A cost-free CURE: using bioinformatics to identify DNA-binding factors at a specific genomic locus

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Undergraduate research experiences (CUREs) offer significant benefits but can face implementation barriers.
• Bioinformatics research presents an accessible, cost-effective, and remote-friendly alternative for CUREs.
• This approach can enhance accessibility for students with disabilities.

Purpose of the Study:

• To describe a novel bioinformatics CURE utilizing publicly available datasets.
• To enable students to discover novel proteins targeting specific genomic loci.
• To provide a flexible and scalable research experience for undergraduates.

Main Methods:

• Leveraging the Galaxy platform for bioinformatics analysis of ChIP-seq datasets.
• Utilizing publicly available genomic and protein datasets.
• Mapping ChIP-seq data to a user-defined genomic locus.

Main Results:

• Students successfully utilized bioinformatics tools to identify potential novel proteins.
• The CURE facilitated the acquisition of basic bioinformatics knowledge and transferable skills.
• Faculty benefited from candidate screening and potential publication of CURE-derived results.

Conclusions:

• This bioinformatics CURE is a viable, accessible, and flexible model for undergraduate research.
• It equips students with essential bioinformatics and scientific communication skills.
• The CURE can be adapted for various high-throughput data types and genomic investigations across species.