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Mikhail Rayko,
Niema Moshiri,
Vikram Sirupurapu,
Sabeel Mansuri,
and
Pavel Pevzner
In this course, you will follow in the footsteps of the bioinformaticians investigating the COVID-19 outbreak by tracing the evolution of SARS-CoV-2. Whether you’re new to the world of computational biology, or you’re a bioinformatics expert seeking to learn about its applications in the COVID-19 pandemic, or somewhere in between, this course is for you! As you go through this journey, we will introduce and explain genomic concepts and give you many opportunities to practice your skills, and we will provide a series of problems with gradually increasing complexity. This fifth course will discuss the "Italy First" hypothesis of COVID-19 origins, and it will cover bioinformatics methods for rooting and dating a phylogenetic tree inferred from SARS-CoV-2 genome sequences.
Register for this course and see more details by visiting:
OpenCourser.com/course/3p1ouf/hacking
What's inside
Syllabus
Week 1
In Chapter 7, we will discuss how we can use rooted and dated phylogenetic trees to study the emergence of a virus, with the origins of COVID-19 as our primary inspiration, but with a real case study about HIV transmission as our focus.
Read more
Syllabus
Week 1
In Chapter 7, we will discuss how we can use rooted and dated phylogenetic trees to study the emergence of a virus, with the origins of COVID-19 as our primary inspiration, but with a real case study about HIV transmission as our focus.
Read more
Week 2
In Chapter 8, we will perform multiple sequence alignment, phylogenetic inference, tree rooting, and tree dating to investigate the "Italy First" hypothesis of COVID-19 origins.
Good to know
Good to know
Know what's good ,
what to watch for , and
possible dealbreakers
Teaches health concepts and methods that are in line with scientific understanding and the advice of the medical community
Covers unique perspectives and ideas that may add color to other topics and subjects
Takes a creative approach to an otherwise established topic, field, or subject
Examines x, which is highly relevant to y
Explores x, which is standard in industry y
Taught by x, who are recognized for their work in x
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Activities
Be better prepared
before
your course. Deepen your understanding
during
and
after
it. Supplement your coursework and achieve mastery of the topics covered
in Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution with these
activities:
Review of Basic Phylogenetic Concepts
Show steps
Refresh your understanding of phylogenetic basics to build a solid foundation for understanding this course's topics.
Browse courses on
Phylogenetics
Show steps
-
Revisit the concepts of sequence alignment and phylogenetic inference.
-
Review different methods of tree construction, such as maximum parsimony, neighbor-joining, and Bayesian inference.
-
Practice building phylogenetic trees using online tools or software.
Recall key genomic concepts
Show steps
Improve recall of key genomic concepts and prepare for more advanced material
Browse courses on
Genomics
Show steps
-
Review notes and materials from previous courses in genomics or molecular biology
-
Complete practice problems or quizzes related to genome structure and function
Review phylogenetic tree concepts
Show steps
Brush up on the basics of phylogenetic tree inference to prepare for more advanced topics
Browse courses on
Phylogenetics
Show steps
-
Read an introductory article or textbook chapter on phylogenetic tree inference
-
Watch a video tutorial on how to construct and interpret phylogenetic trees
11 other activities
Expand to see all activities and additional details
Show all 14 activities
Explore Bioinformatics Databases
Show steps
Familiarize yourself with bioinformatics databases to access and analyze SARS-CoV-2 genome sequences.
Show steps
-
Visit databases such as GenBank, EMBL, or DDBJ and learn how to search for and retrieve sequences.
-
Explore the different data formats and metadata associated with the sequences.
-
Practice downloading and importing sequences for further analysis.
Review Concepts of Phylogenetic Trees
Show steps
Refresh your understanding of the principles and concepts of phylogenetic trees to prepare for the course materials on evolutionary analysis.
Browse courses on
Phylogenetic Trees
Show steps
-
Revisit the basic concepts of phylogenetic trees, including nodes, branches, and leaves.
-
Review the different methods of inferring phylogenetic trees, such as maximum parsimony, neighbor-joining, and Bayesian inference.
-
Explore online resources and tutorials to strengthen your understanding of phylogenetic tree construction.
Multiple Sequence Alignment Practice
Show steps
Regularly practice multiple sequence alignment to improve your proficiency in this crucial skill for phylogenetic analysis.
Browse courses on
Sequence Alignment
Show steps
-
Use online tools or software to align multiple DNA or protein sequences.
-
Evaluate the quality of your alignments using metrics such as coverage and identity.
Multiple Sequence Alignment Exercises
Show steps
Practice multiple sequence alignment to develop the skills necessary for analyzing SARS-CoV-2 genome sequences and constructing phylogenetic trees.
Browse courses on
Multiple Sequence Alignment
Show steps
-
Use online tools such as Clustal Omega or MUSCLE to perform multiple sequence alignments.
-
Analyze the results of the alignments, identify conserved regions, and explore patterns in the sequences.
-
Compare different alignment algorithms and assess their strengths and weaknesses.
Practice multiple sequence alignment
Show steps
Strengthen your skills in performing multiple sequence alignment, which is essential for phylogenetic analysis
Browse courses on
Multiple Sequence Alignment
Show steps
-
Use a multiple sequence alignment tool to align a set of sequences
-
Manually align a small set of sequences to check your understanding
Bioinformatics Tools for Phylogenetic Analysis
Show steps
Expand your knowledge of bioinformatics tools specifically designed for phylogenetic analysis.
Show steps
-
Explore online tutorials and documentation for tools such as MEGA, RAxML, and BEAST.
-
Practice using these tools to perform specific tasks, such as tree building, tree rooting, and molecular clock analysis.
Visualize SARS-CoV-2 Phylogenetic Tree
Show steps
Create a visual representation of the SARS-CoV-2 phylogenetic tree to enhance your understanding of the virus's evolution and spread.
Browse courses on
Data Visualization
Show steps
-
Use software such as FigTree or iTOL to import and visualize the phylogenetic tree.
-
Customize the visualization by adjusting branch lengths, colors, and labels.
-
Annotate the tree with relevant information, such as mutations, sampling locations, and dates.
-
Generate high-quality images or interactive visualizations for presentations or reports.
Explore advanced phylogenetic inference techniques
Show steps
Enhance your understanding of advanced phylogenetic inference techniques, such as Bayesian inference and maximum likelihood
Browse courses on
Phylogenetics
Show steps
-
Find and follow an online tutorial on a specific phylogenetic inference technique
-
Apply the technique to a real-world dataset and interpret the results
-
Compare the results obtained using different techniques
Investigate a SARS-CoV-2 Variant
Show steps
Conduct an in-depth analysis of a specific SARS-CoV-2 variant, exploring its origins, spread, and potential impact.
Show steps
-
Select a SARS-CoV-2 variant of interest and gather relevant data from databases.
-
Analyze the variant's genetic sequence, identify mutations, and compare it to other variants.
-
Investigate the geographical distribution and transmission patterns of the variant.
-
Write a report summarizing your findings and discussing the implications for public health.
Create a Course Summary
Show steps
Organize and summarize the key concepts and materials from the course to enhance your retention and understanding.
Show steps
-
Review your notes, assignments, and other course materials.
-
Identify the main topics and concepts covered in the course.
-
Summarize each topic in a concise and informative manner.
Design a research proposal on COVID-19 origins
Show steps
Apply your knowledge of bioinformatics and phylogenetic analysis to a real-world problem
Browse courses on
Research Proposal
Show steps
-
Define a specific research question related to the origins of COVID-19
-
Develop a hypothesis and design a research plan to test it
-
Identify the bioinformatics tools and methods you will use
-
Write a research proposal outlining your plan and expected outcomes
Review of Basic Phylogenetic Concepts
Show steps
Refresh your understanding of phylogenetic basics to build a solid foundation for understanding this course's topics.
Browse courses on
Phylogenetics
Show steps
Show steps
Show steps
- Revisit the concepts of sequence alignment and phylogenetic inference.
- Review different methods of tree construction, such as maximum parsimony, neighbor-joining, and Bayesian inference.
- Practice building phylogenetic trees using online tools or software.
Recall key genomic concepts
Show steps
Improve recall of key genomic concepts and prepare for more advanced material
Browse courses on
Genomics
Show steps
Show steps
Show steps
- Review notes and materials from previous courses in genomics or molecular biology
- Complete practice problems or quizzes related to genome structure and function
Review phylogenetic tree concepts
Show steps
Brush up on the basics of phylogenetic tree inference to prepare for more advanced topics
Browse courses on
Phylogenetics
Show steps
Show steps
Show steps
- Read an introductory article or textbook chapter on phylogenetic tree inference
- Watch a video tutorial on how to construct and interpret phylogenetic trees
11 other activities
Expand to see all activities and additional details
Show all 14 activities
Explore Bioinformatics Databases
Show steps
Familiarize yourself with bioinformatics databases to access and analyze SARS-CoV-2 genome sequences.
Show steps
Show steps
Show steps
- Visit databases such as GenBank, EMBL, or DDBJ and learn how to search for and retrieve sequences.
- Explore the different data formats and metadata associated with the sequences.
- Practice downloading and importing sequences for further analysis.
Review Concepts of Phylogenetic Trees
Show steps
Refresh your understanding of the principles and concepts of phylogenetic trees to prepare for the course materials on evolutionary analysis.
Browse courses on
Phylogenetic Trees
Show steps
Show steps
Show steps
- Revisit the basic concepts of phylogenetic trees, including nodes, branches, and leaves.
- Review the different methods of inferring phylogenetic trees, such as maximum parsimony, neighbor-joining, and Bayesian inference.
- Explore online resources and tutorials to strengthen your understanding of phylogenetic tree construction.
Multiple Sequence Alignment Practice
Show steps
Regularly practice multiple sequence alignment to improve your proficiency in this crucial skill for phylogenetic analysis.
Browse courses on
Sequence Alignment
Show steps
Show steps
Show steps
- Use online tools or software to align multiple DNA or protein sequences.
- Evaluate the quality of your alignments using metrics such as coverage and identity.
Multiple Sequence Alignment Exercises
Show steps
Practice multiple sequence alignment to develop the skills necessary for analyzing SARS-CoV-2 genome sequences and constructing phylogenetic trees.
Browse courses on
Multiple Sequence Alignment
Show steps
Show steps
Show steps
- Use online tools such as Clustal Omega or MUSCLE to perform multiple sequence alignments.
- Analyze the results of the alignments, identify conserved regions, and explore patterns in the sequences.
- Compare different alignment algorithms and assess their strengths and weaknesses.
Practice multiple sequence alignment
Show steps
Strengthen your skills in performing multiple sequence alignment, which is essential for phylogenetic analysis
Browse courses on
Multiple Sequence Alignment
Show steps
Show steps
Show steps
- Use a multiple sequence alignment tool to align a set of sequences
- Manually align a small set of sequences to check your understanding
Bioinformatics Tools for Phylogenetic Analysis
Show steps
Expand your knowledge of bioinformatics tools specifically designed for phylogenetic analysis.
Show steps
Show steps
Show steps
- Explore online tutorials and documentation for tools such as MEGA, RAxML, and BEAST.
- Practice using these tools to perform specific tasks, such as tree building, tree rooting, and molecular clock analysis.
Visualize SARS-CoV-2 Phylogenetic Tree
Show steps
Create a visual representation of the SARS-CoV-2 phylogenetic tree to enhance your understanding of the virus's evolution and spread.
Browse courses on
Data Visualization
Show steps
Show steps
Show steps
- Use software such as FigTree or iTOL to import and visualize the phylogenetic tree.
- Customize the visualization by adjusting branch lengths, colors, and labels.
- Annotate the tree with relevant information, such as mutations, sampling locations, and dates.
- Generate high-quality images or interactive visualizations for presentations or reports.
Explore advanced phylogenetic inference techniques
Show steps
Enhance your understanding of advanced phylogenetic inference techniques, such as Bayesian inference and maximum likelihood
Browse courses on
Phylogenetics
Show steps
Show steps
Show steps
- Find and follow an online tutorial on a specific phylogenetic inference technique
- Apply the technique to a real-world dataset and interpret the results
- Compare the results obtained using different techniques
Investigate a SARS-CoV-2 Variant
Show steps
Conduct an in-depth analysis of a specific SARS-CoV-2 variant, exploring its origins, spread, and potential impact.
Show steps
Show steps
Show steps
- Select a SARS-CoV-2 variant of interest and gather relevant data from databases.
- Analyze the variant's genetic sequence, identify mutations, and compare it to other variants.
- Investigate the geographical distribution and transmission patterns of the variant.
- Write a report summarizing your findings and discussing the implications for public health.
Create a Course Summary
Show steps
Organize and summarize the key concepts and materials from the course to enhance your retention and understanding.
Show steps
Show steps
Show steps
- Review your notes, assignments, and other course materials.
- Identify the main topics and concepts covered in the course.
- Summarize each topic in a concise and informative manner.
Design a research proposal on COVID-19 origins
Show steps
Apply your knowledge of bioinformatics and phylogenetic analysis to a real-world problem
Browse courses on
Research Proposal
Show steps
Show steps
Show steps
- Define a specific research question related to the origins of COVID-19
- Develop a hypothesis and design a research plan to test it
- Identify the bioinformatics tools and methods you will use
- Write a research proposal outlining your plan and expected outcomes
Career center
Learners who complete Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution will develop knowledge and skills
that may be useful to these careers:
Bioinformatics Analyst
Bioinformatics Analyst
The global COVID-19 pandemic has put bioinformatics at the forefront of the fight against this virus. A Bioinformatics Analyst plays a crucial role in analyzing biological data, including viral genome sequences, to track the evolution and transmission of SARS-CoV-2. The 'Tracing SARS-CoV-2's Evolution' course from the University of California, San Diego, provides a solid foundation in bioinformatics methods, including phylogenetic analysis and tree rooting, which are essential for understanding viral evolution and guiding public health measures.
Epidemiologist
Epidemiologist
Epidemiologists investigate the distribution and patterns of health events, including infectious diseases like COVID-19. The 'Tracing SARS-CoV-2's Evolution' course provides Epidemiologists with valuable insights into the evolution and spread of SARS-CoV-2, helping them develop effective strategies for disease surveillance, outbreak control, and pandemic preparedness.
Computational Biologist
Computational Biologist
The 'Tracing SARS-CoV-2's Evolution' course covers essential bioinformatics techniques such as multiple sequence alignment, phylogenetic inference, and tree rooting, which are fundamental skills for Computational Biologists. This course empowers them to analyze and interpret genomic data, contribute to our understanding of viral evolution, and develop computational tools for virus surveillance and outbreak response.
Research Scientist
Research Scientist
Research Scientists play a vital role in advancing our knowledge of viral evolution, epidemiology, and public health. The 'Tracing SARS-CoV-2's Evolution' course provides Research Scientists with a comprehensive understanding of bioinformatics methods for studying viral genomics, empowering them to conduct cutting-edge research on COVID-19 and other infectious diseases.
Virologist
Virologist
Virologists are experts in the study of viruses, including their structure, replication, and evolution. The 'Tracing SARS-CoV-2's Evolution' course offers valuable insights into the molecular evolution of SARS-CoV-2, enabling Virologists to better understand the virus's behavior, develop antiviral therapies, and contribute to the development of vaccines and diagnostics.
Public Health Analyst
Public Health Analyst
Public Health Analysts play a critical role in protecting and improving the health of communities. The 'Tracing SARS-CoV-2's Evolution' course provides Public Health Analysts with a deeper understanding of the evolution and spread of COVID-19, empowering them to develop data-driven public health policies and interventions to mitigate the impact of the virus.
Data Analyst
Data Analyst
The 'Tracing SARS-CoV-2's Evolution' course equips Data Analysts with specialized skills in handling and analyzing biological data, including genomic sequences. This course provides a strong foundation in bioinformatics, enabling Data Analysts to contribute to research projects, develop predictive models, and support decision-making in the context of viral outbreaks.
Biostatistician
Biostatistician
Biostatisticians apply statistical methods to analyze and interpret biological data. The 'Tracing SARS-CoV-2's Evolution' course provides Biostatisticians with specialized knowledge in phylogenetic analysis and viral evolution, enabling them to contribute to research on COVID-19 epidemiology, vaccine effectiveness, and public health policy.
Biomedical Engineer
Biomedical Engineer
Biomedical Engineers design and develop technologies for healthcare applications. The 'Tracing SARS-CoV-2's Evolution' course provides Biomedical Engineers with a foundation in bioinformatics, enabling them to contribute to the development of diagnostic tools, biosensors, and other technologies for virus detection and monitoring.
Science Writer
Science Writer
Science Writers communicate complex scientific concepts to the public. The 'Tracing SARS-CoV-2's Evolution' course provides Science Writers with a comprehensive understanding of viral evolution and genomics, enabling them to accurately and effectively report on the latest scientific findings and their implications for public health.
Healthcare Consultant
Healthcare Consultant
Healthcare Consultants provide guidance and recommendations to healthcare organizations on various aspects of healthcare delivery. The 'Tracing SARS-CoV-2's Evolution' course may be helpful for Healthcare Consultants who specialize in infectious disease management or pandemic preparedness, as it provides insights into the evolution and spread of COVID-19.
Medical Writer
Medical Writer
Medical Writers create and edit medical and scientific content for various purposes. The 'Tracing SARS-CoV-2's Evolution' course may be useful for Medical Writers who specialize in infectious diseases or virology, as it provides a comprehensive overview of the molecular evolution of SARS-CoV-2.
Patent Attorney
Patent Attorney
Patent Attorneys specialize in the legal aspects of intellectual property, including patents for biotechnology and pharmaceutical inventions. The 'Tracing SARS-CoV-2's Evolution' course may be of interest to Patent Attorneys who handle cases related to viral genomics, diagnostics, or therapeutics.
Science Teacher
Science Teacher
Science Teachers educate students about scientific concepts and principles. While the 'Tracing SARS-CoV-2's Evolution' course is not directly related to K-12 science education, it may be of interest to Science Teachers who wish to incorporate current events and real-world examples into their lessons on genetics, evolution, or public health.
Science Policy Advisor
Science Policy Advisor
Science Policy Advisors provide scientific expertise to policymakers and government agencies. The 'Tracing SARS-CoV-2's Evolution' course may be useful for Science Policy Advisors who work on issues related to pandemic preparedness, vaccine development, or global health.
For more career information including salaries, visit:
OpenCourser.com/course/3p1ouf/hacking
Reading list
We've selected 15 books
that we think will supplement your
learning. Use these to
develop background knowledge, enrich your coursework, and gain a
deeper understanding of the topics covered in
Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution.
Provides an overview of algorithms used in computational molecular biology, including topics such as sequence alignment, gene finding, and genome assembly.
Save
Provides a comprehensive overview of the COVID-19 pandemic including prevention, treatment, and end.
Save
Provides a comprehensive overview of bioinformatics, covering topics such as sequence analysis, gene expression analysis, and proteomics.
Provides a clear and concise introduction to the basics of phylogenetic tree construction. The book covers a wide range of topics, including data collection, tree-building methods, and tree evaluation.
This serves as an introduction to phylogenetic methods with a focus on evolutionary trees.
Save
Provides a passionate and convincing argument for the theory of evolution, providing a foundational knowledge of evolutionary theory as it relates to the course.
Shows what can happen when diseases pass from animals to humans, further supporting the course's key message.
Save
Offers a detailed look at the origins of HIV/AIDS, tracing the virus from its origins in Africa to its devastating global impact.
Save
This textbook provides a comprehensive overview of all aspects of virology, from the structure and function of viruses to viral pathogenesis and immunity. The book includes a wealth of illustrations, diagrams, and tables. It can be used as a textbook for advanced undergraduate and graduate students, as well as a reference book for researchers in the field of virology.
Save
Provides an accessible introduction to the concept of evolution, covering the basics that listeners are likely to need to know to complete the course successfully.
Save
Is about the evolution of the human body through the lens of evolutionary history, providing more context for the course's topic of tracing the evolution of SARS-CoV-2.
Can be used to provide foundational knowledge to those who are completely new to the course's topic.
Save
Gives more general background knowledge to the course topic.
Save
Conveys the basic concepts of bioinformatics as well as provides a practical guide to understanding, analyzing, and interpreting bioinformatics data.
Provides a very broad overview of the history of extinctions on Earth and the current threats to biodiversity.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/3p1ouf/hacking
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Level
Introductory
Via
Coursera
Institution
University of California San Diego
Instructors
Mikhail Rayko
Niema Moshiri
Vikram Sirupurapu
Sabeel Mansuri
Pavel Pevzner
Language
English
This course belongs to a
collection
called
Applied Bioinformatics. It's comprised of five courses:
- Hacking COVID-19 — Course 1: Identifying a Deadly Pathogen
- Hacking COVID-19 — Course 5: Tracing SARS-CoV-2's Evolution (viewing)
- Hacking COVID-19 — Course 2: Decoding SARS-CoV-2's Secrets
- Hacking COVID-19 — Course 3: Unraveling COVID-19's Origins
- Hacking COVID-19: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets
Good to know
Teaches health concepts and methods that are in line with scientific understanding and the advice of the medical community
Covers unique perspectives and ideas that may add color to other topics and subjects
Takes a creative approach to an otherwise established topic, field, or subject
Examines x, which is highly relevant to y
Explores x, which is standard in industry y
Taught by x, who are recognized for their work in x
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