分子进化解密(生物信息学 IV)

Deciphering Molecular Evolution (Bioinformatics IV)

In this course, we will see how evolutionary trees resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans. We will then use methods from computational proteomics to test whether we can reconstruct Tyrannosaurus rex proteins and prove that birds have evolved from dinosaurs.

加州大学圣地亚哥分校

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分子进化解密(生物信息学 IV)

课程概况

In 2003, the deadly Severe Acute Respiratory Syndrome (SARS) virus caused panic as it swept around the globe in a few weeks. But where did SARS come from? By constructing an evolutionary tree of the unknown virus as well as viruses taken from other species, we can not only understand which animal gave us SARS, but also reconstruct its path around the globe. This is just one of many problems in modern biology related to constructing evolutionary trees.

In 2007, a team of biologists announced that some proteins had miraculously survived within a 68 million year old dinosaur fossil. Moreover, they concluded that the amino acid sequences of these dinosaur proteins were nearly identical to sequences in modern-day chickensl. Based on this discovery, famed paleontologist Jack Horner (who partly inspired the character of Dr. Grant from Jurassic Park) hopes to resurrect dinosaurs by genetically re-engineering a chicken. But did these peptides really come from T. rex, or do they represent statistical artifacts or contamination? To answer this question, we will need to explore the field of computational proteomics.

课程大纲

Which Animal Gave Us SARS? (Evolutionary Tree Reconstruction)

The Fastest Outbreak
Transforming Distance Matrices into Evolutionary Trees
Toward An Algorithm for Distance-Based Phylogeny Construction
Additive Phylogeny
Using Least Squares to Construct Approximate Distance-Based Phylogenies
Ultrametric Evolutionary Trees
The Neighbor-Joining Algorithm
Character-Based Tree Reconstruction
The Small Parsimony Problem
The Large Parsimony Problem
Epilogue: Evolutionary Trees Fight Crime

Was T. rex Just a Big Chicken? (Computational Proteomics)
Paleontology Meets Computing
What Proteins Are Present in This Sample?
Decoding an Ideal Spectrum
From Ideal to Real Spectra
Peptide Sequencing
Peptide Identification
Peptide Identification Meets the Infinite Monkey Theorem
Spectral Dictionaries
T. rex Peptides: Treasure Trove of Ancient Proteins or Artifact of Contamination?
Epilogue: From Unmodified to Modified Peptides

背景知识

Comparing Genes, Genomes, and Proteins” is the suggested prerequisite for taking this course, but it is not a strict prerequisite, especially if you have some programming experience.

The programming assignments in this class can be solved using any programming language.

参考资料

The printed course companion is Bioinformatics Algorithms: An Active-Learning Approach, by Compeau & Pevzner.

授课形式

The majority of assessments for the course will consist of exercises and programming assignments. This course covers two chapters taken from Bioinformatics Algorithms: An Active Learning Approach, by Compeau & Pevzner.

Each chapter is also accompanied by a summary quiz and lecture videos.

常见问题

Q: Will I get a statement of accomplishment after completing this class?

Yes. Students who successfully complete the class will receive a statement of accomplishment signed by the instructor.

Q: Can I receive a verified certificate for this course?
Yes. Students 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 2) 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 “Finding Mutations in DNA and Proteins.

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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