Part of the Bioinformatics Specialization »
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. After warming up our algorithmic muscles, we will learn how to
apply popular bioinformatics software tools to real experimental
datasets.
Course at a Glance
About the Course
A genome may look like an incomprehensible string of the letters A, C, G, and T. Yet hidden in the three billion nucleotides of your genome is a secret language. This course offers an introduction to how we can start to understand this language with algorithms.In this course, we will write algorithms to determine where a bacterium starts replicating its genome, a problem with applications in genetic engineering. We will also use randomized algorithms to learn how a cell knows what time of day it is and how the bacterium causing tuberculosis can hide from antibiotics.
Each of the two topics in the course builds the algorithmic knowledge required to address this challenge. In the end of the course, you will be able to apply popular bioinformatics software tools for finding regulatory motifs in experimental data sets and solve our Bioinformatics Application Challenge.
Course Syllabus
Where in the Genome Does Replication Begin? (Algorithmic Warmup):
- Introduction to DNA replication
- Hidden messages in the replication origin
- Some hidden messages are more surprising than others
- An explosion of hidden messages
- The simplest way to replicate DNA
- Asymmetry of replication
- Peculiar statistics of the forward and reverse half-strands
- Some hidden messages are more elusive than others
- A final attempt at finding DnaA boxes in E. coli
- Epilogue: Complications in oriC predictions
- Do we have a "clock" gene?
- Motif finding is more difficult than you think
- Scoring motifs
- From motif finding to finding a median string
- Greedy motif search
- Motif finding meets Oliver Cromwell
- Randomized motif search
- How can a randomized algorithm perform so well?
- Gibbs sampling
- Gibbs sampling in action
- Complications in motif finding
- Epilogue: How does Tuberculosis hibernate to hide from antibiotics?
Recommended Background
If
you are aiming at earning a standard certificate in this class, then
you do not need to have any experience in biology or programming. The
only prerequisite is the enthusiasm to learn about how computational
approaches are used in modern biology :)
If you are aiming at earning a certificate with distinction, then you should either know the basics of programming in the language of your choice (there is no required language for this course) or be willing to learn about programming before the course begins. In this case, we have the following suggestions for resources that will help you quickly learn the basics of programming.
If you are aiming at earning a certificate with distinction, then you should either know the basics of programming in the language of your choice (there is no required language for this course) or be willing to learn about programming before the course begins. In this case, we have the following suggestions for resources that will help you quickly learn the basics of programming.
- The language tracks on Codecademy, particularly the Python track.
- An Introduction to Interactive Programming with Python, the acclaimed Coursera course.
- Introductory problems on Rosalind, a resource for learning bioinformatics created by the course instructors.
Suggested Readings
The printed course companion is Bioinformatics Algorithms: An Active-Learning Approach (2nd edition), by Compeau & Pevzner.
Course Format
This course covers two chapters from Bioinformatics Algorithms: An Active Learning Approach, by Compeau & Pevzner. The course also contains summary quizzes and lecture videos.
To earn a standard certificate in the class, you must complete weekly quizzes in addition to a Bioinformatics Application Challenge in which you apply popular bioinformatics software tools to a real experimental dataset. If you are eager to learn about bioinformatics, you should be able to complete the Application Challenge and earn the course certificate even if you do not know how to program.
To earn a certificate with distinction, rather than complete the Application Challenge, you must complete some programming assignments found in the course's interactive text. The distinction is a "hacker track" that is aimed at learners who know how to program and would like to explore the nuts and bolts of bioinformatics algorithms.
To earn a standard certificate in the class, you must complete weekly quizzes in addition to a Bioinformatics Application Challenge in which you apply popular bioinformatics software tools to a real experimental dataset. If you are eager to learn about bioinformatics, you should be able to complete the Application Challenge and earn the course certificate even if you do not know how to program.
To earn a certificate with distinction, rather than complete the Application Challenge, you must complete some programming assignments found in the course's interactive text. The distinction is a "hacker track" that is aimed at learners who know how to program and would like to explore the nuts and bolts of bioinformatics algorithms.
FAQ
Q: I have never programmed before. Can I still take this class?
Yes you can! The standard certificate is designed for learners who have never programmed before. We do encourage you to learn how to program if you are interested in earning a certificate with distinction, and this course will help you make your first steps towards learning how to program.
Q: The last biology course that I took was in high school (and I fell asleep). Can I still take this class?
Yes you can! We begin by talking about what DNA is, and we explain all of the biological ideas that you will need to succeed in this class.
Q: Will I get a statement of accomplishment after completing this class?
Yes. Learners who successfully complete the class will receive a statement of accomplishment signed by the instructor.Yes you can! The standard certificate is designed for learners who have never programmed before. We do encourage you to learn how to program if you are interested in earning a certificate with distinction, and this course will help you make your first steps towards learning how to program.
Q: The last biology course that I took was in high school (and I fell asleep). Can I still take this class?
Yes you can! We begin by talking about what DNA is, and we explain all of the biological ideas that you will need to succeed in this class.
Q: Will I get a statement of accomplishment after completing this class?
Q: Can I receive a verified certificate for this course?
Yes. Learners who would like a verified certificate can sign up for the course's Signature Track option.
Q: I remember this course used to be part of the larger "Bioinformatics Algorithms (Part 1) course. Why was it split into three courses?
Based on survey feedback, completion data, and studies of other courses, we realized that having shorter courses gives our students more flexibility around their busy schedules. Even though the courses have been split, the overall content remains the same, so we feel confident that we're maintaining learning standards of our material.
Q: What if I earned a voucher for retaking the old course? Can I use it in this course?
Vouchers from the older course will be valid for the newer courses. If you took the original course and earned a voucher, you will be issued a voucher for this course as well as for "Assembling Genomes and Sequencing Antibiotics" and "Comparing Genes, Proteins, and Genomes" (three vouchers total).
Q: Does this mean that the overall cost for earning Verified Certificates in the course is greater now?
Yes. Since there are more courses now, the overall cost for Verified Certificates is greater than before. Coursera offers a Financial Aid program for learners who would face a serious hardship paying for our courses. Plus, if you just want to join and check out our course content, it's still free and available to everyone.
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