TOBIAS

TOBIAS performs genome-wide footprinting analysis of transcription factor (TF) binding dynamics using ATAC-seq data.

Key Features:

• ATAC-seq footprinting: Detects regions of open chromatin and infers TF binding sites from ATAC-seq signal.
• Genome-wide analysis: Performs detailed footprinting across the entire genome to investigate TF dynamics at multiple levels.
• High-throughput TF profiling: Analyzes binding kinetics for hundreds of transcription factors concurrently while maintaining speed and accuracy.
• Algorithmic optimization: Integrates computational algorithms optimized for high accuracy and processing of large datasets.
• Zygotic Genome Activation (ZGA) analysis: Applied to study TF dynamics during ZGA in human and mouse, including Dux-driven TF cascades, interactions with repeat elements, and induction of novel genetic elements.

Scientific Applications:

• Transcriptional regulation studies: Dissects TF binding kinetics and regulatory networks governing gene expression.
• Zygotic genome activation research: Characterizes TF dynamics and cascades during early developmental stages in human and mouse.
• Repeat element and novel element analysis: Investigates TF interactions with repeat elements and the activation of novel genetic elements.

Methodology:

Performs ATAC-seq-based footprinting to identify open chromatin regions and likely TF binding sites, using computational algorithms optimized for accuracy and speed to process large datasets.