Schedule & Readings
Stanford Introduction to Bioengineering
Stanford Introduction to Bioengineering
2026 Spring Quarter
CLASS MEETINGS
Monday, Wednesday, & Friday
Time 1:30-2:20pm, CODA B60
STUDENT HOURS
Come chat with us! This is time set aside by the instructors and TAs to work with you. Use it for help on assignments or to ask any questions about bioengineering or anything at all!
Times (March 30-June 4, excluding holidays):
Mon. 5-6pm
Tue. 5-6pm
Wed. 4-5pm
Thur. 5-6pm
Locations: link (available to enrolled students)
The entire teaching team stands with you, ready and eager to help you learn. Should you need assistance outside of regular student hours, please post a message in Ed Discussion.
SPRING 2026 CLASS SESSION TOPICS SCHEDULE AND PRE-READING ASSIGNMENTS
WEEKS 1 & 2 -- Protein Engineering
30 March - Why engineer biology? Introduction to Syllabus and Course Logistics [lecture slides]
Pre-reading and videos: none
1 April - What are proteins? [lecture slides]
Pre-reading and videos:
What makes living matter special (15 min. video)
What is a protein? (7 min. video)
The Shape and Structure of Proteins (top through Figure 3-16, 25 min. read)
3 April - How does a protein primary sequence impact what a protein does? [lecture slides]
Pre-reading and videos:
How Enzymes Work (5 min. video)
Protein binding interfaces, Binding sites of antibodies (5 min. read)
CRISPR Technology; sections Cas9: From nature to the lab, Cas9 structure-function (10 min. read)
6 April - How do we define, quantify, and measure what proteins do?
Pre-reading and videos: [lecture slides]
Dissociation constant (Kd) and Michaelis-Menten constant (Km) for characterizing binders and enzymes (SLO 4 section, 15 min. read)
How to measure protein-ligand binding (videos explaining the most commonly used techniques)
Surface Plasmon Resonance (2 min.)
Biolayer Interferometry (2 min.)
8 April - How to change what a protein does?
Pre-reading and videos: [lecture slides]
Introduction to Protein Design presented by David Baker (video, 21 min.)
AlphaFold - The Most Useful Thing AI Has Ever Done (video, 24 min.)
10 April - Project Introduction and Framestorming with Proteins
Pre-reading and videos: [lecture slides]
5 challenges we could solve by designing new proteins (David Baker, 10 min. TED video)
Framestorming (5 min. read)
WEEK 3 -- Molecular Devices to Systems Design
13 April - Living logic [lecture slides]
Pre-reading and videos:
George Boole’s Laws of Thought excerpt (Section 11 through end of Section 13, 15 min. read)
Taking Faster and Smarter to New Physical Frontiers (5 min. read)
Essential Genetic Elements Primer for engineering gene expression in bacteria (15 min. read)
Transcriptors & Boolean Integrase Logic (BIL) gates, explained (10 min. video)
15 April - Bioengineering Abstraction: Biomolecules as Devices
Pre-reading and videos: [lecture slides]
Understanding Logic Gates (7 min. video)
Fundamentals of Biodesign (Chapter 2 from BioBuilder, 40 min. read)
17 April - Quantitative Device Modeling
Pre-reading and videos: [lecture slides]
Ordinary differential equation models (5 min. read)
Introduction to biological circuit design (40 min. read)
WEEK 4 -- Physical Devices: Measuring Tools
20 April - Tools for Measuring -- Microscopy [lecture slides]
Pre-reading and videos:
Fluorescent Proteins 101: Green Fluorescent Protein (10 min. read)
Microscopy: What Can You Learn With a Light Microscope (20 min. video)
Self-driving microscopes (video on Prakash lab's Octopi and Global Health impact; 3 min. video)
22 April - Microscopy Field Day [lecture slides]
Pre-reading and videos:
Foldscope: Origami Based Paper Microscopes (note that we will fold a newer version of Foldscope, 15 min. video)
The Foldscope: A Paper Microscope that Costs $1 (3 min. video with inspiring dynamic samples)
Foldscope: Origami-Based Paper Microscope (read the "Introduction" and "Discussion and Conclusions" sections, 15 min. read)
24 April - Mighty Microbiome [lecture slides]
Pre-reading and videos:
What is a microbiome? (3 min. video)
Transforming Immunization: Michael Fischbach's Commensal Bacteria Vaccines (10 min. read)
Why nurturing the gut microbiota could resolve depression and anxiety (15 min. read)
WEEK 5 -- DNA Writing and Reading
27 April - Writing DNA [lecture slides]
Pre-reading and videos:
(1) The Chemical Synthesis of DNA/RNA: Our Gift to Science [instructions — skim the history; pay particular attention to figure 4, 20 min. read]
(2) DNA synthesis technologies to close the gene writing gap [instructions — skim text; pay particular attention to figure 2; STOP before "Technologies for DNA of unlimited length” section, 20 min. read]
29 April - Gene and Genome Assembly [lecture slides]
Pre-reading and videos:
(1a) Complete Synthesis of Gene Reported [instructions — read entire NYT article, 5 min. read]
(1b) Total Synthesis of a Gene [instructions — ponder figure 4 and figure 10, 5 min. interpretation]
(2a ) DNA synthesis technologies to close the gene writing gap [instructions — START at "Technologies for DNA of unlimited length” and study Figure 4, 25 min. read]
(2b) Gibson Assembly® - Building a Synthetic Biology Toolset [instructions — study figure 1 as needed and watch the video, 5 min. interpretation and viewing]
(3) Synthetic chromosomes, genomes, viruses, and cells [instructions — skim to the extent you find interesting, ~10 min.]
(4) Invention of DNA "Page Numbers" Opens Up Vast Possibilities for the Bioeconomy [instructions — read entire Caltech press release but not the primary research article so-referenced, 10 min. read]
1 May - Reading DNA [lecture slides]
Pre-reading and videos:
A Visual Guide to DNA Sequencing, (35 min. read)
WEEK 6 -- DNA Editing and Gene Drives
4 May - Fighting Chip Shortages with Biology [lecture slides]
Pre-reading and videos:
(1) The chip shortage keeps getting worse. Why can’t we just make more? [read, but focus on the graphics and captions; don't linger on the prose sidebars. ~12 min.] (link with full access via stanford.edu account, or PDF version here with Stanford account)
(2) Using nature to grow batteries [instructions — watch. ~15 min.]
(3) Folding DNA to create nanoscale shapes and patterns [instructions — read title and abstract; study Figures 1, 2, and 3. Same as before, but "study" means read the caption and understand what you're looking at — not memorize. ~12 min.]
(4) Roadmap on biological pathways for electronic nanofabrication and materials [instructions — read Section 1. Introduction carefully; read Section 3. Biomolecular nanopatterning...) carefully; skim the remaining main sections by reading only the first paragraph of each and looking at the figures; read Section 6. Conclusions. ~14 min.]
6 May - Editing DNA [lecture slides]
Pre-reading and videos:
CRISPR: Gene editing and beyond (4 min. video)
Interview with Stanley Qi (20 min. read)
8 May - Fighting Screwworms w/ Gene Drives [lecture slides]
Pre-reading and videos:
(1) Setting the scene! [instructions — read entire article. ~8 minutes] (PDF here with Stanford account)
(2) Current State of Emergency! [instructions — read entire article AND read the letter from Congressman Vasquez to Secretary Rollins. ~8 minutes]
(3) How we beat screwworm before! [instructions — read entire article. ~7 minutes]
(4) The new toolkit! [instructions — read and study up to Figure 1 then STOP. ~15 minutes]
(5) Science and civil society! [instructions — read entire article. ~8 minutes]
WEEK 7 -- Directed Evolution and Generative Biology [lecture slides]
11 May - Directed Evolution
Pre-reading and videos:
[optional but recommended reading, participation points for Mon. class period will not be a typical pre-reading/video quiz] Directed evolution of enzymes and binding proteins (Nobel Prize in Chemistry 2018)
13 May - Generative Biology [lecture slides]
Pre-reading and videos:
BindCraft -- open source protein binder design (5 min. read)
Building Evo 2: A Frontier DNA Language Model (5 min. video)
15 May - Evolution and AI for bioengineering, continued [lecture slides]
(no additional readings or videos, in-class activity/quiz on lecture concepts presented in class during the week)
WEEK 8 -- Engineering for Human and Planet Health
18 May - Fighting Fear w/ Glowing Plants
Pre-reading and videos (< 30min. for all readings together):
[introduction and summary] https://www.scientificamerican.com/article/how-does-a-bioluminescent-petunia-glow/
[going to market] https://www.nature.com/articles/d41586-024-00383-3
[FAQs] https://light.bio/pages/faqs
[Sacred plants?] https://en.wikipedia.org/wiki/Sanjivani_(Hinduism)
20 May - Fighting Cancer w/ CAR-T Cells
Pre-reading and videos:
CAR T-cell therapy explained: Manufacturing process and how it works (3 min. video)
CAR T Cells: Engineering Patients’ Immune Cells to Treat Their Cancers (20 min. read)
Early CAR T trial story (4 min. video)
22 May - Fighting Medicine Shortages w/ Brewing, special guest Dr. Christina Smolke, Founder and CEO Antheia Therapeutics
Pre-reading and videos: (as you complete these readings, come up with a question to ask Dr. Smolke in the class session)
1. The problem (3 min); ASHP Drug Shortages Statistics; https://www.ashp.org/drug-shortages/shortage-resources/drug-shortages-statistics [parse live dashboard; understand what is going on]
2. The science & the scientist (8 min); "A Conversation with Christina Smolke.” ACS Central Science, 2016. https://pubs.acs.org/doi/10.1021/acscentsci.6b00029 [read]
3. The homebrew preprint (5 min); "Complete absence of thebaine biosynthesis under home-brew fermentation conditions.” bioRxiv, August 2015. https://doi.org/10.1101/024299 [read]
4. The company origin (7 min); "Can This Silicon Valley Startup Bioengineer a Less Addictive Opioid?” https://www.fastcompany.com/3066129/can-antheias-opioid-producing-yeast-one-day-challenge-big-pharma [read]
5. Commercial reality, this year (3 min); "Antheia Raises Additional $24 Million to Complete Series C Financing, Bringing Total Funds Raised to More than $175 Million Over Past Year" https://antheia.bio/antheia-raises-additional-24-million-to-complete-series-c-financing-bringing-total-funds-raised-to-more-than-175-million-over-past-year/ [read]
WEEK 9 -- Bioengineering Beyond the Bench
25 May - no class - Memorial Day
27 May - Biosecurity
Pre-reading and videos:
1. "Biotechnology Research in an Age of Terrorism” (aka the "Fink Report”) (20 minutes); US National Academies, 2004; https://www.nationalacademies.org/read/10827/chapter/2 [READ executive summary only]
2. "AI just created a working virus. The U.S. isn't prepared for that.” (5 minutes); Washington Post, September 25, 2025. https://www.washingtonpost.com/opinions/2025/09/25/artificial-intelligence-advance-virus-created/ [READ entirely]
3. "Biosecurity Really: A Strategy for Victory.” (25 minutes) Hoover Institution, October 2025. https://www.hoover.org/sites/default/files/research/docs/Moront_BiosecurityReally_web-251007.pdf [READ: Preface, Chapter 1, and Chapter 5]
29 May - Bioculture: Can Hip-hop save Bioengineering?
Pre-reading and videos:
1. Stewart Brand (Stanford ’60) on Pace Layering https://longnow.org/ideas/pace-layers/ [read all, ~10 min]
2. Kraftwerk and the roots of computing culture https://consequence.net/2021/05/kraftwerk-computer-world-40-anniversary-essay/ [read all, ~10 min]
3. Nobel Laureates Letter Supporting GMOs (2016) https://www.supportprecisionagriculture.org/nobel-laureate-gmo-letter_rjr.html [read all, ~5 min]
4. Agapakis & Tolaas, "Selfmade” https://www.smithsonianmag.com/science-nature/cheese-made-from-bacteria-between-toes-and-other-bizarre-bio-art-180949486/ [read all, ~10 min]
5. Donna Haraway & Drew Endy, "Tools for Multispecies Futures” Journal of Design and Science (JoDS), MIT Press
https://jods.mitpress.mit.edu/pub/issue4-haraway-endy [read all, ~20 min]
WEEK 10 -- Bioengineering Beyond the Bench and Wrapup
1 June - Bio-what-else-now?!
3 June - Reflection & Lookahead