Microbiome Informatics (M8161)¶
Read on for Microbiology 8161: Microbiome Informatics (Fall 2023). Here, you’ll find a list of topics covered by the course and a set of references (if available) on this website.
Conceptual instructor:
Prof. Matthew B. Sullivan
Practical instructors:
Dr. Ahmed Zayed
Dr. Ben Bolduc
Dr. Mike Sovic
Dr. Dean Vik
Teaching assistants
Dr. Marion Urvoy
Dr. Ricardo Pavan
Course learning objectives: This course seeks to inspire creativity and innovation for answering fundamental microbiological questions using sequence data. Specific learning objectives include the following:
Gain exposure to approaches for studying the function, structure and evolutionary history of genes observed in sequence datasets.
Learn approaches for organizing sequence datasets into organismal units using marker genes (e.g., 16S) and shotgun metagenomics data.
Learn ecological statistical approaches to discern community structure and ecological drivers from large-scale metagenomic datasets.
Introduction to other sequence-based datasets including viral metagenomes, as well as metatranscriptomics, metaproteomics, metabolomics, etc.
Design, implement and interpret an informatics group project to further biological understanding of microbes.
Lecture Schedule
Week 1: Intro to the Course and OSC (see OSC Introduction and Guide)
Week 2: OSC and HPC, Review 5161
Week 3: Genome-resolved MetaG + Intro to R for Microbiome Science
Week 4: Introduction to R Parts 2 + 3, Genome-resolved MetaG workflow
Week 5: Ecological stats primer and hands-on applications
Week 6: Select projects and transition to project phase
Week 7: In-class troubleshoot project work (MAGs, DRAM)
Week 8: Project report-outs
Week 9: In-class troubleshoot project work (GTDB for microbial work, virus ID and taxonomy if viruses)
Week 10: Project report-outs
Week 11: Literature context, what are the low-hanging fruit analyses to do?
Week 12: In-class troubleshoot project work (varies upon needs)
Week 13: Project report-outs
Week 14: In-class troubleshoot project work (varies upon needs)
Week 15: Project presentations
Week 16: Project presentations
Finals week: Final paper due!