Microbial 'omics


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a post by A. Murat Eren (Meren)

Table of Contents

Welcome, and thank you for your interest!

The link to the registration form is at the end of this post. But we will assume that you have read everything on this page! :)

Motivation

The primary aim of this seminar series is 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.

Seminar format

Each week there will be a seminar, and each seminar will be composed of two sections: lecture, and discussion.

Lecture part

Lectures will take approximately an hour and will use slides for presentation.

Discussion part

Discussions will take and additional 30 to 45 minutes and will be dedicated to questions, exchange of ideas, and practical considerations. Although the target audience is beginners, our sessions will undoubtedly include researchers who are experienced on the topic and will be encouraged to take part in discussions.

Logistics

If you are registered for a given week, you will get an e-mail 15 minutes before the start time with URLs that will enable you to follow the session.

We will primarily use Zoom for lectures. If you plan to attend, please download the latest version of Zoom beforehand. If you already have Zoom installed on your computer, please make sure it is up to date. On the Zoom call, any participant will be able to unmute themselves to ask questions verbally, or use the chat window to do it in written form during the lecture or discussion sections. A person who will be identified at the beginning of each seminar will interrupt the speaker at appropriate times and brings up questions from the chat window.

In parallel, we will also use YouTube to stream the content live. Those who are registered for the seminar series will also be given a YouTube URL. This way, if there are more people than our Zoom account can accommodate, they will follow the seminar and discussions through YouTube.

There will be a 20 to 40 second delay between Zoom and YouTube.

Lecturers

Schedule

Every lecture will take place on a Wednesday at 9am Chicago Time (CST) (see what time it corresponds to in your city), and recording of the lecture (minus the discussions) will appear here after a few days.

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):

Registration

Seminars are free to attend and open to anyone! If you have registered, you will get an e-mail five to fifteen minutes before the beginning of the seminar on each Wednesday. Please be patient and don’t forget to keep an eye on your JUNK or SPAM folders :) If you have not registered, you still can attend. Please keep an eye on Meren’s Twitter account or Anvi’o Slack channel (link below) for URLs to Zoom and YouTube streams.

Questions?

Please use the comments section down below or find us on Slack.

Questions? Concerns? Find us on

Thank you very much for your interest.