Aim and content

This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee.

Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.

Learning objectives

A student who has met the objectives of the course will be able to:

1. Ability to describe biological systems with mathematical models
2. Ability to simulate, analyze, and compare different types of mathematical models
3. Have insight into biological processes through joint mathematical-experimental approaches
4. Ability to interpret data quantitative through models for hypothesis testing

Content

The course introduces a variety of computational/mathematical techniques for modeling and analysis of biological systems. Topics include properties of gene-regulatory and signaling networks; network reconstruction from data; stochastic modeling to study single-cell variation, and physiological modeling.
Also covered will be general introductions to bacterial viruses, phages, modeling host-pathogen population dynamics as well as major topics within antibiotic resistance.

The following topics will be covered:

• Introduction to Systems Biology and show examples of well-known mathematical models in molecular and cell biology, neuroscience, ecology, and evolution.

• Boolean models of gene regulatory networks and tools for inferring gene interactions from expression level data. Hand-on exercises on model simulation and identification from data. Presentation and discussion on previous papers using Boolean models in the context of modeling different biological pathways

• Modeling gene expression process using different equation models. Hand-on exercises on simulating these models in Microsoft Excel, R, MATLAB, and Mathematica, Discussion of how key parameters (transcription/translation rates, mRNA/protein decay rates) are measured and their genome-wide physiological values from bacterial to mammalian cells.

• Design principle of biological network from feedback to feedforward loops. Motif detection in large biological networks. Function roles of these types of regulation, and how they modulate the dynamic responses of biological systems with case studies drawn from microbiology.

• Introduction to biological toggle switches and clocks. Detailed case studies of the lysis-lysogeny switch in lambda phage and cellular decision-making in human viruses.

• Introduction to single-cell biology and heterogeneity that arises even within the same isoclonal population. Stochastic modeling of gene expression and regulation to understand the origins and consequences of inter-cellular variation and it in the context of antibiotic resistance.

• Modeling population dynamics of host-pathogen interaction with a specific focus on bacteriophages and their intracellular mechanisms of host cell lysis.

Participants

The participants will be PhD students from the graduate programs as well as PhD at the graduate program at Science, UCPH. Also, it will be relevant for PhD students at nearby universities including Technical University of Denmark and Lund University.

Basic background in linear algebra and programming. A background in cell/molecular biology will be helpful but not required for the class. Additional mathematical/biological reading material may be given to individual students to bring their background at par with the class.

Relevance to graduate programmes

The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:

Molecular Microbiology and infection

Public Health and Epidemiology

Biostatistics and Bioinformatics

Language

English

Form

Lectures, group work and discussion

Course director

Hanne Ingmer, Professor, Department of Veterinary and Animal Sciences, hi@sund.ku.dk

Teachers

Abhyudai Singh, Professor at University of Delaware, absingh@udel.edu
Hanne Ingmer, Professor, SUND, hi@sund.ku.dk
Freja Cecilie Mikkelsen, Graduate student SUND, freja.mikkelsen@sund.ku.dk
Ifigeneia Kyrkou, Post doc SUND, ifigeneia.kyrkou@sund.ku.dk

Dates

31/3 – 4/4 2025

Course location

Frederiksberg Campus, UCPH.

Registration

Please register before 28/2 2025.

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules.
Applications from other participants will be considered after the last day of enrolment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.