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Peter Karp,
Niema Moshiri,
Mikhail Rayko,
Vikram Sirupurapu,
Sabeel Mansuri,
and
Pavel Pevzner
Pathway Bioinformatics is a subfield of Bioinformatics that is concerned with computationally deriving functional insights from genomic data through analysis of molecular networks. This course will present principles and techniques from Pathway Bioinformatics, and will apply these methodologies to the search for drug targets for SARS-CoV-2. The course will begin by discussing motivations for Pathway Bioinformatics, and by presenting an overview of metabolism and of metabolic pathways. Next it will discuss machine representation of pathway data, and methods for pathway visualization. The course will describe how the metabolic pathways of an organism can be inferred from genome data, and how pathways can be used to interpret high-throughput data such as transcriptomics data. It will show how to predict the essential genes of an organism via reachability analysis, and then present a metabolic analysis of human metabolism when interacting with SARS-CoV-2 to predict SARS-CoV-2 drug targets.
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What's inside
Syllabus
Traffic lights
Traffic lights
Read about what's good
what should give you pause and
possible dealbreakers
Useful for students interested in biomedical science
Provides a strong foundation for beginners in Pathway Bioinformatics
Taught by experts in the field of bioinformatics and computational biology
Helps develop expertise in pathway visualization, analysis, and prediction
Does not require extensive background knowledge in the subject
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Reviews summary
Advanced drug target bioinformatics analysis
According to learners, "Hacking COVID-19: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets" is a highly specialized and valuable course, particularly for those with a strong background in bioinformatics and molecular biology. Students frequently praise the expert instructor, whose clear explanations make complex topics accessible. The course provides a timely and relevant focus, applying pathway bioinformatics to real-world problems like SARS-CoV-2 drug target identification through practical case studies. However, several students caution that it is not for beginners and can be very challenging without prior knowledge, especially as it's the fourth course in a specialization. More recent reviews suggest content is updated.
Course content appears to be regularly updated, reflecting research.
"I appreciate the updated content reflecting recent research."
"The course seems to maintain its relevance by incorporating new information and research trends."
Effectively builds upon and concludes a larger course series.
"This course is part of a larger specialization, and building on the previous courses really helps."
"This course builds very well on the previous parts of the specialization."
"This is a fantastic course, especially as the capstone of the specialization."
Applies concepts to real-world challenges like COVID-19 drug targets.
"Excellent deep dive into applying pathway bioinformatics to a real-world problem like COVID-19."
"I particularly appreciated the hands-on case study on SARS-CoV-2; it directly applied the concepts."
"The practical application of metabolic pathway analysis to a real-world health crisis like COVID-19 made it incredibly engaging."
Instructor's deep expertise ensures clear and engaging content.
"The instructor, Dr. Palsson, is a true expert, and his explanations of metabolic pathway analysis are incredibly clear..."
"The instructor's expertise shines through."
"The instructor's expertise is evident throughout."
Demands solid foundation in bioinformatics and molecular biology.
"This course is definitely not for beginners; you need a strong foundation in molecular biology and some scripting experience."
"I enrolled hoping to gain some insight into drug targeting, but I was completely lost. The course is way too advanced..."
"I struggled with the computational aspects, and the forum discussions weren't always enough to clarify my doubts."
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: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets with these
activities:
Read an article about Systems Biology
Show steps
Refresh your understanding of Systems Biology to better understand the fundamental concepts and topics that will be covered throughout the course.
Browse courses on
Systems Biology
Show steps
-
Research scholarly articles on Systems Biology.
-
Identify concepts and terms that are central to the field.
Compile a literature review on Pathway Bioinformatics
Show steps
Enhances understanding of Pathway Bioinformatics by exposing you to a wide range of research and perspectives.
Show steps
-
Identify relevant literature sources
-
Read and summarize the literature
-
Organize and synthesize the findings
Review metabolism and metabolic pathways
Show steps
This will help you build a stronger foundation of knowledge in metabolism and its pathways, which can be helpful in understanding the fundamentals of this course.
Browse courses on
Metabolism
Show steps
-
Review the basic principles of metabolism, including anabolism and catabolism
-
Identify the different types of metabolic pathways, such as glycolysis, the citric acid cycle, and the electron transport chain
-
Understand the role of enzymes in metabolic pathways
Five other activities
Expand to see all activities and additional details
Show all eight activities
Form a study group to discuss course concepts
Show steps
Encourages active learning, collaboration, and peer-to-peer knowledge exchange.
Show steps
-
Find other students who are interested in forming a study group
-
Set regular meeting times and discuss course topics
Guided tutorials on pathway visualization tools
Show steps
This activity will equip you with the skills to use pathway visualization tools, enabling you to effectively analyze and interpret metabolic pathways.
Show steps
-
Explore online tutorials or documentation for pathway visualization tools
-
Follow the instructions to import and visualize metabolic pathways
-
Practice customizing and manipulating the visualization settings to optimize your analysis
Practice predicting metabolic pathways
Show steps
Engaging in practice drills will reinforce your understanding of metabolic pathways and prepare you for more advanced work in the field.
Show steps
-
Use online tools or resources to predict metabolic pathways based on given data
-
Compare your predictions with known metabolic pathways to evaluate your accuracy
-
Identify areas where your predictions differ from known pathways and research to understand the reasons for the discrepancies
Practice Reachability Analysis
Show steps
Deepens understanding of reachability analysis by having you apply the technique to different datasets.
Browse courses on
Reachability Analysis
Show steps
-
Find an appropriate dataset
-
Identify the nodes and edges in the graph
-
Apply reachability analysis to the graph
-
Analyze the results of the analysis
Create a metabolic model of a simple organism
Show steps
Provides hands-on experience with metabolic modeling and helps solidify understanding of pathway bioinformatics.
Show steps
-
Choose an organism to model
-
Gather data on the organism's metabolism
-
Construct a metabolic model using software
-
Validate and refine the model
Read an article about Systems Biology
Show steps
Refresh your understanding of Systems Biology to better understand the fundamental concepts and topics that will be covered throughout the course.
Browse courses on
Systems Biology
Show steps
Show steps
Show steps
- Research scholarly articles on Systems Biology.
- Identify concepts and terms that are central to the field.
Compile a literature review on Pathway Bioinformatics
Show steps
Enhances understanding of Pathway Bioinformatics by exposing you to a wide range of research and perspectives.
Show steps
Show steps
Show steps
- Identify relevant literature sources
- Read and summarize the literature
- Organize and synthesize the findings
Review metabolism and metabolic pathways
Show steps
This will help you build a stronger foundation of knowledge in metabolism and its pathways, which can be helpful in understanding the fundamentals of this course.
Browse courses on
Metabolism
Show steps
Show steps
Show steps
- Review the basic principles of metabolism, including anabolism and catabolism
- Identify the different types of metabolic pathways, such as glycolysis, the citric acid cycle, and the electron transport chain
- Understand the role of enzymes in metabolic pathways
Five other activities
Expand to see all activities and additional details
Show all eight activities
Form a study group to discuss course concepts
Show steps
Encourages active learning, collaboration, and peer-to-peer knowledge exchange.
Show steps
Show steps
Show steps
- Find other students who are interested in forming a study group
- Set regular meeting times and discuss course topics
Guided tutorials on pathway visualization tools
Show steps
This activity will equip you with the skills to use pathway visualization tools, enabling you to effectively analyze and interpret metabolic pathways.
Show steps
Show steps
Show steps
- Explore online tutorials or documentation for pathway visualization tools
- Follow the instructions to import and visualize metabolic pathways
- Practice customizing and manipulating the visualization settings to optimize your analysis
Practice predicting metabolic pathways
Show steps
Engaging in practice drills will reinforce your understanding of metabolic pathways and prepare you for more advanced work in the field.
Show steps
Show steps
Show steps
- Use online tools or resources to predict metabolic pathways based on given data
- Compare your predictions with known metabolic pathways to evaluate your accuracy
- Identify areas where your predictions differ from known pathways and research to understand the reasons for the discrepancies
Practice Reachability Analysis
Show steps
Deepens understanding of reachability analysis by having you apply the technique to different datasets.
Browse courses on
Reachability Analysis
Show steps
Show steps
Show steps
- Find an appropriate dataset
- Identify the nodes and edges in the graph
- Apply reachability analysis to the graph
- Analyze the results of the analysis
Create a metabolic model of a simple organism
Show steps
Provides hands-on experience with metabolic modeling and helps solidify understanding of pathway bioinformatics.
Show steps
Show steps
Show steps
- Choose an organism to model
- Gather data on the organism's metabolism
- Construct a metabolic model using software
- Validate and refine the model
Career center
Learners who complete Hacking COVID-19: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets will develop knowledge and skills
that may be useful to these careers:
Systems Biologist
Systems Biologist
A Systems Biologist uses systems biology to study the interactions between different components of a biological system, such as cells, organs, and organisms. Systems Biologists may specialize in a particular area, such as human systems biology, plant systems biology, or microbial systems biology. This course may be useful to a Systems Biologist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Metabolic Engineer
Metabolic Engineer
A Metabolic Engineer uses metabolic engineering to design and construct new metabolic pathways for the production of chemicals and fuels. Metabolic Engineers may specialize in a particular area, such as biofuels, pharmaceuticals, or food production. This course may be useful to a Metabolic Engineer because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Drug Discovery Scientist
Drug Discovery Scientist
A Drug Discovery Scientist researches and develops new drugs for the treatment of diseases. Drug Discovery Scientists may specialize in a particular area, such as oncology, infectious diseases, or neurology. This course may be useful to a Drug Discovery Scientist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Pharmaceutical Scientist
Pharmaceutical Scientist
A Pharmaceutical Scientist researches, develops, and manufactures new drugs for the treatment of diseases. Pharmaceutical Scientists may specialize in a particular area, such as drug discovery, drug development, or drug manufacturing. This course may be useful to a Pharmaceutical Scientist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Virologist
Virologist
A Virologist studies viruses and their interactions with other organisms. Virologists may specialize in a particular area, such as human virology, plant virology, or microbial virology. This course may be useful to a Virologist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Microbiologist
Microbiologist
A Microbiologist studies microorganisms, such as bacteria, viruses, and fungi. Microbiologists may specialize in a particular area, such as medical microbiology, environmental microbiology, or industrial microbiology. This course may be useful to a Microbiologist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Computational Biologist
Computational Biologist
A Computational Biologist uses computational tools and techniques to solve problems in biology and medicine. Computational Biologists may specialize in a particular area, such as genomics, proteomics, or metabolomics. This course may be useful to a Computational Biologist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Genomics Scientist
Genomics Scientist
A Genomics Scientist researches the structure, function, and evolution of genomes. Genomics Scientists may specialize in a particular area, such as human genomics, plant genomics, or microbial genomics. This course may be useful to a Genomics Scientist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Bioinformatics Scientist
Bioinformatics Scientist
A Bioinformatics Scientist researches, develops, and implements bioinformatics tools and databases for use in the analysis of biological data. Bioinformatics Scientists may specialize in a particular area, such as genomics, proteomics, or metabolomics. This course may be useful to a Bioinformatics Scientist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Proteomics Scientist
Proteomics Scientist
A Proteomics Scientist researches the structure, function, and evolution of proteins. Proteomics Scientists may specialize in a particular area, such as human proteomics, plant proteomics, or microbial proteomics. This course may be useful to a Proteomics Scientist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Toxicologist
Toxicologist
A Toxicologist studies the effects of toxic substances on living organisms. Toxicologists may specialize in a particular area, such as environmental toxicology, occupational toxicology, or forensic toxicology. This course may be useful to a Toxicologist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Machine Learning Engineer
Machine Learning Engineer
A Machine Learning Engineer develops and implements machine learning models for use in a variety of applications, such as image recognition, natural language processing, and fraud detection. Machine Learning Engineers may specialize in a particular area, such as supervised learning, unsupervised learning, or reinforcement learning. This course may be useful to a Machine Learning Engineer because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Data Scientist
Data Scientist
A Data Scientist uses data to solve problems in a variety of industries, including healthcare, finance, and retail. Data Scientists may specialize in a particular area, such as machine learning, statistics, or data visualization. This course may be useful to a Data Scientist because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
Researcher
Researcher
A Researcher conducts research in a variety of fields, including science, engineering, and medicine. Researchers may specialize in a particular area, such as cancer research, climate change research, or educational research. This course may be useful to a Researcher because it provides an overview of pathway bioinformatics and its applications to drug target discovery.
For more career information including salaries, visit:
OpenCourser.com/course/w6kng1/hacking
Reading list
We've selected six 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: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets.
Save
This textbook is more advanced and would serve as a great textbook replacement for this course. It comprehensively covers the field of bioinformatics with a focus on sequence and genome analysis.
This comprehensive guide to bioinformatics methods and techniques would serve as a valuable reference tool, particularly for those who are new to the field or who are looking to dig deeper into specific topics.
Can be used as a basic textbook with a focus on bioinformatics principles. It may prove valuable for building a foundational knowledge of how to handle and analyze biological data.
This advanced textbook provides a broad overview of the field of molecular biology. Its inclusion on this list is due to its relevance to the course topic of drug target identification. However, its depth may make it more suitable as a reference tool than a core text for the course.
Offers an accessible introduction to the field of systems biology, with a focus on the design principles of biological circuits. While it may not directly align with the specific topic of drug target identification, it could provide valuable background knowledge for those who are new to the area.
Save
This general microbiology textbook provides an accessible overview of the fundamental principles of microbiology. It could help to provide essential background knowledge for those who are new to the field.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/w6kng1/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
Peter Karp
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
- Hacking COVID-19: Metabolic Pathway Analysis Yields SARS-CoV-2 Drug Targets (viewing)
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