Acerca del Curso
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 by using algorithms to find hidden messages in DNA.
What do these hidden messages say? In the first chapter of the course, hidden DNA messages indicate where a bacterium starts replicating its genome, a problem with applications in genetic engineering and beyond. In the second chapter, hidden DNA messages tell us how organisms know whether it is day or night as well as how the bacterium causing tuberculosis is able to hide from antibiotics. We will see howrandomized algorithms, which toss coins and roll dice, can be used to find these messages.
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.
The Bioinformatics Specialization to which this class belongs covers exactly the same material as the core bioinformatics class in the "Bioinformatics and Systems Biology" program at the University of California at San Diego, one of the top bioinformatics programs in the world. In other words, you will have exactly the same lectures and homework assignments as students at UCSD. Moreover, many leading universities have adopted this material in their offline classes. Our goal is to provide you with the same high-quality materials that these students study in their offline classes.
Check out the following video to see why Semyon Kruglyak, Senior Director of Informatics Research at Illumina wants to interview you if you excel in the Bioinformatics Specialization!
Programa del Curso
- 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?
Where in the Genome Does Replication Begin? (Algorithmic Warmup):
Which DNA Patterns Play the Role of Molecular Clocks? (Randomized Algorithms)
Bioinformatics Application Challenge: Searching for regulatory motifs in Mycobacterium tuberculosis
