课程信息
4.8
154 个评分
34 个审阅
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....
Stacks

Course 2 of 7 in the

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Beginner Level

初级

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Approx. 15 hours to complete

建议:3 hours/week...
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English

字幕:English, Chinese (Simplified)...

您将获得的技能

AlgorithmsPython ProgrammingWhole Genome SequencingDynamic Programming
Stacks

Course 2 of 7 in the

Globe

100% 在线课程

立即开始,按照自己的计划学习。
Calendar

可灵活调整截止日期

根据您的日程表重置截止日期。
Beginner Level

初级

Clock

Approx. 15 hours to complete

建议:3 hours/week...
Comment Dots

English

字幕:English, Chinese (Simplified)...

教学大纲 - 您将从这门课程中学到什么

Week
1
Clock
完成时间为 4 小时

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 个视频(共 36 分钟), 2 个阅读材料, 3 个测验
Video8 个视频
FIELD TRIP!4分钟
What Is Genome Sequencing?6分钟
Exploding Newspapers4分钟
The String Reconstruction Problem3分钟
String Reconstruction as a Hamiltonian Path Problem3分钟
String Reconstruction as an Eulerian Path Problem5分钟
Similar Problems with Different Fates 3分钟
Reading2 个阅读材料
Course Details10分钟
Week 1 FAQs (Optional)分钟
Quiz1 个练习
Week 1 Quiz15分钟
Week
2
Clock
完成时间为 3 小时

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 个视频(共 28 分钟), 1 个阅读材料, 3 个测验
Video5 个视频
Euler's Theorem 6分钟
Assembling Read-Pairs 8分钟
De Bruijn Graphs Face Harsh Realities of Assembly 4分钟
Returning to Konigsberg 1分钟
Reading1 个阅读材料
Week 2 FAQs (Optional)分钟
Quiz1 个练习
Week 2 Quiz15分钟
Week
3
Clock
完成时间为 4 小时

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 个视频(共 27 分钟), 1 个阅读材料, 3 个测验
Video5 个视频
How Do Bacteria Make Antibiotics? 8分钟
Sequencing Antibiotics by Shattering Them into Pieces 4分钟
A Brute Force Algorithm for Cyclopeptide Sequencing 3分钟
Cyclopeptide Sequencing with Branch and Bound 6分钟
Reading1 个阅读材料
Week 3 FAQs (Optional)分钟
Quiz1 个练习
Week 3 Quiz15分钟
Week
4
Clock
完成时间为 3 小时

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 个视频(共 18 分钟), 1 个阅读材料, 3 个测验
Video4 个视频
From 20 to More than 100 Amino Acids 2分钟
The Spectral Convolution Saves the Day 6分钟
The Truth About Spectra 2分钟
Reading1 个阅读材料
Week 4 FAQs (Optional)分钟
Quiz1 个练习
Week 4 Quiz15分钟
4.8
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热门审阅

创建者 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.

创建者 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).

讲师

Pavel Pevzner

Professor
Department of Computer Science and Engineering

Phillip Compeau

Visiting Researcher
Department of Computer Science & Engineering

关于 University of California San Diego

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关于 Bioinformatics 专项课程

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

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