Genomics & Bioengineering
New measurement tools reveal individual cells, human cell atlases, molecular traces in blood, immune clones, and microbial ecosystems. A video-first introduction to genomics and bioengineering.
2 modules · 6 lessons · 0.7h · mastery threshold 80
Watch videos free — no sign-inBackground for Research in the Stephen Quake Lab This independent educational primer introduces scientific concepts relevant to research themes in the Stephen Quake Lab at Stanford University. It is not an official Stanford University or Stephen Quake Lab course and does not imply endorsement or affiliation. For ambitious high-school students and early undergraduates with high-school biology and DNA/RNA/protein basics; probability is helpful. Approximately 40–45 minutes including six video-first lessons and assessments. Mastery-only certificate eligibility at 80%, without a capstone or Research Defense.
Module 1
Microfluidics, single-cell transcriptomes, and human reference atlases.
Module 2
Cell-free nucleic acids, immune repertoires, and microbial ecology.
Cell-free DNA and liquid biopsy
Interpret fragmented extracellular DNA as a molecular mixture.
Cell-free RNA and tissue-of-origin inference
Explain why cfRNA can carry expression information but source inference needs assumptions.
Genome versus transcriptome and bulk versus single-cell measurement
Distinguish genome, transcriptome and bulk versus single-cell information.
Human cell atlases and reference transcriptomes
Use cell-atlas reference profiles while accounting for sampling and capture bias.
Immune repertoire sequencing and clonal dynamics
Interpret immune clone counts without inferring antigen or complete tissue coverage.
Measurement technology, scale, and microfluidics
Explain how microfluidic scale, isolation and valves change what can be measured.
Metagenomics and quantitative microbial ecology
Separate microbial DNA detection from viability, infection and causal ecology.
Molecular counting in prenatal and transplant monitoring
Relate counting noise, placental DNA and donor DNA to scoped screening and monitoring principles.
Reference atlases, mixture models, and deconvolution
Describe reference-based mixture deconvolution, validation and identifiability limits.
Single-cell RNA sequencing, cell types, and cell states
Interpret RNA matrices, cell types and states without equating clusters with biological identities.
Single-molecule measurement and measurement-driven discovery
Distinguish individual-molecule measurements from averages and sole-invention claims.
Tabula Sapiens and cross-tissue cellular diversity
Explain the consortium atlas and cross-tissue diversity within its donor and tissue scope.