Introduction to Popular `Omics Strategies

Table of Contents


The purpose of this document is to share the details of the course “Introduction to Popular `Omics Strategies”. In the following sections you will find the course description, learning objectives, plan, schedule, attendance and grading policies, as well as other key information that is critical for the course attendees to consider.

Course Details

This course is a part of the module “Applied Molecular Ecology” (mar260) taught by Prof. Dr. A. Murat Eren (Meren) and Prof. Dr. Iliana Baums.

Course Details  
Name Introduction to Popular ‘Omics Strategies
Number 5.12.262
Type Lecture
Credits 2
Language English

In addition to this course, the module mar260 contains three additional components that each participant of this course is expected to also attend,

  • Applied Microbial 'Omics (5.12.263, Seminar / Exercise, Meren, Course Plan: HTML, PDF)
  • Coastal Conservation in the 'Omics Age (5.12.260, Lecture, Iliana Baums)
  • Readings/Exercises in Coastal Conservation (5.12.261, Seminar, Iliana Baums)

Please familiarize yourself with the details of the remaining courses using the appropriate documentation provided for the other components.

Faculty and Communication

The lectures in the Introduction to Popular 'Omics Strategies will be primarily delivered by Meren. However, additional experts will take part in the design and/or delivery of various sections. The following table lists individuals who will be involved in the course, and their contact information:

Name Role Expertise Contact information
Meren Professor Microbial Ecology, Computer Science
Iva Veseli Postdoc Microbial Ecology, Computer Science
Jessika Füssel Postdoc Microbial Metabolism, Biogeochemistry
Florian Trigodet Postdoc Microbiology, Bioinformatics

Throughout the semester (and beyond) you can reach out via email with any question to Meren, who should be your first contact for anything related to the course activities unless specified otherwise anytime throughout the semester.

Description and Learning Objectives

Every ecological niche our planet has to offer is home to an astonishing number of microbial cells that form complex communities. The last several years witnessed tremendous advances in molecular and computational approaches which now offer unprecedented access to these 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. The primary aim of this course is to empower its participants and enable them to study the ecology, evolution, and functioning of naturally occurring microbial populations and recognize the current conceptual framework that helps us wrap our collective mind around the most diverse form of life on our planet.

Introduction to Popular 'Omics Strategies is a lecture with a companion seminar, Applied Microbial 'Omics. The lecture is designed to introduce its participants to the extent of microbial diversity on Earth and its impact on key biogeochemical processes, and strategies by which we characterize and study microbial life in naturally occurring systems to answer fundamental questions in microbial ecology and evolution. Participants will learn about the theoretical underpinnings of popular 'omics data types and their contemporary applications. These data types include genomics, metagenomics, metatranscriptomics, metaepitranscriptomics, as well as various 'omics data analysis approaches such as metabolic reconstruction in genomes and metagenomes, metagenomic read recruitment, pangenomics, phylogenomics, and microbial population genetics.

The learning objectives of the course includes the following:

  • To explain microbial diversity in naturally occurring systems and their evolution.

  • To recognize data-enabled means to study microbial ecosystems.

  • To introduce state-of-the-art ‘omics approaches and data types to characterize naturally occurring microbial diversity.

  • To improve discussion, analytical, presentation and writing skills.


To maximize benefit, the participants of this course are expected to be familiar with the central dogma of molecular biology, and able to answer what is a gene, a genome, a transcript, or a protein, and have at least a preliminary understanding of the principles in ecology and evolution, such as the basics of taxonomy and broad ecological principles that maintain complex ecosystems.

The course will require its participants to read and understand contemporary literature written in English.

Content Delivery

The primary mode of course content delivery will be through slides, where Meren will explain core concepts, data types, and analysis strategies. There will often be extensive discussions over these slides, which will require active, verbal participation by the attendees. Slides will be available on Stud.IP after each lecture.

After each lecture, the attendees will be given suggested readings from the recent literature that covers relevant topics and/or their real-world applications to contemporary questions in marine microbiology, oceanography, marine conservation, and beyond.

Please note that preparation and participation will play a key role in your success. For an effective learning experience please consider (1) taking a brief look at the suggested reading material of a given week in the course plan before coming to the lecture to familiarize yourself with the topic through online resources (~1 hour of study), (2) participate the lecture actively by asking questions and attending discussions, and (3) read the suggested material carefully soon after the lecture (~3 hours of study).

Attendance Policy

Each participant is expected to attend each lecture in person (unless a legitimate reason for absence that is recognized by the University is in effect). The attendance will be recorded by a strategy that we call class citizenship, which aims to help the course director to have an overall understanding of the evolution of the course.

The class citizenship demands every participant to send a class citizenship email to at the end of each lecture. The class citizenship email must be composed of two parts:

  • A brief summary of the main concepts discussed during the class, interpreted by the attendee in their own words.

  • A short question that is relevant to a concept or idea discussed during the lecture, yet remained unclear.

The last 5 minutes of every lecture will be dedicated to class citizenship emails, therefore the attendees will leave the class without having to remember doing it later. The class citizenship emails that are sent after the end of the class will not be taken into consideration as a mark of attendance.

The title of the class citizenship email must follow this pattern word-by-word:

ITPOS Citizenship: DD/MM/YY

For instance, the following would be the appropriate title for this email for the first lecture:

ITPOS Citizenship: 16/10/23

The best class citizenship emails are those that are brief, genuine, and insightful. In an ideal world the emails should be no less than 50 words, and no more than 150 words. Please do not send notes you take throughout the class. You should use the last 5 minutes of the lecture to gather your thoughts, and come up with a summary of what you can remember. Here is an example class citizenship email:

Summary: Today we discussed what is phylogenomics, how phylogenomic trees are built, and why single-copy core genes are suitable for building phylogenomics trees. We also discussed the relationship between phylogenetics, phylogenomics, and pangenomics with respect to the fraction of genome used and the evolutionary distance that they can cover.

Question: Since phylogenomics and pangenomics are both useful for inferring evolutionary distances, it seems to me that integrating both methods in a systematic way would yield a more reliable tree. But it looks like the field only uses phylogenomics and pangenomics separately, is there a reason for that?

Course Plan

Please note that each lecture takes place on Mondays, between 10:15 - 12:00, at VARIOUS LOCATIONS (see below).

16/10/23 :: Course logistics

  • Discussion Leaders:

    • Meren
    • Iliana
  • Discussion Topic. Course Logistics and Introductions with Meren and Iliana. If we have time, we will start with a brief introduction to microbial life on Earth, and will continue next week.

  • Suggested Reading:

    • The Course Syllabus :)

23/10/23 :: A brief introduction to microbial life on Earth

  • Discussion Leaders:

    • Meren
  • Learning Objectives:

    • Describe the extent of microbial diversity on Earth, their involvement in key biogeochemical processes, as well as human health and disease
    • Remember seminal studies that contributed to our understanding of the diversity, functioning, and metabolic potential of naturally occurring microbial communities and approaches to study them
    • Explain the old and new intellectual and technical challenges that prevent us from defining fundamental units of microbial life, and the art of moving forward without any answers
  • Suggested Reading:

  • Even More to Suggested Resources for the Ambitious:

    • Seeing the Invisible, Op-Docs, The New York Times (a short and cute video on microbial life for a lay audience).
    • Meet Your Microbes, Jonathan Eisen, TED Talk (an easy-to-follow introduction to microbes for a lay audience).
    • How Giant Tube Worms Survive at Hydrothermal Vents, Ed Yong, PBS Digital Studies (Ed Yong is a very successful science journalist, who talks about hydrothermal vent microbes with Colleen Cavanaugh, who made significant contributions to our understanding of microbial symbioses).
    • Overview of how next-generation sequencing works, Eric Chow (a very useful and easy-to-follow lecture on the general principles of sequencing with Illumina, Oxford Nanopore, and PacBio).

30/10/23 :: An overview of data-driven strategies to survey environmental microbiomes

  • Discussion Leaders:

    • Meren
  • Learning Objectives:

    • Recognize currently available 'omics data types (such as metagenomics, and metatranscriptomics), approaches (such as pangenomics, and phylogenomics), and questions they can and can not answer
    • Recognize the available computational solutions to gain insights into fundamental questions in microbiology and their brief history
    • Explain the power of metagenomic read recruitment and interpret ecological and evolutionary insights we can infer through this strategy
  • Suggested Reading:

06/11/23 :: Genome-resolved metagenomics: opportunities and pitfalls

13/11/23 :: Pangenomics: comparative genomics in the era of genomic explosion

20/11/23 :: Metapangenomics: integrated interpretations of pangenomes and metagenomes

27/11/23 :: Phylogenomics: inferring evolutionary relationships between microorganisms

04/12/23 :: A Group Discussion Over Course Proposals

  • Meeting Location:

    • W15 0-027
  • Discussion Leaders:

    • Meren
  • Learning Objectives:

    • Learn how to write a compelling proposal

11/12/23 :: Inferring microbial metabolism in genomes and metagenomes

18/12/23 :: Microbial population genetics: tools, terminology, and open questions

08/01/24 :: Structure-informed interpretations of microbial population genetics

15/01/24 :: Genomic dynamism: inversions, diversity generating retroelements, and more

22/01/24 :: Metaepitranscriptomics: translational regulation and its ecological implications

29/01/24 :: Linking metabolomics and (meta)genomics: opportunities and limitations

Evaluation and Grading

The evaluation of the attendee performance in this course (along with all the other three in the module “Applied Molecular Ecology” (mar260) will be based on two items to be returned by each attendee individually: (1) a research pre-proposal (which will provide the basis for the full proposals due at the end of class) and a final research proposal.

Writing research proposals provide one with a critical skill that will be useful regardless of the profession one chooses to pursue after an undergraduate education. The primary purpose of a research proposal is to persuade others that your idea (in this case science) is worthy of committing resources to, and you are the best person to implement it. The final research proposals will be graded based on their ability to address the following questions:

  • Is the proposal contains a novel research objective that is relevant to the “Applied Molecular Ecology” (mar260) module content?
  • Does it make a strong case given what is known and what is unknown?
  • Does it adequately and accurately cite the existing literature?
  • Does it suggest the use of methods that are relevant and effective to address the research question?
  • Does the investigator demonstrate their ability to use the proposed methods?
  • Does the proposal includes a discussion of expected outcomes, potential risks, and how to mitigate risks?
  • Does it include a reasonable budget and a meaningful timeline to carry out the proposed research objectives?
  • Does the proposal written in a clear, concise, and accurate manner that is expected of scientific work?

Upon the submission of the pre-proposal, smaller teams of students will serve as a “peer-review panel” and discuss each pre-proposal. The names of participants who wrote these proposals will not be known to the class. The panel will take place in class for all participants. The purpose of the panel is to provide feedback on how well the proposal was able to convey ideas. Participants are expected to improve their short pre-proposals based on the feedback they received from the peer-review panels and submit their full proposal as their final project.

The participants will be provided with detailed instructions on how to come up with a proposal idea, what resources are available to carry out the projects, how to format the pre-proposal and final proposals and how to evaluate them in panel.

It is challenging to think of a topic for research that can be done in a short amount of time with limited resources. Therefore, the course directors (Meren and Iliana) will meet with each of the course participants individually to discuss their proposal idea, tell them whether it is feasible, and help them with resources. To initiate this discussion, you will hand in a one-paragraph research idea early in the semester.

The grading scale for this module is as follows:

Grade Threshold
1.0 95%
1.3 90%
1.7 85%
2.0 80%
2.3 75%
2.7 70%
3.0 65%
3.3 60%
3.7 55%
4.0 50%

Examination Policy

Please find all relevant university policies here:

Academic Integrity

All UOL policies regarding ethics and honorable behavior apply to this. Academic integrity is the pursuit of scholarly activity free from fraud and deception and is an educational objective of this class. All University policies regarding academic integrity apply to this course. Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabricating of information or citations, facilitating acts of academic dishonesty by others, having unauthorized possession of examinations, submitting work of another person or work previously used without informing the instructor, or tampering with the academic work of other students. For any material or ideas obtained from other sources, such as the text or things you see on the web, in the library, etc., a source reference must be given. Direct quotes from any source must be identified as such.

Disability Access Statement

UOL welcomes students with disabilities and students with care obligations for their children or close relatives into the University’s educational programs. In order to receive consideration for reasonable accommodations, you must contact the Prüfungsausschuss. Please let Meren and/or Iliana know at the beginning of the semester what accommodations were approved for you.