Understanding principles of biochemical genetics with computational biology
Apply advanced biochemistry and bioinformatics techniques to solve problems in drug discovery and genomic integrity research through virtual pipelines.
Aayudh Das
DREAM Venture Labs
Fridays at 5:00 P.M. ET / 2:00 P.M. PT
8 weeks, 2-3 hours per weekDescription
This Build Project provides undergraduate students with a comprehensive, hands-on experience in translational biochemistry and computational biology, focusing on real-world applications in drug discovery and genomic integrity. You will engage in designing and analyzing CRISPR-Cas9 knockout screens using next-generation sequencing (NGS), develop virtual pipelines for structural variant detection using Optical Genome Mapping (OGM), and perform protein abundance analysis from LC-MS data using R. Through guided supervision, you will gain practical experience with industry-standard tools and databases such as dbVAR, and ClinVar, while also learning to synthesize their findings into professional scientific reports. The project bridges fundamental biochemical principles with bioinformatics and emerging genomic technologies to prepare students for careers in biotechnology and biomedical research.
Application timeline
What you will learn
- Design and implement CRISPR knockout screening pipelines using next-generation sequencing (NGS) data and tools such as BWA, Samtools, and CRISPResso.
- Analyze structural variants using Optical Genome Mapping (OGM) and interpret findings with reference databases like dbVAR, ClinVar, and gnomAD.
- Quantify protein abundance using LC-MS data and perform statistical analysis in R, including visualization with heatmaps and volcano plots.
- Translate genomic and proteomic data into biologically meaningful insights relevant to drug discovery, particularly in identifying oncogenes and therapeutic targets.
- Develop publication-quality reports and visualizations that effectively communicate research findings to scientific and industry audiences.
Project workshops
Prerequisites
- A solid understanding of DNA structure and function, including how mutations such as insertions, deletions, and structural variants affect gene expression and protein function.
- Familiarity with the central dogma of molecular biology (DNA > RNA > Protein), and how CRISPR-Cas9 edits the genome by inducing double-strand breaks followed by DNA repair mechanisms like NHEJ and HDR.
- Basic experience with data analysis tools such as Excel or R, especially for generating plots and interpreting trends from tabular datasets (e.g., variant counts or protein abundances).
- The ability to interpret scientific figures (e.g., heatmaps, volcano plots, gene models) and translate data into concise written conclusions.
- Willingness to explore new bioinformatics tools and databases (such as COSMIC, gnomAD, and ClinVar) with guided instruction and troubleshooting support.
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About the Fellow
Aayudh Das
DREAM Venture Labs
Visit Aayudh's LinkedInAayudh Das is a Biochemistry Build Fellow at Dream Venture Labs, where he works with students leading projects in biochemistry and genomics. Aayudh is a Senior Scientist, Research & Development at Garuda Therapeutics, where he focuses on qualification and validation of amplicon sequencing (NGS)-based onco-panel pipelines to detect oncogenic variants in drug products. His work includes building pipelines for variant calling (Strelka2 and GATK4) with WGS to uncover oncogenes in human iPSCs, and validating CRISPR knockouts while identifying off-target effects using NGS-based targeted sequencing. He also develops pipelines for single-cell sequencing (scRNA) analysis to study hematopoietic stem cell expressions and manages computational biology teams while mentoring research associates and interns. With 10 years of experience in biochemistry, genomics, and computational biology, Aayudh holds an M.S. in Biochemistry and a Ph.D. in Biology (Genomics and Evolution). A fun fact about Aayudh: He always thought he'd be a stand-up comedian so naturally, he ended up in academia and then in industry.