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Named a top 50 MOOC of all time by Class Central! This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat. In the first half of the course, we investigate DNA replication, and ask the question, where in the genome does DNA replication begin? We will see that we can answer this question for many bacteria using only some straightforward algorithms to look for hidden messages in the genome. In the second half of the course, we examine a different biological question, when we ask which DNA patterns play the role of molecular clocks. The cells in your body manage to maintain a circadian rhythm, but how is this achieved on the level of DNA? Once again, we will see that by knowing which hidden messages to look for, we can start to understand the amazingly complex language of DNA. Perhaps surprisingly, we will apply randomized algorithms, which roll dice and flip coins in order to solve problems. Finally, you will get your hands dirty and apply existing software tools to find recurring biological motifs within genes that are responsible for helping Mycobacterium tuberculosis go "dormant" within a host for many years before causing an active infection.
Syllabus
- Week 1 - Week 1: Welcome!
Welcome to class!
This course will focus on two questions at the forefront of modern computational biology, along with the algorithmic approaches we will use to solve them in parentheses:
- Weeks 1-2: Where in the Genome Does DNA Replication ...
- Week 2 - Week 2: Finding Replication Origins
Welcome to Week 2 of class!
This week, we will examine the biological details of how DNA replication is carried out in the cell. We will then see how to use these details to help us design an intelligent algorithmic approach looking for the replica...
- Week 3 - Week 3: Hunting for Regulatory Motifs
Welcome to Week 3 of class!
This week, we begin a new chapter, titled "Which DNA Patterns Play the Role of Molecular Clocks?" At the bottom of this message is this week's Bioinformatics Cartoon. What does a late night casino trip with two 18th...
- Week 4 - Week 4: How Rolling Dice Helps Us Find Regulatory Motifs
Welcome to Week 4 of class!
Last week, we encountered a few introductory motif-finding algorithms. This week, we will see how to improve upon these motif-finding approaches by designing randomized algorithms that can "roll dice" to find motifs.
- Week 5 - Week 5: Bioinformatics Application Challenge
Welcome to week 5 of the class! This week, we will apply popular motif-finding software in order to hunt for motifs in a real biological dataset.
Instructors
Pavel Pevzner
Professor
Department of Computer Science and Engineering
Phillip Compeau
Visiting Researcher
Department of Computer Science & Engineering
Content Designer
The University of California, San Diego is a public land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the southernmost of the University of California's ten campuses and offers more than 200 undergraduate and graduate degree programs, enrolling 33,096 undergraduate students and 9,872 graduate students.
UC San Diego is considered one of the best universities in the world. Several publications have ranked UC San Diego's Departments of Biological Sciences and Computer Science among the top 10 in the world.
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