About this course: 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.
Who is this class for: This course is primarily aimed at undergraduate-level learners in computer science, biology, or a related field who are interested in learning about how the intersection of these two disciplines represents an important frontier in modern science.
Created by:Â Â University of California San Diego
Taught by:Â Â Pavel Pevzner, Professor
Department of Computer Science and Engineering
Taught by:Â Â Phillip Compeau, Visiting Researcher
Department of Computer Science & Engineering
| Basic Info | Course 1 of 7 in the Bioinformatics Specialization |
| Level | Beginner |
| Commitment | 4-10 hours/week |
| Language | English |
| How To Pass | Pass all graded assignments to complete the course. |
| User Ratings |
Syllabus
WEEK 1
Week 1: Welcome!
<p>Welcome to class!</p><p>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:</p><ol><li>Weeks 1-2: Where in the Genome Does DNA Replication Begin? (<em>Algorithmic Warmup</em>)</li><li>Weeks 3-4: Which DNA Patterns Play the Role of Molecular Clocks? (<em>Randomized Algorithms</em>)</li></ol><p>Week 5 will consist of a Bioinformatics Application Challenge in which you will get to apply software for finding DNA motifs to a real biological dataset.</p><p>Each of the two chapters in the course is accompanied by a Bioinformatics Cartoon created by Randall Christopher and serving as a chapter header in the Specialization's bestselling <a href="http://bioinformaticsalgorithms.com" target="_blank">print companion</a>. You can find the first chapter's cartoon at the bottom of this message. What does a cryptic message leading to buried treasure have to do with biology? We hope you will join us to find out!</p><p><img src="http://bioinformaticsalgorithms.com/images/cover/replication_cropped.jpg" title="Image: http://bioinformaticsalgorithms.com/images/cover/chapter1_cropped.jpg" width="500"></p><p><a href="http://compeau.cbd.cmu.edu" target="_blank"><img src="http://bioinformaticsalgorithms.com/images/Compeau_caricature.jpg" width ="150"></a> <a href="http://cseweb.ucsd.edu/~ppevzner/" target="_blank"><img src="http://bioinformaticsalgorithms.com/images/Pevzner_caricature.jpg" width ="150"></a></p><p>Phillip and Pavel</p>
3 videos, 3 readings
- Reading: Course Details
- LTI Item: Stepik Interactive Text for Week 1
- Video: Where in the Genome Does DNA Replication Begin? (Part 1) (11:37)
- Video: Where in the Genome Does DNA Replication Begin? (Part 2) (06:24)
- Reading: Week 1 FAQs (Optional)
- Reading: What is Pseudocode? (Optional)
Graded: Week 1 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 1
WEEK 2
Week 2: Finding Replication Origins
<p>Welcome to Week 2 of class!</p>
<p>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 replication origin in a bacterial genome.</p>
2 videos, 1 reading
- LTI Item: Stepik Interactive Text for Week 2
- Video: Where in the Genome Does DNA Replication Begin? (Part 4) (04:10)
- Reading: Week 2 FAQs (Optional)
Graded: Week 2 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 2
WEEK 3
Week 3: Hunting for Regulatory Motifs
<p>Welcome to Week 3 of class!</p>
<p>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 Century French mathematicians have in common with finding molecular clocks? Start learning to find out...</p>
<p><img src="https://d396qusza40orc.cloudfront.net/bioinformatics%2Fimages%2Fchapter3_final.jpg" title="Image: https://d396qusza40orc.cloudfront.net/bioinformatics%2Fimages%2Fchapter3_final.jpg" width="528"></p>
3 videos, 1 reading
- LTI Item: Stepik Interactive Text for Week 3
- Video: From Implanted Patterns to Regulatory Motifs (Part 2) (05:06)
- Video: From Implanted Patterns to Regulatory Motifs (Part 3) (07:22)
- Reading: Week 3 FAQs (Optional)
Graded: Week 3 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 3
WEEK 4
Week 4: How Rolling Dice Helps Us Find Regulatory Motifs
<p>Welcome to Week 4 of class!</p>
<p>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.</p>
3 videos, 1 reading
- LTI Item: Stepik Interactive Text for Week 4
- Video: How Rolling Dice Helps Us Find Regulatory Motifs (Part 2) (05:37)
- Video: How Rolling Dice Helps Us Find Regulatory Motifs (Part 3) (07:46)
- Reading: Week 4 FAQs (Optional)
Graded: Week 4 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 4
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.
Graded: Bioinformatics Application Challenge
FAQs
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Ratings and Reviews
I couldn't finish successfully last question but I don't know why. I believe I understand the meaning of the question
One of the best online courses I've ever taken. Since I come from a biotechnology background, this course was particularly relevant for me in terms of its depth and thoroughness. Seriously considering a future in computational biology, thanks to this course.
Well prepared course although sometimes tough due to algorithmization tasks even for people with programming background.
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JM
Great course. Good introduction to applying computer science to real biology problems. Only cons to this course is that it tries to split the line between biologists wanting to learn more bioinformatics and data scientists wanting to learn bioinformatics which boils down to the coding being tough and at times not well explained and there not being enough explanation for the biology part. I wouldn't take this if you don't have any coding skills because without working through the coding challenges the course isn't useful and for those with what would be more novice coding skills (like me) be prepared to spend a lot of time on this course. Well worth the challenge.