Table of Contents
Welcome, and thank you for your interest! The microbial ‘omics seminar series of 2020 is now over, but in this page you can find the recorded lectures.
Motivation
The primary aim of this seminar series was to give a broad introduction to some of the key concepts and strategies that enable us to study the ecology, evolution, and functioning of naturally occurring microbial populations.
The last several years witnessed tremendous advances in molecular and computational approaches which now offer unprecedented access to naturally occurring microbial communities through new ‘omics strategies. Developing an overall understanding of these strategies -including the ability to identify their appropriate applications and shortcomings- has quietly become a de facto necessity in the journey of an independent life scientist.
While most of these strategies are quite accessible thanks to the increasing number of computational tools and pipelines, without a complete understanding of the key concepts, exploiting available computational solutions to address unique scientific questions remain difficult. The purpose of the seminar series is to offer some introductions to key concepts, without talking about tools or their practical applications.
Target audience
The target audience of this seminar series is beginners from all backgrounds who are interested in microbial ‘omics.
Even if you have never been exposed to the strategies the seminars will cover, you will likely to be able to follow the content and discussions.
Seminars will use simple terms and simple language as much as possible.
Lecturers
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Meren: Assistant Professor in the Department of Medicine and the Committee on Microbiology at the University of Chicago, and a Fellow of the Marine Biological Laboratory.
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Roland Hatzenpichler, Assistant Professor in the Department of Chemistry and Biochemistry, the Thermal Biology Institute, and the Center for Biofilm Engineering at Montana State University. Roland led a discussion on what we do not learn about microbial associations from sequencing alone.
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Jessica Mark Welch, Associate Scientist in the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory. Jessica led a discussion on what we do not learn about microbial interactions from sequencing alone.
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Mike Lee: Research Scientist at the Ames Research Center, National Aeronautics and Space Administration (NASA). Mike led the discussion on Phylogenomics.
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Iva Veseli: Graduate Student in the Biophysical Sciences Program at the University of Chicago. Iva answered questions asked on the chat window on the Zoom call, or bring them up with the lecturer(s).
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Emily Fogarty: Graduate Student in the Committee on Microbiology at the University of Chicago. Emily answered questions asked on the chat window during the YouTube live stream.
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Andrea Watson: Graduate Student in the Committee on Microbiology at the University of Chicago. Andrea documented questions asked at the Zoom environment and YouTube live stream under each lecture video.
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Jessica Pan: Undergraduate Student at Massachusetts Institute of Technology. Jessica transcribed the lecture content and generated subtitles for YouTube videos.
Lectures
July 8, 2020
A brief introduction to microbial life, and popular ‘omics approaches and data types
The video of the first week’s lecture (if you click on the title, you will find the outline and timestamps of independent sections of the talk on YouTube):
July 15, 2020
The power of metagenomic read recruitment
The video of the second week’s lecture. Please see questions asked and responses given, as well as the outline and timestamps of independent sections of the talk on YouTube:
July 22, 2020
Genome-resolved metagenomics: key concepts in reconstructing genomes from metagenomes
July 29, 2020
Pangenomics: comparative genomics in the era of genomic explosion
The video of the lecture (please find timestamps for individual chapters and written Q&A’s on YouTube):
August 5, 2020
Metapangenomics: A nexus between pangenomes and metagenomes
The video of the lecture (please find timestamps for individual chapters and written Q&A’s on YouTube):
August 12, 2020
Phylogenomics: inferring evolutionary relationships between microorganisms
The video of the lecture (please find timestamps for individual chapters and written Q&A’s on YouTube):
Future
We are hoping to put together another seminar series later on bioinformatics approaches that give access to ‘omics strategies covered in this introductory seminar series. Meanwhile, please use the comments section down below or find us on Disord if you have any comments or suggestions.
Thank you very much for your interest!