NucPosDB

NucPosDB curates nucleosome positioning and cell-free DNA (cfDNA) datasets to support studies of gene regulation, nucleosome dynamics, and cfDNA-based clinical diagnostics.

Key Features:

• Extensive dataset curation: Curates ~400 publications on nucleosome positioning across cell lines and in situ conditions, including MNase-seq datasets and cfDNA data from over 10,000 patients and healthy volunteers.
• Nucleosomics and cfDNA biology: Supports nucleosomics analysis by leveraging that apoptotic nucleases preferentially cut DNA between nucleosomes, so short cfDNA fragments reflect original nucleosome positions.
• Stable nucleosome occupancy regions: Contains regions with stable nucleosome occupancy across individuals under various conditions.
• Computational tools and predictive algorithms: Includes a catalogue of computational tools for analyzing nucleosome positioning and cfDNA experiments and theoretical algorithms that predict nucleosome positioning preferences from DNA sequence.
• Research and diagnostic datasets: Provides comprehensive datasets to study gene regulatory processes, explore variability across medical conditions, and train computational models for cfDNA-based patient diagnostics.

Scientific Applications:

• Liquid biopsy nucleosomics: Enables analysis of cfDNA fragment patterns to infer nucleosome positioning for liquid biopsy research and diagnostics.
• Gene regulation and epigenetics: Supports investigations into nucleosome organization and its role in transcriptional regulation and chromatin structure.
• Computational model development: Supplies datasets and algorithmic resources for training and benchmarking models that predict nucleosome positioning and diagnose patients from cfDNA.
• Comparative studies of nucleosome dynamics: Facilitates comparison of nucleosome positioning and cfDNA fragmentomic variability across health and disease states.

Methodology:

Provides a catalogue of computational tools for nucleosome positioning and cfDNA analysis and theoretical algorithms that predict nucleosome positioning preferences from DNA sequence.