Representations and Algorithms for Computational Molecular Biology


Stanford School of Medicine



The explosion of molecular data continues to fuel academic and industry interest in biomedical informatics. This is an exciting time in bioinformatics, and there is great potential for harnessing information produced by genome sequencing projects for medical diagnostic and therapeutic uses.

This course provides an introduction to computing with DNA, RNA, proteins and small molecules. Learn how to program both basic and advanced algorithms for sequence analysis, 3D structure analysis and high-throughput functional data analysis. Receive hands-on experience with the algorithms used in the field.

Note on Course Availability

This course is typically offered Autumn quarter.

The course schedule is displayed for planning purposes – courses can be modified, changed, or cancelled. Course availability will be considered finalized on the first day of open enrollment. For quarterly enrollment dates, please refer to our graduate certificate homepage.

What you will learn

  • Computing with strings
  • Phylogenetic tree construction and hidden Markov models
  • Protein structural computations, structure prediction and threading techniques
  • Molecular dynamics and energy minimization
  • Statistical analysis of 3D biological data and integration of data sources
  • Machine learning (clustering and classification)
  • Natural language text processing


CS106B; CS161 is recommended.


Non-Degree Option students are required to enroll for 4 units.
3 unit enrollment is only allowed with instructor approval.

014 Autumn 2020-21 Online

Not Yet Available

Dates:September 14 - November 20, 2020
Units: 3.00-4.00
Instructors: Russ Altman
Delivery Option:
For Credit $4,056.00-$5,408.00

Pre-registration Dates: August 10 to September 4, 2020

Pre-registration for this course will secure your enrollment request and ensure timely processing of your application for potential course approval. Please note: course enrollment will be confirmed after September 1, 2020; after completing your pre-registration, no further action is required on your part.


This course may not currently be available to learners in some states and territories.