Nucleome Data Bank

Nucleome Data Bank simulates and analyzes the three-dimensional organization and dynamics of genomes to link epigenetic information with experimental Hi-C and FISH observations.

Key Features:

• Simulation Pipeline: Performs physics-based simulations of chromosomal structural dynamics using the MEGABASE + MiChroM computational pipeline with epigenetic inputs from the ENCODE database to reproduce Hi-C and FISH observations.
• Chromosomal Sub-compartment Annotation: Generates chromosomal sub-compartment annotations directly from epigenetic inputs without relying on DNA-DNA proximity ligation data.
• Structural Genomics Data Hosting: Hosts experimental and computational structural genomics datasets and simulated genome structures for analysis.
• Visualization of Genomic Features: Overlays one-dimensional genetic and epigenetic data onto three-dimensional chromosomal structures to analyze spatial distributions of genomic features.

Scientific Applications:

• Genome Structure Analysis: Simulating 3D genome architecture to elucidate the physical organization and functional implications of genomic elements.
• Epigenetics Research: Integrating epigenetic markers with structural simulations to study how epigenetic modifications influence chromosomal dynamics and genome function.
• Integrative Genomics: Combining experimental Hi-C and FISH datasets with epigenetic data and simulations to enable comprehensive analyses of genetic and epigenetic interactions in three-dimensional genome context.

Methodology:

Physics-based simulations using the MEGABASE + MiChroM pipeline with epigenetic inputs from the ENCODE database, simulation of chromosomal trajectories to reproduce Hi-C and FISH observations, and derivation of chromosomal sub-compartment annotations from epigenetic inputs without DNA-DNA proximity ligation data.