About this Course
4.5
40 ratings
11 reviews
Specialization

Course 4 of 7 in the

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Flexible deadlines

Flexible deadlines

Reset deadlines in accordance to your schedule.
Beginner Level

Beginner Level

Hours to complete

Approx. 17 hours to complete

Suggested: 3 hours/week...
Available languages

English

Subtitles: English
Specialization

Course 4 of 7 in the

100% online

100% online

Start instantly and learn at your own schedule.
Flexible deadlines

Flexible deadlines

Reset deadlines in accordance to your schedule.
Beginner Level

Beginner Level

Hours to complete

Approx. 17 hours to complete

Suggested: 3 hours/week...
Available languages

English

Subtitles: English

Syllabus - What you will learn from this course

Week
1
Hours to complete
3 hours to complete

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>...
Reading
5 videos (Total 34 min), 2 readings, 3 quizzes
Video5 videos
The Fastest Outbreak 5m
Transforming Distance Matrices into Evolutionary Trees 6m
Toward an Algorithm for Distance-Based Phylogeny Construction 8m
Additive Phylogeny 9m
Reading2 readings
Course Details10m
Week 1 FAQs (Optional)
Quiz1 practice exercise
Week 1 Quiz15m
Week
2
Hours to complete
3 hours to complete

Week 2: More 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>...
Reading
3 videos (Total 17 min), 1 reading, 3 quizzes
Video3 videos
Ultrametric Trees 6m
The Neighbor-Joining Algorithm 7m
Reading1 reading
Week 2 FAQs (Optional)
Quiz1 practice exercise
Week 2 Quiz15m
Week
3
Hours to complete
4 hours to complete

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>...
Reading
4 videos (Total 20 min), 1 reading, 3 quizzes
Video4 videos
The Small Parsimony Algorithm 8m
The Large Parsimony Algorithm 3m
Evolutionary Tree Reconstruction in the Modern Era 5m
Reading1 reading
Week 3 FAQs (Optional)
Quiz1 practice exercise
Week 3 Quiz15m
Week
4
Hours to complete
1 hour to complete

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>...
Reading
4 videos (Total 26 min), 1 reading, 2 quizzes
Video4 videos
Decoding an Ideal Spectrum 5m
From Ideal to Real Spectra 5m
Peptide Sequencing 7m
Reading1 reading
Note on This Week's Assignments10m
Quiz1 practice exercise
Week 4 Quiz15m
4.5
11 ReviewsChevron Right

Top Reviews

By RGJul 20th 2017

Covers the most important algorithms for phylogenetic trees. Fascinating exam

Instructors

Avatar

Pavel Pevzner

Professor
Department of Computer Science and Engineering
Avatar

Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering

About 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....

About the Bioinformatics Specialization

Join Us in a Top 50 MOOC of All Time! How do we sequence and compare genomes? How do we identify the genetic basis for disease? How do we construct an evolutionary Tree of Life for all species on Earth? When you complete this Specialization, you will learn how to answer many questions in modern biology that have become inseparable from the computational approaches used to solve them. You will also obtain a toolkit of existing software resources built on these computational approaches and that are used by thousands of biologists every day in one of the fastest growing fields in science. Although this Specialization centers on computational topics, you do not need to know how to program in order to complete it. If you are interested in programming, we feature an "Honors Track" (called "hacker track" in previous runs of the course). The Honors Track allows you to implement the bioinformatics algorithms that you will encounter along the way in dozens of automatically graded coding challenges. By completing the Honors Track, you will be a bioinformatics software professional! Learn more about the Bioinformatics Specialization (including why we are wearing these crazy outfits) by watching our introductory video. You can purchase the Specialization's print companion, Bioinformatics Algorithms: An Active Learning Approach, from the textbook website. Our first course, "Finding Hidden Messages in DNA", was named a top-50 MOOC of all time by Class Central!...
Bioinformatics

Frequently Asked Questions

  • Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.

  • When you enroll in the course, you get access to all of the courses in the Specialization, and you earn a certificate when you complete the work. Your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.

More questions? Visit the Learner Help Center.