Molecular Evolution (Bioinformatics IV)

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Opleiderscore: starstarstarstar_borderstar_border 6,3 Coursera heeft een gemiddelde beoordeling van 6,3 (uit 4 ervaringen)

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Beschrijving

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About 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. H…

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When you enroll for courses through Coursera you get to choose for a paid plan or for a free plan

  • Free plan: No certicification and/or audit only. You will have access to all course materials except graded items.
  • Paid plan: Commit to earning a Certificate—it's a trusted, shareable way to showcase your new skills.

About 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.

Who is this class for: This course is primarily aimed at undergraduate-level learners in computer science, biology, or a related field who are interested in learning about how the intersection of these two disciplines represents an important frontier in modern science.

Created by:  University of California, San Diego
  • Taught by:  Pavel Pevzner, Professor

    Department of Computer Science and Engineering
  • Taught by:  Phillip Compeau, Visiting Researcher

    Department of Computer Science & Engineering
Basic Info Course 4 of 7 in the Bioinformatics Specialization Level Beginner Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.4 stars Average User Rating 4.4See what learners said Coursework

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University of California, San Diego UC San Diego is an academic powerhouse and economic engine, recognized as one of the top 10 public universities by U.S. News and World Report. Innovation is central to who we are and what we do. Here, students learn that knowledge isn't just acquired in the classroom—life is their laboratory.

Syllabus


WEEK 1


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&nbsp;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?&nbsp;(<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>


5 videos, 2 readings expand


  1. Video: (Check Out Our Wacky Course Intro Video!)
  2. Reading: Course Details
  3. LTI Item: Stepik Interactive Text for Week 1
  4. Video: The Fastest Outbreak
  5. Video: Transforming Distance Matrices into Evolutionary Trees
  6. Video: Toward an Algorithm for Distance-Based Phylogeny Construction
  7. Video: Additive Phylogeny
  8. Reading: Week 1 FAQs (Optional)

Graded: Week 1 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 1

WEEK 2


Week 2: Algorithms for Constructing Trees from Distance Matrices



<p>Welcome to Week 2 of class!</p> <p>Last week, we started to see how evolutionary trees can be constructed from distance matrices. &nbsp;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.</p>


3 videos, 1 reading expand


  1. LTI Item: Stepik Interactive Text for Week 2
  2. Video: Using Least Squares to Construct Distance-Based Phylogenies
  3. Video: Ultrametric Trees
  4. Video: The Neighbor-Joining Algorithm
  5. Reading: Week 2 FAQs (Optional)

Graded: Week 2 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 2

WEEK 3


Week 3: Constructing Evolutionary Trees from Characters



<p>Welcome to week 3 of class!</p> <p>Over the last two weeks, we have seen several different algorithms for constructing evolutionary trees from distance matrices.</p> <p>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.</p>


4 videos, 1 reading expand


  1. LTI Item: Stepik Interactive Text for Week 3
  2. Video: Character-Based Tree Reconstruction
  3. Video: The Small Parsimony Algorithm
  4. Video: The Large Parsimony Algorithm
  5. Video: Evolutionary Tree Reconstruction in the Modern Era
  6. Reading: Week 3 FAQs (Optional)

Graded: Week 3 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 3

WEEK 4


Week 4



<p>Welcome to week 4 of the class!</p> <p>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 <em>T. rex&nbsp;</em>look so much like a chicken? And why is the monkey typing frantically? Keep learning to find out!</p> <p><img src="http://bioinformaticsalgorithms.com/images/cover/proteomics_cropped.jpg" title="Image: http://bioinformaticsalgorithms.com/images/cover/proteomics_cropped.jpg" width="528"></p>


4 videos, 1 reading expand


  1. Reading: Note on This Week's Assignments
  2. Video: Paleontology Meets Computing
  3. Video: Decoding an Ideal Spectrum
  4. Video: From Ideal to Real Spectra
  5. Video: Peptide Sequencing

Graded: Week 4 Quiz
Graded: Stepik Code Challenges for Week 4

WEEK 5


Week 5: Resolving the T. rex Peptides Mystery?



<p>Welcome to week 5 of class!</p> <p>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.</p>


5 videos, 1 reading expand


  1. Reading: Note on This Week's Content
  2. Video: Peptide Identification
  3. Video: Spectral Dictionaries
  4. Video: The Ostrich Hemoglobin Riddle
  5. Video: Searching for Post-Translational Modifications
  6. Video: Spectral Alignment Algorithm

Graded: Week 5 Quiz
Graded: Stepik Code Challenges for Week 5

WEEK 6


Week 6: Bioinformatics Application Challenge



<p>Welcome to the sixth and final week of the course!</p> <p>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.</p>




    Graded: Bioinformatics Application Challenge

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