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来自 University of California San Diego 的课程

分子进化 (生物信息学 IV)

38 个评分

University of California San Diego

分子进化 (生物信息学 IV)

38 个评分

课程 4（共 7 门，Specialization Bioinformatics）

In the previous course in the Specialization, we learned how to compare genes, proteins, and genomes. One way we can use these methods is in order to construct a "Tree of Life" showing how a large collection of related organisms have evolved over time. In the first half of the course, we will discuss approaches for evolutionary tree construction that have been the subject of some of the most cited scientific papers of all time, and show how they can resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans. In the second half of the course, we will shift gears and examine the old claim that birds evolved from dinosaurs. How can we prove this? In particular, we will examine a result that claimed that peptides harvested from a T. rex fossil closely matched peptides found in chickens. In particular, we will use methods from computational proteomics to ask how we could assess whether this result is valid or due to some form of contamination. Finally, you will learn how to apply popular bioinformatics software tools to reconstruct an evolutionary tree of ebolaviruses and identify the source of the recent Ebola epidemic that caused global headlines.

从本节课中

Week 1: Introduction to Evolutionary Tree Construction

<p>Welcome to our class!</p><p>In this class, we will consider the following two central biological questions (the computational approaches needed to solve them are shown in parentheses):</p><ol><li>Weeks 1-3: Which Animal Gave Us SARS? (<i>Evolutionary tree construction</i>)</li><li>Weeks 4-5: Was <em>T. rex</em> Just a Big Chicken? (<em>Combinatorial Algorithms</em>)</li></ol><p>In Week 6, you will complete a Bioinformatics Application Challenge to apply evolutionary tree construction algorithms in order to determine the origin of the recent ebola outbreak in Africa.</p><p>As in previous courses, each of these two chapters is accompanied by a Bioinformatics Cartoon created by talented artist 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 do stick bugs and bats have to do with deadly viruses? And how can bioinformatics be used to stop these viruses in their tracks? Start learning today and find out!</p><p><img src="http://bioinformaticsalgorithms.com/images/cover/evolution_cropped.jpg" title="Image: http://bioinformaticsalgorithms.com/images/cover/evolution_cropped.jpg" width="528"></p>

(Check Out Our Wacky Course Intro Video!)3:30

与讲师见面

Pavel Pevzner
Professor
Department of Computer Science and Engineering
Phillip Compeau
Visiting Researcher
Department of Computer Science & Engineering

In 2003, a doctor flew to Hong Kong to attend a wedding and

he brought with him a mysterious, deadly virus that he had caught from patients he

was treating in Mainland, China.

Unfortunately, the doctor never made it to the wedding.

And he died two weeks later.

But not before he had infected several other people from different countries

who were staying on the same floor of his hotel.

And within a month, this mysterious virus was wreaking havoc and

causing panic around the world.

>> But where did this virus come from and how did it spread around the globe?

To solve this mystery, we will construct an evolutionary tree for

similar viruses from different species

in order to determine which species started the epidemic.

Studying viruses that cause epidemics is just one of the many

applications of evolutionary trees, which range from catching criminals

to identifying the birth place of human civilization.

When we construct evolutionary trees, we use genomes of present day species.

To get inside into how the species have evolved from their ancestor,

but can we reconstruct the genes and proteins from extinct species?

>> Speaking of extinct species, when I was seven years old I saw the movie

Jurassic Park, and it made me dream of one day getting to see a real life dinosaur.

Fortunately, I'm not alone.

Famous paleontologist, Jack Horner, has the same dream and

this shared dream of ours took 1 small step toward reality when

in 2007 Horner and his colleagues identified protein fragments

that had miraculously survived in a T-Rex fossil for 68 million years.

But because these proteins were very similar to chicken proteins,

they presented the first genetic evidence for

the hypothesis that birds had evolved from dinosaurs.

In fact, Horner was so

inspired by this discovery that he even published a book about how researchers

could one day genetically modify a chicken into a real life T-Rex.

>> But what in the world do have to do with these dinosaur fossils?

It turns out that since all for protein sequencing make errors,

some scientists, myself included, doubted whether Horner

had really found any evidence of Jurassic project.

But which side is correct?

We hope that you will join us and decide for yourself.

>> Although these instructors may appear crazy,

they are not quite as mad as they look.

Dr. Pavel Pevzner is a distinguished professor of computer science at

the University of California, San Diego and a leading authority on bioinformatics.

He's dressed this way because he sometimes thinks that he is a sheriff of

bioinformatics, a frontier discipline under pinning

the digital revolution in biology and personalized medicine.

Dr. Phillip Compeau is an Assistant Professor of Computer Science at

Carnegie Mellon University, to learn why he is dressed this way,

you'll need to take this course or

read the textbook, Bioinformatics Algorithms An Active Learning Approach,

coauthored by the two speakers.

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