Genome Sequencing (Bioinformatics II)

Go to Course: https://www.coursera.org/learn/genome-sequencing

Introduction

# Course Review: Genome Sequencing (Bioinformatics II) on Coursera If you're curious about the fascinating world of genome sequencing and how it paves the way for personalized medicine, the "Genome Sequencing (Bioinformatics II)" course on Coursera offers an exciting journey into this critical area of bioinformatics. This course aims to bridge the gap between theoretical knowledge and practical application, pulling back the curtain on the complexities involved in assembling genomes and sequencing antibiotics. ## Course Overview The primary objective of this course is to impart a robust understanding of two essential questions in modern computational biology: 1. **How do we assemble genomes using graph algorithms?** 2. **How do we sequence antibiotics using brute force algorithms?** The course’s unique approach combines visual aids—namely whimsical Bioinformatics Cartoons by the talented San Diego artist Randall Christopher—with potent algorithmic techniques to elucidate complex concepts. ### Syllabus Breakdown #### Week 1: Introduction to Genome Sequencing The course kicks off with a warm welcome, introducing students to the intricacies of genome sequencing and setting the stage for deeper exploration. The playful cartoons establish an engaging narrative, while the overview includes foundational concepts necessary for genome assembly. #### Week 2: Applying Euler's Theorem to Assemble Genomes Building on geometrical and mathematical principles, this week reveals how a 300-year-old theorem can facilitate the assembly of genomes from millions of DNA fragments. This is an excellent illustration of how historical knowledge can converge with cutting-edge technology. #### Week 3: Sequencing Antibiotics Venturing into antibiotic sequencing, students are introduced to brute force algorithms for determining the amino acid sequences of antibiotics. This week emphasizes the practical applications of the theoretical knowledge from previous lessons. #### Week 4: From Ideal to Real Spectra for Antibiotics Sequencing In this week, the focus shifts to the development of sophisticated algorithms that manage real-world challenges, such as spectra containing false or missing masses. It is a crucial lesson in adapting theoretical approaches to handle the unpredictableness of biological data. #### Week 5: Bioinformatics Application Challenge! The final week culminates in a real-world application challenge where students can apply what they've learned to analyze sequencing data from a dangerous pathogenic bacterium. This not only reinforces knowledge but also provides valuable experience relevant to current scientific challenges. ## What Makes This Course Stand Out - **Engaging Content:** The combination of cartoons and in-depth discussions allows complex topics to be more digestible, keeping students engaged and, importantly, entertained. - **Practical Applications:** Emphasizing real-world applications encourages learners to think critically about how bioinformatics can be used in health and disease management, particularly antibiotics—a hot topic in today's biological sciences. - **Multi-disciplinary Approach:** The course covers graph theory and brute force algorithms, showcasing the interplay between mathematics and biology in solving real-world problems. ## Recommendation Whether you are a student pursuing a career in bioinformatics, a researcher looking to expand your knowledge, or simply someone fascinated by the potential of genomics, the "Genome Sequencing (Bioinformatics II)" course is highly recommended. The skilled instructors guide you through the course with clarity and enthusiasm, fostering a supportive learning environment that encourages intellectual curiosity. A solid understanding of biology and basic programming concepts will undoubtedly enrich your experience, but even beginners can find value in the content provided. By enrolling in this course, you not only acquire knowledge about sequencing but also contribute to a deeper understanding of the vast potentials of personalized medicine. Embark on this educational journey to unravel the mysteries of genome sequencing and be part of a field that holds immense promise for the future of healthcare!

Syllabus

Week 1: Introduction to Genome Sequencing

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:

1. Weeks 1-2: How Do We Assemble Genomes? (Graph Algorithms)
2. How Do We Sequence Antibiotics? (Brute Force Algorithms)

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!

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.

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.

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.

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.