Teaching

Systems, Integrative and Quantitative Biology

Winter semester 2026/2027 · Faculty of Natural Sciences, Comenius University in Bratislava

What this course is about

Living systems are made of components that interact in ways that often make it impossible to reduce a phenotype to a single part, such as one gene. Technological advances of the past two decades have made it possible to characterise biological processes at the level of the entire system, and at the various levels of complexity in between, giving rise to a new field: systems biology.

In this course we study the field through its primary literature. Each week we take one research paper, either a seminal work that shaped the field or a recent state-of-the-art study, and take it apart figure by figure. By the end of the semester you should

• have an overview of the foundational papers of systems biology and of where the field stands today,
• be able to read a research figure critically: understand what was measured and how, what the figure shows, what it does not show, and whether the authors’ interpretation holds,
• be more confident presenting scientific results and arguing about them in a scientific debate, in English.

How a session works

The first session (22 September) is an introduction. No preparation is needed: I will present the course, and then we will work through the first paper together as a group to demonstrate how the figure presentations and the discussion work. Figures for the second session will be assigned at the end of the first one.

From the second session onwards, each 90-minute session has the same structure:

1. Short lecture (about 20 min). I introduce the context of the week’s paper: the biological question, the historical setting, the key methods or concepts you need to follow the data.
2. Figure presentations (about 50 min). The main figures of the paper are divided among the students. Each student presents one figure (about 5 minutes), followed by questions from the group.
3. General discussion (about 20 min). We put the figures back together: What does the paper claim? Is the evidence convincing? What would we have done differently? What came next in the field?

What is expected of you

Before each session (except the introductory first one)

• Read the whole paper, not only your figure. The discussion only works if everyone knows what the paper is about.
• Prepare your assigned figure. For each panel be ready to explain: what is on the axes, what was measured and how (check the methods and supplementary material where needed), what the result is, and what the authors conclude from it.
• Form your own opinion. Do you agree with the authors’ interpretation? What are the caveats, alternative explanations, or missing controls?

Presenting a figure

• No slides. You present directly from the figure as printed in the paper (it will be on the screen); the point is to explain and defend the data, not to design a presentation.
• Structure: question the figure addresses → experimental or computational approach → what is shown → conclusion → your critical assessment.
• Aim for about 5 minutes, then be ready to take questions.
• Figures are assigned one week in advance, at the end of the previous session. Depending on the class size, expect to present roughly every one to two weeks.

During the session

• Participate. Ask questions, challenge interpretations, offer alternatives. Participation in the discussion is assessed every week, not only your own presentation.
• Attendance is required. The course is entirely on-site and there is no way to substitute for the discussion. If you have to miss a session, let me know in advance by e-mail.

Assessment

Assessment is continuous throughout the semester; there is no final exam. The introductory first session is not assessed. From the second session onwards, every week you receive a grade (A – FX) for

• the quality of your figure presentation (clarity, correctness, depth of understanding, critical assessment), and
• your participation in the discussion.

The final grade is a weighted average of these weekly assessments, 60 % figure presentations and 40 % discussion participation, on the standard Comenius University scale:

Schedule

Teaching in the winter semester 2026/2027 runs from 21 September to 18 December 2026 (13 weeks). Tuesday 17 November is a state holiday and rector’s free day, so there is no class that week. The rector’s free day on Friday 30 October and the dean’s free day around All Saints’ Day do not affect this course.

We read strictly one paper per session. The course is organised in two parts. Part I follows the classical route from genes to functions and phenotypes: expression patterns, functional annotation, deletion phenotypes, natural variation and the quantitative economy of the cell. Part II turns to phenotypes that emerge from the interplay of many genes and cells: network rewiring, physical interactions, cell-to-cell variability, and the single-cell technologies and models that let us observe and predict them.

Part I – From genes to functions and phenotypes

Part II – Emergent phenotypes

Schedule and papers may be adjusted during the semester; changes will be announced in class and on this page.