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Molecular Evolution (Bioinformatics IV)

Molecular Evolution (Bioinformatics IV)

Name: Molecular Evolution (Bioinformatics IV)
Rating: 4.493670886075949 (79 reviews)

This course is part of Bioinformatics Specialization

Instructors: Pavel Pevzner

18,254 already enrolled

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6 modules

Gain insight into a topic and learn the fundamentals.

79 reviews

Intermediate level

Some related experience required

2 weeks to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

6 modules

Gain insight into a topic and learn the fundamentals.

79 reviews

Intermediate level

Some related experience required

2 weeks to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

Skills you'll gain

Details to know

Shareable certificate

Add to your LinkedIn profile

Assessments

5 assignments¹

AI Graded see disclaimer

Taught in English

91% of learners achieved a positive career outcome

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This course is part of the Bioinformatics Specialization

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There are 6 modules in this course

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.

Module details

Welcome to our class!In this class, we will consider the following two central biological questions (the computational approaches needed to solve them are shown in parentheses):<ol><li>Weeks 1-3: Which Animal Gave Us SARS? (Evolutionary tree construction)</li><li>Weeks 4-5: Was T. rex Just a Big Chicken? (Combinatorial Algorithms)</li></ol>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.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!<img src="http://bioinformaticsalgorithms.com/images/cover/evolution_cropped.jpg" title="Image: http://bioinformaticsalgorithms.com/images/cover/evolution_cropped.jpg" width="528">

What's included

5 videos2 readings1 assignment2 app items

5 videosTotal 34 minutes

(Check Out Our Wacky Course Intro Video!)4 minutes
The Fastest Outbreak 5 minutes
Transforming Distance Matrices into Evolutionary Trees 6 minutes
Toward an Algorithm for Distance-Based Phylogeny Construction 9 minutes
Additive Phylogeny 10 minutes

2 readingsTotal 10 minutes

Course Details10 minutes
Week 1 FAQs (Optional)0 minutes

1 assignmentTotal 15 minutes

Week 1 Quiz15 minutes

2 app itemsTotal 150 minutes

Open in order to Sync Your Progress: Interactive Text for Week 10 minutes
Interactive Text for Week 1150 minutes

Welcome to Week 2 of class! Last week, we started to see how evolutionary trees can be constructed from distance matrices.  This week, we will encounter additional algorithms for this purpose, including the neighbor-joining algorithm, which has become one of the top-ten most cited papers in all of science since its introduction three decades ago.

What's included

3 videos1 reading1 assignment2 app items

3 videosTotal 17 minutes

Using Least Squares to Construct Distance-Based Phylogenies 3 minutes
Ultrametric Trees 7 minutes
The Neighbor-Joining Algorithm 8 minutes

1 reading

Week 2 FAQs (Optional)0 minutes

1 assignmentTotal 15 minutes

Week 2 Quiz15 minutes

2 app itemsTotal 150 minutes

Open in order to Sync Your Progress: Interactive Text for Week 20 minutes
Interactive Text for Week 2150 minutes

Welcome to week 3 of class! Over the last two weeks, we have seen several different algorithms for constructing evolutionary trees from distance matrices. This week, we will conclude the current chapter by considering what happens if we use properties called "characters" instead of distances. We will also see how to infer the ancestral states of organisms in an evolutionary tree, and consider whether it is possible to define an efficient algorithm for this task.

What's included

4 videos1 reading1 assignment2 app items

4 videosTotal 20 minutes

Character-Based Tree Reconstruction 3 minutes
The Small Parsimony Algorithm 9 minutes
The Large Parsimony Algorithm 3 minutes
Evolutionary Tree Reconstruction in the Modern Era 6 minutes

1 reading

Week 3 FAQs (Optional)0 minutes

1 assignmentTotal 15 minutes

Week 3 Quiz15 minutes

2 app itemsTotal 210 minutes

Open in order to Sync Your Progress: Interactive Text for Week 30 minutes
Interactive Text for Week 3210 minutes

Welcome to week 4 of the class! Did birds evolve from dinosaurs? Over the next two weeks, we will see how we could analyze molecular evidence in support of this theory. You can find this week's Bioinformatics Cartoon from Randall Christopher at the bottom of this E-mail. Why does the T. rex look so much like a chicken? And why is the monkey typing frantically? Keep learning to find out! <img src="http://bioinformaticsalgorithms.com/images/cover/proteomics_cropped.jpg" title="Image: http://bioinformaticsalgorithms.com/images/cover/proteomics_cropped.jpg" width="528">

What's included

4 videos1 assignment2 app items

Welcome to week 5 of class! Last week, we asked whether it is possible for dinosaur peptides to survive locked inside of a fossil for 65 million years. This week, we will see what this question has to do with statistics; in the process, we will see how a monkey typing out symbols on a typewriter can be used to address it.

What's included

5 videos1 assignment2 app items

5 videosTotal 44 minutes

Peptide Identification 5 minutes
Spectral Dictionaries 7 minutes
The Ostrich Hemoglobin Riddle 15 minutes
Searching for Post-Translational Modifications 5 minutes
Spectral Alignment Algorithm 11 minutes

1 assignmentTotal 15 minutes

Week 5 Quiz15 minutes

2 app itemsTotal 60 minutes

Open in order to Sync Your Progress: Interactive Text for Week 50 minutes
Interactive Text for Week 560 minutes

Welcome to the sixth and final week of the course! In this week's Bioinformatics Application Challenge, we will use reconstruct an evolutionary tree of ebolaviruses and use it to determine the origin of the pathogen that caused the recent outbreak in Africa.

What's included

1 peer review

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Instructors

Pavel Pevzner

University of California San Diego

16 Courses907,973 learners

Phillip Compeau

University of California San Diego

8 Courses323,928 learners

Offered by

University of California San Diego

Learner reviews

5 stars
69.62%
4 stars
17.72%
3 stars
8.86%
2 stars
0%
1 star
3.79%

Showing 3 of 79

Reviewed on Dec 4, 2016

At some point several instructors lost necessary passion to keep us focused. Otherwise it was a very informed and enjoyable presentation. Historical references are extremely important.

Reviewed on Mar 30, 2021

Good course for improving algorithmic skills and keep learning something new

Reviewed on Jul 19, 2017

Covers the most important algorithms for phylogenetic trees. Fascinating exam

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