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所在平台: Coursera |
课程主页: https://www.coursera.org/learn/genome-sequencing
课程评论：没有评论
课程名称：基因组测序（生物信息学 II） 课程概述：您可能听说过基因组测序及其在个性化医学中的潜力，但基因组测序到底意味着什么呢？生物学家目前无法像阅读一本书那样逐字逐句阅读整个基因组的核苷酸，但他们可以读取较短的DNA片段。在本课程中，我们将探讨如何利用图论将这些短片段组装成完整的基因组。此外，我们还会学习蛮力算法，并将其应用于测序一种称为抗生素的小型蛋白质。 课程的前半部分将介绍生物学家无法像阅读书籍那样逐步读取一个人类基因组的30亿个核苷酸，但可以读取较短的DNA片段。我们将通过图论的应用来阐释如何将这些短片段组装成一个最大的拼图。 课程后半部分将讨论抗生素，这一主题正变得尤为重要，因为耐药细菌（如MRSA）正在增加。抗生素是药物，但在分子水平上它们是由细菌工程化制造的小型蛋白质，用于消灭其敌人。确定构成这些抗生素的氨基酸序列是一个重要的研究问题，与组装基因组的工作类似。我们将看到蛮力算法如何尝试每一种可能的解决方案，从而识别自然存在的抗生素，以便能够在实验室中进行合成。 最后，您将学习如何使用流行的生物信息学软件工具来测序一种已获得耐药性的致死性金黄色葡萄球菌的基因组。 课程大纲： - 第一周：基因组测序简介 - 内容：本课程将关注现代计算生物学的两个前沿问题，以及我们将使用的算法方法。 - 第二周：应用欧拉定理组装基因组 - 内容：了解如何利用300年前的数学定理，从数百万个小DNA片段中组装基因组。 - 第三周：抗生素测序 - 内容：学习如何运用蛮力算法确定构成抗生素的氨基酸序列。 - 第四周：从理想到实际的抗生素测序光谱 - 内容：开发更复杂的算法，处理含有许多错误和缺失质量的光谱进行抗生素肽测序。 - 第五周：生物信息学应用挑战！ - 内容：应用基因组组装工具处理危险病原菌的测序数据。 通过本课程的学习，您将获得关于基因组测序与抗生素测序的深刻理解，并掌握相应的生物信息学分析工具。
Name:Week 1: Introduction to Genome Sequencing
Description:
Welcome to class!
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:
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 print companion. 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!
Name:Week 2: Applying Euler's Theorem to Assemble Genomes
Description:
Welcome to Week 2 of class!
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.
Name:Week 3: Sequencing Antibiotics
Description:
Welcome to Week 3 of class!
This week, we begin a new chapter, titled "How Do We Sequence Antibiotics?" In this chapter, we will learn how to determine the amino acid sequences making up antibiotics using brute force algorithms.
Below is this week's Bioinformatics Cartoon.
Name:Week 4: From Ideal to Real Spectra for Antibiotics Sequencing
Description:
Welcome to Week 4 of class!
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.
Name:Week 5: Bioinformatics Application Challenge!
Description: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.
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.
