Acerca de este Curso
4.5
39 ratings
11 reviews
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....
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Beginner Level

Nivel principiante

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Sugerido: 3 hours/week

Aprox. 16 horas para completar
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English

Subtítulos: English
Globe

Cursos 100 % en línea

Comienza de inmediato y aprende a tu propio ritmo.
Calendar

Fechas límite flexibles

Restablece las fechas límite en función de tus horarios.
Beginner Level

Nivel principiante

Clock

Sugerido: 3 hours/week

Aprox. 16 horas para completar
Comment Dots

English

Subtítulos: English

Programa - Qué aprenderás en este curso

1

Sección
Clock
3 horas para completar

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 lecturas
Course Details10m
Week 1 FAQs (Optional)m
Quiz1 ejercicio de práctica
Week 1 Quiz15m

2

Sección
Clock
3 horas para completar

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 lectura
Week 2 FAQs (Optional)m
Quiz1 ejercicio de práctica
Week 2 Quiz15m

3

Sección
Clock
4 horas para completar

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 lectura
Week 3 FAQs (Optional)m
Quiz1 ejercicio de práctica
Week 3 Quiz15m

4

Sección
Clock
1 hora para completar

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 lectura
Note on This Week's Assignments10m
Quiz1 ejercicio de práctica
Week 4 Quiz15m
4.5

Principales revisiones

por RGJul 20th 2017

Covers the most important algorithms for phylogenetic trees. Fascinating exam

Instructores

Pavel Pevzner

Professor
Department of Computer Science and Engineering

Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering

Acerca de 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....

Acerca del programa especializado Bioinformatics

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

Preguntas Frecuentes

  • 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.

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