Computational methods for analysing multiscale 3D genome organization
Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …
characterization of the spatial organization and folding of the genome in the nucleus. In …
Explainable artificial intelligence for omics data: a systematic mapping study
Researchers increasingly turn to explainable artificial intelligence (XAI) to analyze omics
data and gain insights into the underlying biological processes. Yet, given the …
data and gain insights into the underlying biological processes. Yet, given the …
[HTML][HTML] Topology regulatory elements: From shaping genome architecture to gene regulation
The importance of 3D genome topology in the control of gene expression is becoming
increasingly apparent, while regulatory mechanisms remain incompletely understood …
increasingly apparent, while regulatory mechanisms remain incompletely understood …
Knowledge-augmented Graph Machine Learning for Drug Discovery: From Precision to Interpretability
Conventional Artificial Intelligence models are heavily limited in handling complex
biomedical structures (such as 2D or 3D protein and molecule structures) and providing …
biomedical structures (such as 2D or 3D protein and molecule structures) and providing …
In silico discovery of repetitive elements as key sequence determinants of 3D genome folding
Natural and experimental genetic variants can modify DNA loops and insulating boundaries
to tune transcription, but it is unknown how sequence perturbations affect chromatin …
to tune transcription, but it is unknown how sequence perturbations affect chromatin …
Best practices for interpretable machine learning in computational biology
Advances in machine learning (ML) have enabled the development of next-generation
prediction models for complex computational biology problems. These developments have …
prediction models for complex computational biology problems. These developments have …
A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains
J Xu, X Xu, D Huang, Y Luo, L Lin, X Bai… - Nature …, 2024 - nature.com
Topologically associating domains (TADs), megabase-scale features of chromatin spatial
architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the …
architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the …
UNADON: transformer-based model to predict genome-wide chromosome spatial position
Motivation The spatial positioning of chromosomes relative to functional nuclear bodies is
intertwined with genome functions such as transcription. However, the sequence patterns …
intertwined with genome functions such as transcription. However, the sequence patterns …
Artificial Intelligence in Plastic Surgery: Advancements, Applications, and Future
Artificial intelligence (AI) is revolutionizing plastic surgery through its remarkable
advancements in various domains such as image analysis, robotic assistance, predictive …
advancements in various domains such as image analysis, robotic assistance, predictive …
Toward understanding the role of genomic repeat elements in neurodegenerative diseases
Z An, A Jiang, J Chen - Neural Regeneration Research, 2025 - journals.lww.com
Neurodegenerative diseases cause great medical and economic burdens for both patients
and society; however, the complex molecular mechanisms thereof are not yet well …
and society; however, the complex molecular mechanisms thereof are not yet well …