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Niema Moshiri,
Mikhail Rayko,
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 investigating the origins 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 third course will only discuss the multiple sequence alignment and maximum-likelihood phylogenetic inference of SARS-CoV-2 genomes, but future courses in this series will explore follow-up bioinformatics analyses used in the COVID-19 pandemic.
Register for this course and see more details by visiting:
OpenCourser.com/course/f0dnoy/hacking
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What's inside
Syllabus
Week 1
In Chapter 5, we will use sequence alignment to explore the "Artificial Origin Hypothesis" about the origin of SARS-CoV-2.
Week 2
In Chapter 6, we will use phylogenetics to explore the "Direct Zoonotic Transfer" and "Intermediate Host" hypotheses about the origin of SARS-CoV-2.
Read more
Syllabus
Week 1
In Chapter 5, we will use sequence alignment to explore the "Artificial Origin Hypothesis" about the origin of SARS-CoV-2.
Week 2
In Chapter 6, we will use phylogenetics to explore the "Direct Zoonotic Transfer" and "Intermediate Host" hypotheses about the origin of SARS-CoV-2.
Read more
Traffic lights
Traffic lights
Read about what's good
what should give you pause and
possible dealbreakers
Investigates the origins of SARS-CoV-2
Explores genomic concepts
Suitable for beginners in computational biology
Provides opportunities for skill practice
Taught by bioinformatics experts at UC San Diego
Part of a series of courses on COVID-19 bioinformatics
Save this course
Create your own learning path.
Save this course to your list so you can find it easily later.
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Reviews summary
Bioinformatics on covid-19 origins
According to learners, this course provides an incredibly clear and engaging exploration of SARS-CoV-2 origins, particularly for those new to serious bioinformatics applications or keen on specific epidemiological questions. Students found the lectures well-structured and easy to follow, appreciating how problems increased in complexity gradually. It is highly praised for successfully bridging theoretical bioinformatics with critical real-world applications in public health crises. While overwhelmingly positive, a few learners noted some advanced phylogenetic concepts felt a bit rushed or that the course assumes a certain level of prior biological knowledge, which might challenge those from a purely computational background. Overall, it's considered a valuable and brilliant course for understanding viral origin tracing methods.
Problems increase in complexity gradually, aiding confidence building.
"The problems increased in complexity gradually, which was perfect for building confidence."
"I appreciated the logical progression from alignment to phylogenetics."
"The exercises reinforced the theoretical concepts well, building up skills progressively."
Effectively bridges theory and real-world application in epidemiological questions.
"...filled a significant gap in my understanding of how these techniques are applied to real-world epidemiological questions."
"It successfully bridges the gap between theoretical bioinformatics and its critical application in public health crises."
"I gained valuable insights into the methods used to trace viral origins, which reinforced theoretical concepts well."
Lectures are well-organized and easy to follow, making complex topics accessible.
"This course provided an incredibly clear and engaging exploration of SARS-CoV-2 origins. The lectures on sequence alignment and phylogenetics were well-structured and easy to follow..."
"The instructors did a good job of breaking down complex concepts."
"The clarity of the lectures and the practical problems were outstanding."
Some wished for more diverse or challenging real-world datasets.
"My only minor critique is that I wished there were more real-world datasets to work with, beyond just the core examples."
"I felt some parts could be more challenging, but overall, it delivers on its promise."
"I would have liked to see a broader range of problem sets to deepen my skills further."
Course pacing and content assume some prior biological or computational background.
"...I found some parts a bit rushed, especially the more advanced phylogenetic concepts."
"It assumes a certain level of prior biological knowledge, which wasn't always explicitly stated."
"For someone coming from a purely computational background, some of the biological context was hard to grasp quickly."
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 3: Unraveling COVID-19's Origins with these
activities:
Review Basic Biology
Show steps
A basic understanding of biology will help you understand the origin of SARS-CoV-2.
Browse courses on
Biology
Show steps
-
Review your notes from high school or college biology classes.
-
Read a basic biology textbook.
Read 'Virus Taxonomy: Classification and Nomenclature of Viruses'
Show steps
This book provides a comprehensive overview of the taxonomy of viruses, including SARS-CoV-2.
View
Virus Taxonomy, Deluxe Edition with Online...
on Amazon
Show steps
-
Read the chapters on the taxonomy of coronaviruses.
-
Read the chapter on the nomenclature of SARS-CoV-2.
Follow Tutorials on Bioinformatics Tools
Show steps
There are many online tutorials that can help you learn how to use bioinformatics tools.
Show steps
-
Find tutorials on multiple sequence alignment.
-
Find tutorials on phylogenetic inference.
-
Follow the tutorials and complete the exercises.
Six other activities
Expand to see all activities and additional details
Show all nine activities
Practice Sequence Alignment
Show steps
Practice aligning SARS-CoV-2 sequences to improve your understanding of sequence alignment techniques.
Browse courses on
Sequence Alignment
Show steps
-
Gather SARS-CoV-2 sequences from a public database.
-
Choose a sequence alignment tool and align the sequences.
-
Analyze the alignment results and identify conserved regions.
Practice Multiple Sequence Alignment
Show steps
Multiple sequence alignment is a fundamental skill in bioinformatics, and practicing it will help you understand the origin of SARS-CoV-2.
Browse courses on
Multiple Sequence Alignment
Show steps
-
Read the chapter on multiple sequence alignment in the course textbook.
-
Complete the practice exercises provided in the textbook.
-
Find additional practice exercises online or in other textbooks.
Practice Phylogenetic Inference
Show steps
Phylogenetic inference is a powerful tool for understanding the evolutionary history of SARS-CoV-2.
Show steps
-
Read the chapter on phylogenetic inference in the course textbook.
-
Complete the practice exercises provided in the textbook.
-
Find additional practice exercises online or in other textbooks.
Introduction to Maximum-Likelihood Phylogenetic Inference
Show steps
Enhance your understanding of phylogenetic inference methods used to study the evolution of SARS-CoV-2.
Show steps
-
Find online tutorials on maximum-likelihood phylogenetic inference.
-
Follow the tutorials to build a phylogenetic tree using SARS-CoV-2 sequences.
-
Interpret the tree and discuss the evolutionary relationships among SARS-CoV-2 strains.
Create a Phylogenetic Tree
Show steps
Creating a phylogenetic tree is a great way to visualize the evolutionary history of SARS-CoV-2.
Browse courses on
Phylogenetics
Show steps
-
Choose a dataset of SARS-CoV-2 genomes.
-
Align the genomes using a multiple sequence aligner.
-
Build a phylogenetic tree using a phylogenetic inference program.
-
Visualize the phylogenetic tree.
Create a Visual Summary of SARS-CoV-2 Evolution
Show steps
Reinforce your understanding of SARS-CoV-2 evolution by creating a visual summary of the phylogenetic analysis.
Browse courses on
Phylogenetic Analysis
Show steps
-
Gather data on SARS-CoV-2 evolution from scientific literature.
-
Choose a data visualization tool and create a visual representation of the data.
-
Share your visualization with others and discuss the implications of the findings.
Review Basic Biology
Show steps
A basic understanding of biology will help you understand the origin of SARS-CoV-2.
Browse courses on
Biology
Show steps
Show steps
Show steps
- Review your notes from high school or college biology classes.
- Read a basic biology textbook.
Read 'Virus Taxonomy: Classification and Nomenclature of Viruses'
Show steps
This book provides a comprehensive overview of the taxonomy of viruses, including SARS-CoV-2.
View
Virus Taxonomy, Deluxe Edition with Online...
on Amazon
Show steps
Show steps
Show steps
- Read the chapters on the taxonomy of coronaviruses.
- Read the chapter on the nomenclature of SARS-CoV-2.
Follow Tutorials on Bioinformatics Tools
Show steps
There are many online tutorials that can help you learn how to use bioinformatics tools.
Show steps
Show steps
Show steps
- Find tutorials on multiple sequence alignment.
- Find tutorials on phylogenetic inference.
- Follow the tutorials and complete the exercises.
Six other activities
Expand to see all activities and additional details
Show all nine activities
Practice Sequence Alignment
Show steps
Practice aligning SARS-CoV-2 sequences to improve your understanding of sequence alignment techniques.
Browse courses on
Sequence Alignment
Show steps
Show steps
Show steps
- Gather SARS-CoV-2 sequences from a public database.
- Choose a sequence alignment tool and align the sequences.
- Analyze the alignment results and identify conserved regions.
Practice Multiple Sequence Alignment
Show steps
Multiple sequence alignment is a fundamental skill in bioinformatics, and practicing it will help you understand the origin of SARS-CoV-2.
Browse courses on
Multiple Sequence Alignment
Show steps
Show steps
Show steps
- Read the chapter on multiple sequence alignment in the course textbook.
- Complete the practice exercises provided in the textbook.
- Find additional practice exercises online or in other textbooks.
Practice Phylogenetic Inference
Show steps
Phylogenetic inference is a powerful tool for understanding the evolutionary history of SARS-CoV-2.
Show steps
Show steps
Show steps
- Read the chapter on phylogenetic inference in the course textbook.
- Complete the practice exercises provided in the textbook.
- Find additional practice exercises online or in other textbooks.
Introduction to Maximum-Likelihood Phylogenetic Inference
Show steps
Enhance your understanding of phylogenetic inference methods used to study the evolution of SARS-CoV-2.
Show steps
Show steps
Show steps
- Find online tutorials on maximum-likelihood phylogenetic inference.
- Follow the tutorials to build a phylogenetic tree using SARS-CoV-2 sequences.
- Interpret the tree and discuss the evolutionary relationships among SARS-CoV-2 strains.
Create a Phylogenetic Tree
Show steps
Creating a phylogenetic tree is a great way to visualize the evolutionary history of SARS-CoV-2.
Browse courses on
Phylogenetics
Show steps
Show steps
Show steps
- Choose a dataset of SARS-CoV-2 genomes.
- Align the genomes using a multiple sequence aligner.
- Build a phylogenetic tree using a phylogenetic inference program.
- Visualize the phylogenetic tree.
Create a Visual Summary of SARS-CoV-2 Evolution
Show steps
Reinforce your understanding of SARS-CoV-2 evolution by creating a visual summary of the phylogenetic analysis.
Browse courses on
Phylogenetic Analysis
Show steps
Show steps
Show steps
- Gather data on SARS-CoV-2 evolution from scientific literature.
- Choose a data visualization tool and create a visual representation of the data.
- Share your visualization with others and discuss the implications of the findings.
Career center
Learners who complete Hacking COVID-19 — Course 3: Unraveling COVID-19's Origins will develop knowledge and skills
that may be useful to these careers:
Computational Biologist
Computational Biologist
A Computational Biologist researches biological systems using computational methods, such as data analysis and mathematical modeling. This course may help build a foundation for this career by giving learners experience with genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, all of which are essential skills for a Computational Biologist.
Bioinformatician
Bioinformatician
A Bioinformatician uses computational tools to analyze biological data. This course may help build a foundation for this career by providing learners with experience in essential bioinformatics skills, such as genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference.
Epidemiologist
Epidemiologist
An Epidemiologist investigates the causes and spread of diseases. This course may be useful for an Epidemiologist by providing experience with phylogenetic inference, which is a technique used to study the evolution and spread of diseases.
Microbiologist
Microbiologist
A Microbiologist studies microorganisms, such as bacteria and viruses. This course may be useful for a Microbiologist by providing experience with genomic concepts and phylogenetic inference, which are techniques used to study the evolution and diversity of microorganisms.
Virologist
Virologist
A Virologist studies viruses. This course may be useful for a Virologist by providing experience with genomic concepts and phylogenetic inference, which are techniques used to study the evolution and diversity of viruses.
Physician-Scientist
Physician-Scientist
A Physician-Scientist is a medical doctor who also conducts research. This course may be useful for a Physician-Scientist by providing experience with bioinformatics techniques, such as genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to study the genetic basis of diseases.
Data Scientist
Data Scientist
A Data Scientist uses data to solve problems. This course may be useful for a Data Scientist by providing experience with data analysis techniques, such as genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to analyze large datasets.
Software Engineer
Software Engineer
A Software Engineer designs, develops, and maintains software systems. This course may be useful for a Software Engineer by providing experience with data analysis techniques, such as genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to develop software for the healthcare industry.
Science Writer
Science Writer
A Science Writer communicates complex scientific information to a general audience. This course may be useful for a Science Writer by providing experience with genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to explain complex scientific concepts to a general audience.
Teacher
Teacher
A Teacher educates students at all levels. This course may be useful for a Teacher by providing experience with genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to teach students about biology and the scientific process.
Policy Analyst
Policy Analyst
A Policy Analyst develops and analyzes policies. This course may be useful for a Policy Analyst by providing experience with data analysis techniques, such as genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to analyze the impact of policies on public health.
Science Communicator
Science Communicator
A Science Communicator translates complex scientific information into language that the public can understand. This course may be useful for a Science Communicator by providing experience with genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to explain complex scientific concepts to the public.
Healthcare Consultant
Healthcare Consultant
A Healthcare Consultant helps healthcare organizations improve their performance. This course may be useful for a Healthcare Consultant by providing experience with data analysis techniques, such as genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to analyze healthcare data and identify areas for improvement.
Medical Writer
Medical Writer
A Medical Writer creates written content for the healthcare industry. This course may be useful for a Medical Writer by providing experience with genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to write about complex scientific topics for a variety of audiences.
Patent Attorney
Patent Attorney
A Patent Attorney helps clients obtain and protect patents. This course may be useful for a Patent Attorney by providing experience with genomic concepts, multiple sequence alignment, and maximum-likelihood phylogenetic inference, which can be used to understand the technical aspects of patents in the healthcare industry.
For more career information including salaries, visit:
OpenCourser.com/course/f0dnoy/hacking
Reading list
We've selected 11 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 3: Unraveling COVID-19's Origins.
This practical guide provides a comprehensive overview of bioinformatics tools and techniques. It covers topics such as sequence analysis, gene expression analysis, and protein structure prediction.
This textbook provides a comprehensive overview of sequence analysis methods. It covers topics such as sequence alignment, phylogenetic analysis, and gene expression analysis.
This textbook provides a comprehensive overview of phylogenetic analysis methods. It covers topics such as tree reconstruction, model selection, and hypothesis testing.
Save
This popular science book provides a comprehensive overview of human evolution. It covers topics such as human origins, the development of language, and the evolution of culture.
Save
This popular science book provides a strong argument for the theory of evolution. It covers topics such as the fossil record, the genetic code, and the evolution of the human brain.
Save
This popular science book provides a comprehensive overview of the evolution of the human body. It covers topics such as the origin of life, the development of vertebrates, and the evolution of the human brain.
This popular science book provides a sweeping overview of human history. It covers topics such as the development of agriculture, the rise of civilization, and the future of humanity.
This popular science book provides a comprehensive overview of the history of mass extinctions. It covers topics such as the extinction of the dinosaurs, the rise of mammals, and the current extinction crisis.
Save
This popular science book provides a comprehensive overview of island biogeography. It covers topics such as the evolution of island species, the impact of humans on islands, and the future of island ecosystems.
This popular science book provides a comprehensive overview of the history of mass extinctions. It covers topics such as the extinction of the dinosaurs, the rise of mammals, and the current extinction crisis.
Save
This popular science book provides a comprehensive overview of the history of genetics. It covers topics such as the discovery of DNA, the development of genetic engineering, and the future of genetics.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/f0dnoy/hacking
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Similar courses
Similar courses are unavailable at this time. Please try again later.
Level
Introductory
Via
Coursera
Institution
University of California San Diego
Instructors
Niema Moshiri
Mikhail Rayko
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
- Hacking COVID-19 — Course 2: Decoding SARS-CoV-2's Secrets
- Hacking COVID-19 — Course 3: Unraveling COVID-19's Origins (viewing)
- Hacking COVID-19: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets
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