Open Access Teaching

I make the material for all classes I teach available on github. These are released under the unrestrictive unlicense, which allows end users to use the teaching material however they wish.

Chalkboard biochemistry lectures

These are a set of 10-15 minute videos that aim to hit some of the core concepts in biochemistry. These videos aim to develop intuition and focus on big ideas rather than details. They are designed to complement, not replace, a standard lecture and reading material for each topic.

Biochem and cellular physiology (B281H)

Material

Course objectives

  • Survey the key molecular and cellular features shared by all organisms on earth, revealing how life can be understood in physical and chemical terms.
  • Begin to develop intuition and analytical tools to think about life quantitatively and molecularly.
  • Introduce several key, universal systems that are shared across organisms:
    • Serine protease
    • Hemoglobin
    • Glycolysis/gluconeogenesis
    • Citric Acid Cycle
    • Electron transport chain
    • ATP synthase

Scientific programming (CH410/510)

Material

Conceptual Goals

By the end of the course, students should understand:

  • Basic python: data types, key words, control, functions and imports
  • Core python extensions for scientists: scipy, numpy, and jupyter
  • Strategies for dissecting problems and formulating solutions in code
  • Where to go to pick up skills in the future as the need arises

Skill Goals

By the end of the course, students should be able to:

  • Write basic python programs from scratch

  • Identify existing libraries for a problem and learn how to use them

  • Generate arbitrarily complex custom plots

  • Simulate experimental sampling

  • Manipulate scientific datasets of the following types (at a basic level):

  • High-throughput sequencing data

  • Chemical structure data from databases such as the PDB

Advanced Biochemistry (CH662)

Material

Course objectives

  • Prepare PhD students to do research in molecular biology by helping them think molecularly and by introducing tools to study binding interactions.
  • This will be achieved by:
    • Introducing students to controlling conceptual frameworks in biochemistry, with an emphasis on quantitative reasoning.
    • Introducing methods used to study biomolecular properties and function, with an emphasis on binding interactions.
  • By the end of this course:
    • Understand the difference between microscopic and macroscopic phenomena and know the conceptual tools used by biochemists to link the two scales.
    • Be able to employ simple mathematical models to describe both the thermodynamics and kinetics of biomolecluar interactions.
    • Reason about the effects of mutations on molecular structure.
    • Have a working understanding of a collection of methods used to probe molecular mechanisms, with an emphasis on those used for binding interactions.