About this Course
4.8
158 ratings
34 reviews
Specialization

Course 2 of 7 in the

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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. 15 hours to complete

Suggested: 3 hours/week...
Available languages

English

Subtitles: English, Chinese (Simplified)...

Skills you will gain

AlgorithmsPython ProgrammingWhole Genome SequencingDynamic Programming
Specialization

Course 2 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. 15 hours to complete

Suggested: 3 hours/week...
Available languages

English

Subtitles: English, Chinese (Simplified)...

Syllabus - What you will learn from this course

Week
1
Hours to complete
4 hours to complete

Week 1: Introduction to Genome Sequencing

<p>Welcome to class!</p><p>This course will focus on two questions at the forefront of modern computational biology, along with the algorithmic approaches we will use to solve them in parentheses:</p><ol><li>Weeks 1-2: How Do We Assemble Genomes? (<i>Graph Algorithms</i>)</li><li>How Do We Sequence Antibiotics? (<i>Brute Force Algorithms</i>)</li></ol><p>Each of the two chapters of content in the class is accompanied by a Bioinformatics Cartoon created by talented San Diego 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 does a time machine trip to 1735, a stack of newspapers, a jigsaw puzzle, and a giant ant invading a riverside city have to do with putting together a genome? Start learning today to find out!</p><p><img src="https://d396qusza40orc.cloudfront.net/bioinformatics%2Fimages%2Fchapter4_final_lr.jpg" title="Image: https://d396qusza40orc.cloudfront.net/bioinformatics%2Fimages%2Fchapter4_final_lr.jpg" width="528"></p>...
Reading
8 videos (Total 36 min), 2 readings, 3 quizzes
Video8 videos
FIELD TRIP!4m
What Is Genome Sequencing?6m
Exploding Newspapers4m
The String Reconstruction Problem3m
String Reconstruction as a Hamiltonian Path Problem3m
String Reconstruction as an Eulerian Path Problem5m
Similar Problems with Different Fates 3m
Reading2 readings
Course Details10m
Week 1 FAQs (Optional)m
Quiz1 practice exercise
Week 1 Quiz15m
Week
2
Hours to complete
3 hours to complete

Week 2: Applying Euler's Theorem to Assemble Genomes

<p>Welcome to Week 2 of class!</p> <p>This week in class, we will see how a 300 year-old mathematical theorem will help us assemble a genome from millions of tiny pieces of DNA.</p>...
Reading
5 videos (Total 28 min), 1 reading, 3 quizzes
Video5 videos
Euler's Theorem 6m
Assembling Read-Pairs 8m
De Bruijn Graphs Face Harsh Realities of Assembly 4m
Returning to Konigsberg 1m
Reading1 reading
Week 2 FAQs (Optional)m
Quiz1 practice exercise
Week 2 Quiz15m
Week
3
Hours to complete
4 hours to complete

Week 3: Sequencing Antibiotics

<p>Welcome to Week 3 of class!</p> <p>This week, we begin a new chapter, titled "How Do We Sequence Antibiotics?" &nbsp;In this chapter, we will learn&nbsp;how to determine the amino acid sequences making up antibiotics using brute force algorithms.</p> <p>Below is this week's Bioinformatics Cartoon.</p> <p><img src="https://d396qusza40orc.cloudfront.net/bioinformatics%2Fimages%2Fchapter2_final.jpg" title="Image: https://d396qusza40orc.cloudfront.net/bioinformatics%2Fimages%2Fchapter2_final.jpg" width="528"></p>...
Reading
5 videos (Total 27 min), 1 reading, 3 quizzes
Video5 videos
How Do Bacteria Make Antibiotics? 8m
Sequencing Antibiotics by Shattering Them into Pieces 4m
A Brute Force Algorithm for Cyclopeptide Sequencing 3m
Cyclopeptide Sequencing with Branch and Bound 6m
Reading1 reading
Week 3 FAQs (Optional)m
Quiz1 practice exercise
Week 3 Quiz15m
Week
4
Hours to complete
3 hours to complete

Week 4: From Ideal to Real Spectra for Antibiotics Sequencing

<p>Welcome to Week 4 of class!</p> <p>Last week, we discussed how to sequence an antibiotic peptide from an ideal spectrum. This week, we will see how to develop more sophisticated algorithms for antibiotic peptide sequencing that are able to handle spectra with many false and missing masses.</p>...
Reading
4 videos (Total 18 min), 1 reading, 3 quizzes
Video4 videos
From 20 to More than 100 Amino Acids 2m
The Spectral Convolution Saves the Day 6m
The Truth About Spectra 2m
Reading1 reading
Week 4 FAQs (Optional)m
Quiz1 practice exercise
Week 4 Quiz15m
4.8
34 ReviewsChevron Right
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50%

started a new career after completing these courses
Career Benefit

83%

got a tangible career benefit from this course

Top Reviews

By SVJan 10th 2017

Great course to explore a bit of Bioinformatics for those with no background in Bioinformatics. I love the way the content has been provided, its interactivity increases the interest in the course.

By MPDec 8th 2017

I like the real-world tasks, especially the assembly on the final exam. Some of the programming tasks, such as the antibiotic noisy spectrum assembly, are challenging (which is good).

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.