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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

Hacking COVID-19 — Course 4: Searching for Drug Targets
In this course, we will use pathway bioinformatics techniques to search for potential COVID-19 drug targets.

Good to know

Know what's good
, what to watch for
, 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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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
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
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
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
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Form a study group to discuss course concepts
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
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
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
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
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

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:
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

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.
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.
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.

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