Genome Sequencing (Bioinformatics II)

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Description

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  • Paid plan: Commit to earning a Certificate—it's a trusted, shareable way to showcase your new skills.

About this course: You may have heard a lot about genome sequencing and its potential to usher in an era of personalized medicine, but what does it mean to sequence a genome? Biologists still cannot read the nucleotides of an entire genome as you would read a book from beginning to end. However, they can read short pieces of DNA. In this course, we will see how graph theory can be used to assemble genomes from these short pieces. We will further learn about brute force algorithms and apply them to sequencing mini-proteins called antibiotics. In the first half of the course, we will see that biologists cannot read the 3 billion nucleotides of a human genome as you would read a book from …

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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: You may have heard a lot about genome sequencing and its potential to usher in an era of personalized medicine, but what does it mean to sequence a genome? Biologists still cannot read the nucleotides of an entire genome as you would read a book from beginning to end. However, they can read short pieces of DNA. In this course, we will see how graph theory can be used to assemble genomes from these short pieces. We will further learn about brute force algorithms and apply them to sequencing mini-proteins called antibiotics. In the first half of the course, we will see that biologists cannot read the 3 billion nucleotides of a human genome as you would read a book from beginning to end. However, they can read shorter fragments of DNA. In this course, we will see how graph theory can be used to assemble genomes from these short pieces in what amounts to the largest jigsaw puzzle ever put together. In the second half of the course, we will discuss antibiotics, a topic of great relevance as antimicrobial-resistant bacteria like MRSA are on the rise. You know antibiotics as drugs, but on the molecular level they are short mini-proteins that have been engineered by bacteria to kill their enemies. Determining the sequence of amino acids making up one of these antibiotics is an important research problem, and one that is similar to that of sequencing a genome by assembling tiny fragments of DNA. We will see how brute force algorithms that try every possible solution are able to identify naturally occurring antibiotics so that they can be synthesized in a lab. Finally, you will learn how to apply popular bioinformatics software tools to sequence the genome of a deadly Staphylococcus bacterium that has acquired antibiotics resistance.

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 2 of 7 in the Bioinformatics Specialization Level Beginner Language English, Subtitles: Chinese (Simplified) How To Pass Pass all graded assignments to complete the course. User Ratings 4.7 stars Average User Rating 4.7See what learners said Coursework

Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.

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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 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>


8 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: FIELD TRIP!
  5. Video: What Is Genome Sequencing?
  6. Video: Exploding Newspapers
  7. Video: The String Reconstruction Problem
  8. Video: String Reconstruction as a Hamiltonian Path Problem
  9. Video: String Reconstruction as an Eulerian Path Problem
  10. Video: Similar Problems with Different Fates
  11. 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: 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>


5 videos, 1 reading expand


  1. LTI Item: Stepik Interactive Text for Week 2
  2. Video: De Bruijn Graphs
  3. Video: Euler's Theorem
  4. Video: Assembling Read-Pairs
  5. Video: De Bruijn Graphs Face Harsh Realities of Assembly
  6. Video: Returning to Konigsberg
  7. 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: 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>


5 videos, 1 reading expand


  1. LTI Item: Stepik Interactive Text for Week 3
  2. Video: The Discovery of Antibiotics
  3. Video: How Do Bacteria Make Antibiotics?
  4. Video: Sequencing Antibiotics by Shattering Them into Pieces
  5. Video: A Brute Force Algorithm for Cyclopeptide Sequencing
  6. Video: Cyclopeptide Sequencing with Branch and Bound
  7. 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: 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>


4 videos, 1 reading expand


  1. LTI Item: Stepik Interactive Text for Week 4
  2. Video: Adapting Sequencing for Spectra with Errors
  3. Video: From 20 to than 100 Amino Acids
  4. Video: The Spectral Convolution Saves the Day
  5. Video: The Truth About Spectra
  6. Reading: Week 4 FAQs (Optional)

Graded: Week 4 Quiz
Graded: Open in order to Sync Your Progress: Stepik Interactive Text for Week 4

WEEK 5


Week 5: Bioinformatics Application Challenge!
Welcome to Week 5 of class! This week, we will see how to apply genome assembly tools to sequencing data from a dangerous pathogenic bacterium.




    Graded: Bioinformatics Application Challenge
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