Genomics: Decoding the Universal Language of Life

About this course: What is a genome? A genome contains all of the information that a cell needs to develop, function, and reproduce itself, and all the information needed for those cells to come together to form a person, plant, or animal. Genomes contain an organism’s complete set of genes, and also the even tinier genetic structures that help regulate when and how those genes are used. The ability to regrow a torn ligament, the clues that might predict the onset of mental illness, the nutritional potential of crops, and even the history of life itself, are all encoded in genomes. By taking this course, you will discover how scientists are deciphering the language of genomes to learn how to develop sustainable food and fuel supplies, improve disease treatment and prevention, and protect our environment. Professor Robinson is the main instructor for this course. In addition, each module features several guest instructors. These guest instructors come from diverse fields of study—biology, physics, computer science, and many others—and pursue diverse research goals, yet they share a common interest in genomic approaches and technologies. The guest instructors include: - Elizabeth (Lisa) Ainsworth, Associate Professor of Plant Biology - Mark Band, Director of the Functional Genomics Facility - Alison Bell, Associate Professor of Animal Biology - Jenny Drnevich, Functional Genomics Bioinformatics Specialist with High-Performance Biological Computing - Christopher Fields, Associate Director of High-Performance Biological Computing - Bruce Fouke, Director of the Roy J. Carver Biotechnology Center - Glenn Fried, Director of the Carl R. Woese Institute for Genomic Biology Core Facilities - Nigel Goldenfeld, Professor of Physics - Brendan Harley, Assistant Professor of Chemical and Biomolecular Engineering - Alvaro Hernandez, Director of the High-Throughput Sequencing and Genotyping Facility - Victor Jongeneel, former NCSA Director of Bioinformatics and former Director of High-Performance Biological Computing - Kingsley Boateng, Senior Research Specialist with the Carl R. Woese Institute for Genomic Biology Core Facilities - Stephen Long, Professor of Plant Biology and Crop Sciences - Ruby Mendenhall, Associate Professor of African American Studies - William Metcalf, Professor of Microbiology - Karen Sears, Assistant Professor of Animal Biology - Saurabh Sinha, Associate Professor of Computer Science - Lisa Stubbs, Professor of Cell and Developmental Biology - Rachel Whitaker, Associate Professor of Microbiology - Derek Wildman, Professor of Molecular and Integrative Physiology - Peter Yau, Director of the Protein Sciences Facility

Who is this class for: If you are curious about how genes work, why microbes are the masters of the chemical world, when we will be able to use DNA sequencing to predict disease risk, or what makes genetically modified plants different from their relatives, this course is right for you.

Created by:  University of Illinois at Urbana-Champaign

• Taught by:  Gene E. Robinson, Director, Carl R. Woese Institute for Genomic Biology; Swanlund Chair; Center for Advanced Study Professor of Entomology and Neuroscience

Level Beginner Commitment 6 weeks of study; 6-8 hours/week Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.5 stars Average User Rating 4.5See what learners said Coursework

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

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University of Illinois at Urbana-Champaign The University of Illinois at Urbana-Champaign is a world leader in research, teaching and public engagement, distinguished by the breadth of its programs, broad academic excellence, and internationally renowned faculty and alumni. Illinois serves the world by creating knowledge, preparing students for lives of impact, and finding solutions to critical societal needs.

Syllabus


WEEK 1


Course Orientation
You will become familiar with the course, your classmates, and our learning environment. The orientation will also help you obtain the technical skills required for the course.


2 videos, 4 readings, 2 practice quizzes expand

1. Video: Welcome to Genomics: Decoding the Universal Language of Life! (Course Overview)
2. Video: What Is Genomics?
3. Reading: Syllabus
4. Reading: About the Discussion Forums
5. Practice Quiz: Orientation Quiz
6. Practice Quiz: Demographics Survey
7. Reading: Updating Your Profile
8. Discussion Prompt: Getting to Know Your Classmates
9. Reading: Social Media

What Is a Genome and Why Do We Care?



Genes, genomes, DNA: these words have slipped into our daily news cycles and our awareness, but what they actually mean often remains unclear. In these lessons, we aim to give you, not just the Biology 101 explanation of what a genome is, but a real-life perspective on why you already care about genomics – perhaps in ways you didn’t even realize. Are you interested in where your food comes from, what health conditions you are most likely to develop, what fish will share your aquarium most successfully? Genomes are a key to finding a better answer to these and other everyday questions.


11 videos, 2 practice quizzes expand

1. Video: Module 1 Overview
2. Video: The Book of Life
3. Video: Two Flavors of Research: Exploration and Application
4. Video: What Is Genomics Good For?
5. Practice Quiz: All Roads Lead through Genomics
6. Video: Reverse-Engineering the Machinery of Life
7. Video: Basic Components of Life
8. Video: What Is Life?
9. Video: Why Does Life Exist?
10. Video: How Do We Recognize Life?
11. Practice Quiz: Life: Here and There, Now and Then
12. Video: Analyzing Living Cells
13. Video: Module 1 Conclusion
14. Discussion Prompt: Week 1 Discussion

Graded: Week 1 Quiz
Graded: Week 1 Graded Discussion Activity
Graded: Week 1 Honors Assignment

WEEK 2


What Were the First Genomes Like and How Do They Work Now?



You may have seen DNA visually represented in different ways: a twisted ladder, a tangle of string, an array of sloppy X shapes, a row of letters. But what is DNA actually doing, and how does it relate to genes and the genome? How are scientists able to move from studying the physical structure of the genome to understanding its functionality? This module will help you become more comfortable with these ideas.


11 videos, 2 practice quizzes expand

1. Video: Module 2 Overview
2. Video: Understanding Complex Systems
3. Video: What Is DNA?
4. Video: What Is a Genome?
5. Video: The Grammar of Genomes
6. Practice Quiz: Genome Nuts and Bolts
7. Video: How Do We Read Genomes?
8. Video: Genomics and Computing: P2P
9. Practice Quiz: Genome Sequencing
10. Video: High-Performance Biological Computing
11. Video: Equalizing Access to Genomics of Health
12. Video: Challenges in Supercomputing (Optional)
13. Video: Module 2 Conclusion
14. Discussion Prompt: Week 2 Discussion

Graded: Week 2 Quiz
Graded: Week 2 Graded Discussion Activity
Graded: Week 2 Honors Assignment

WEEK 3


How Can We Use Genomes to Understand the Healthy Body and Fight Diseases?



Often, we hear about genes only when something goes wrong – when mutations, mistakes made in the DNA sequence, cause a disease like cancer cystic fibrosis. But what happens inside our cells that leads from a mutation in DNA to the physical symptoms of a disease? Why do some mutations cause positive outcomes, or no change at all? To answer these questions, we take a closer look at how information flows from genes, to RNA, to proteins, to all the physical structures and processes that make up living things.


14 videos, 3 practice quizzes expand

1. Video: Module 3 Overview
2. Video: Biology's Big Two
3. Video: The Gene to Protein Pipeline
4. Video: What Do Proteins Do, and How?
5. Video: How Do Proteins Evolve?
6. Video: Horizontal Gene Transfer: Caring About DNA Sharing
7. Practice Quiz: The Central Dogma
8. Video: Why Do We Study Microbes?
9. Video: Antibiotics and the Microbial Arms Race
10. Practice Quiz: Microbes and Drug Resistance
11. Video: The Revolution of Protein Science
12. Video: The Protein Science Facility at the CBC
13. Video: Complexity from Simplicity
14. Video: Pathways to Understanding the Mind
15. Video: Mapping the Genomic Landscape
16. Practice Quiz: Gene Interactions
17. Video: Module 3 Conclusion
18. Discussion Prompt: Week 3 Discussion

Graded: Week 3 Quiz
Graded: Week 3 Graded Discussion Activity
Graded: Week 3 Honors Assignment

WEEK 4


What Can Genomes Tell Us About How to Grow New Organs or New Crops?



If all the cells in all the tissues and organs of our bodies have the same genome, how is it that they can look so different? How does a hair cell, a white blood cell, or a brain cell know what to do or where to go? The answer can be found by looking beyond the structure of the genome, into the timing of its activities. Recognizing how the information stored in the genome can be used in flexible ways shows us how living things can develop and change over time.


13 videos, 4 practice quizzes expand

1. Video: Module 4 Overview
2. Video: Changing the Nature of Medicine
3. Video: The Identity Crisis of Newborn Cells
4. Video: Biomaterials & Human Health
5. Practice Quiz: Guiding Tissue Growth
6. Video: Why Study Development in Mammals?
7. Video: Studying Limb Development: Four Thumbs Up?
8. Video: The Who, Where, and When of Genes in Development
9. Practice Quiz: Endless Forms
10. Video: Adaptation & Evolution
11. Video: What Is a Genetically Modified Organism?
12. Video: Ozone and Plant Health
13. Video: Preparing Crops for Climate Change
14. Practice Quiz: Adapting to Change
15. Video: Fear of GMOs
16. Practice Quiz: Concerns About GMOs
17. Video: Module 4 Conclusion
18. Discussion Prompt: Week 4 Discussion

Graded: Week 4 Quiz
Graded: Week 4 Graded Discussion Activity
Graded: Week 4 Honors Assignment

WEEK 5


How Might Genomes Allow Us to Predict Health Problems Before They Occur?



You may have heard of "nature vs. nurture" or the modern day response, "nature AND nurture!" But how does "nurture," the environment, act through the genome? Can the biological effects of experience be passed from one generation to the next? And what does all of this have to do with everyday issues, like our physical and mental health? A closer look at two mechanisms that help regulate the activity for genes, epigenetic modifications and transcription factors, provides some answers.


16 videos, 3 practice quizzes expand

1. Video: Module 5 Overview
2. Video: The Dynamic Genome
3. Video: Experience across Generations
4. Video: Health: This Time, It's Personal
5. Video: The Proper Study of Humankind
6. Video: Predicting Problems in Pregnancy
7. Practice Quiz: Marks of Experience
8. Video: Reading the Blueprint of Life
9. Video: The Hierarchy of Genes
10. Video: Gene Regulation & Social Behavior
11. Video: Mapping the Punctuation of the Genome
12. Practice Quiz: Parsing Gene Regulation
13. Video: DNA Services Facility
14. Video: Variety: The Spice of Life
15. Video: Behavioral Syndromes
16. Video: Lamarck in the 21st Century
17. Video: Genes, Brains, and Social Behavior
18. Practice Quiz: Animal Personalities
19. Video: Module 5 Conclusion
20. Discussion Prompt: Week 5 Discussion

Graded: Week 5 Quiz
Graded: Week 5 Graded Discussion Activity
Graded: Week 5 Honors Assignment

WEEK 6


How Do the Genomes of Ecosystem Members Cooperate or Conflict?



The world is a big and sometimes incomprehensibly complex place. Just as no gene in the genome acts in isolation, no living thing on this planet exists in isolation. In this final module of the course, we explore some of the rich, complicated interactions between living things, their genomes, and the world that surrounds them.


10 videos, 4 practice quizzes expand

1. Video: Module 6 Overview
2. Video: Microbial Diversity: Worlds within Worlds
3. Video: Microbial Love and War
4. Video: Ecosystems of the Human Body
5. Practice Quiz: Microscopic Worlds
6. Video: What Are We Eating Tomorrow?
7. Video: The Second Green Revolution
8. Practice Quiz: Rethinking Photosynthesis
9. Video: Supporting Genomic Research
10. Video: Challenges to Community Health
11. Video: Dreams of a Better World
12. Practice Quiz: Science and Society
13. Video: Module 6 Conclusion
14. Discussion Prompt: Week 6 Discussion
15. Discussion Prompt: Final Reflections
16. Practice Quiz: End of Course Survey

Graded: Week 6 Quiz
Graded: Week 6 Graded Discussion Activity
Graded: Week 6 Honors Assignment