...
Homo Sapiens Chromosomal Location Ontology: A Framework for Genomic Data in Biomedical Knowledge Graphs.
Scientific data
Jan 11, 2025
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...
Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies.
American journal of human genetics
Sep 12, 2024
Large-scale, multi-ethnic whole-genome sequencing (WGS) studies, such as the National Human Genome Research Institute Genome Sequencing Program's Centers for Common Disease Genomics (CCDG), play an important role in increasing diversity for genetic r...
Deep Learning Sequence Models for Transcriptional Regulation.
Annual review of genomics and human genetics
Aug 6, 2024
Deciphering the regulatory code of gene expression and interpreting the transcriptional effects of genome variation are critical challenges in human genetics. Modern experimental technologies have resulted in an abundance of data, enabling the develo...
Genome analysis through image processing with deep learning models.
Journal of human genetics
Jul 31, 2024
Genomic sequences are traditionally represented as strings of characters: A (adenine), C (cytosine), G (guanine), and T (thymine). However, an alternative approach involves depicting sequence-related information through image representations, such as...
INDELpred: Improving the prediction and interpretation of indel pathogenicity within the clinical genome.
HGG advances
Jul 10, 2024
Small insertions and deletions (indels) are critical yet challenging genetic variations with significant clinical implications. However, the identification of pathogenic indels from neutral variants in clinical contexts remains an understudied proble...
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