PhD courses

This graduate course in evolutionary biology emphasises the various evolutionary processes rather than descriptions of states, patterns and the methods to establish them. It covers all levels of biological organisation and temporal and spatial scales. It does so by a conceptual and general approach, although ample reference will be made to well-known organisms and biological systems. When appropriate, examples from experimental evolution will be discussed from a theoretical perspective.

Course organisation

The course will be run for 5 days in one week. The course will have elements from genetics (molecular, population, quantitative), ecology, developmental biology and palaeontology. There is mathematics, but not beyond basic algebra and simple calculus. The course is explicitly interdisciplinary and synthesising.

Time-period

We give the course every year in the autumn. The course will be held in the Ecology building, Sölvegatan 37, Lund. The next time we will give the course is 25–29 November 2024.

Credits

Completion of the course renders 2 credits.

Registration

Send an email to Tobias Uller. A limited number of places are available!

Contact person

Tobias Uller
Researcher
E-mail: Tobias [dot] Uller [at] biol [dot] lu [dot] se

The course is about the Department of Biology, PhD student rights and responsibilities, the history of biology, introduction to the philosophy of science, scientific publishing, science and society, and sustainable graduate education.

Course organisation

The course consists of lectures, seminars and written assignments.

Time-period

3–7 March 2025.

Credits

Completion of the course renders 1.5 credits.

Registration

You register by sending an email to Klas Flärdh. Write "Registration – intro course 2024 as a subject and your name and unit affiliation in the main body.

Contact

Klas Flärdh
Professor

Telephone: +46 46 222 85 84
Email: Klas [dot] Flardh [at] biol [dot] lu [dot] se

Dennis Hasselquist
Professor
Telephone: +46 46 222 37 08
Email: Dennis [dot] Hasselquist [at] biol [dot] lu [dot] se

This course gives an introduction to the use of microscopy-based methods in life science today. Both PhD students and master’s students are welcome to take this course. The emphasis is on fluorescence microscopy and theoretical principles of confocal microscopy and image deconvolution. We give an overview of different types of advanced research microscopes and the principles of the most common advanced methods. Another important aspect is the preparation and optimisation of samples for microscopy, both fixed samples and tissue sections, as well as living samples. The course also includes a theoretical introduction to digital visualisation, with emphasis on fluorescence-based methods, including a brief introduction to ImageJ and basic analysis of digital images.

Course organisation

In addition to lectures, seminars, and demonstrations, the course includes two projects. A literature project and a practical bio-imaging project.

Time-period

We give the course once a year in the latter part of the spring term.

Registration

Send an e-mail to David O'Carroll.

Credits

Completion of the course renders 7.5 credits.

Contact person

David O'Carroll
Professor
Telephone: +46 46 222 95 77
Email: David [dot] OCarroll [at] biol [dot] lu [dot] se

In this course, the world's leading authorities in sensory ecology are invited to Lund to deliver an outstanding program of lectures covering all animal senses.

Time-period

We give this course in September/October every second year. Next time 22 September to 5 October 2024.

Registration

Places will be allocated on a first-in-first-served basis until the maximum number of places is filled (40 places). You must include a poster title in the form and send in a poster abstract before the registration time ends. More information about the course and how you apply.

Course fee

Unfortunately, due to the worsened financial climate, the course is no longer subsidised, and we are forced to raise the course fee significantly. In 2024 the course fee will be 15,500 SEK.

Credits

Completion of the course renders 6 credits.

Contact

All inquiries should be directed to Sensory [dot] Ecology [at] biol [dot] lu [dot] se.

In this course, you will get an introduction to R, and learn about binomial-, poisson- and normal distribution, descriptive statistics and graphs, hypotheses testing, t-test, ANOVAs, correlation, regression, multiple and non-linear regression, chi-square, G-tests, log-linear modelling, logistic regression and survival, discriminant, PCA and cluster analyses.

Course organisation

We usually run the course two days a week for 7-8 weeks during November–January, with lectures in the mornings and exercises in the afternoons. Participants may need to spend some time on the exercises between scheduled events. For your planning, you will have access to the exercises in advance.

Registration

Please e-mail questions and enrolment requests to Øystein Opedal.

Credits

Completion of the course renders 7.5 credits.

Contact person

Øystein Opedal
Associate senior lecturer
Telephone: +47 922 331 89
Email: Oystein [dot] Opedal [at] biol [dot] lu [dot] se

The course covers PCR-based DNA/RNA analysis from sampling to evaluation of results, with a specific focus on real-time quantitative PCR (qPCR). The aim of the course is to improve the understanding of the biochemical and physical principles that govern PCR, thus giving the participants the tools for designing, optimising, validating, troubleshooting and using PCR/qPCR assays.

Included topics are

• absolute and relative quantification of DNA/RNA
• limit of detection
• optimisation of PCR
• primer/probe design
• contamination and quality control
• validation of PCR methods
• sample preparation (DNA/RNA)
• understanding and relieving PCR inhibition (pre-PCR processing)
• forensic DNA analysis.

Laboratory exercises are integrated with the lectures and serve to illustrate essential theoretical aspects of PCR design and optimisation. The obtained results will be thoroughly discussed within the course. 

Additionally, various PCR-based methods and techniques will be presented and discussed, including

• gene expression
• digital PCR
• high resolution melting (HRM)
• massively parallel sequencing (MPS). 

Finally, all students will give an oral literature presentation on a chosen topic related to PCR methodology. Course literature, lab manuals and lecture slides will be provided on the first day of the course.

The course leader performs research in the areas of diagnostic PCR, forensic DNA analysis, and pre-PCR processing. The course was started by Professor Peter Rådström in 1997, and real-time quantitative PCR has been applied in the course since 1999.

Course leader

Johannes Hedman
Adjunct Associate Professor, Division of Applied Microbiology
Faculty of Technology (LTH)
Lund University
and
Specialist, National Forensic Centre
Swedish Police Authority
E-mail: johannes [dot] hedman [at] tmb [dot] lth [dot] se (johannes[dot]hedman[at]tmb[dot]lth[dot]se)

Course period

13–17 October 2025

The course is intended for PhD students in life sciences, such as biology, ecology, chemical ecology, analytical or medical chemistry or related fields of science. This is a hands-on course in combined gas chromatography and mass spectrometry (GC-MS). You will learn how to prepare samples for and operate a GC-MS. 

The course includes lectures in sampling preparation, extraction methods and practical considerations when analysing volatile compounds, mixed with practical exercises. The practical part of the course is to construct and evaluate different methods of sample preparation and GC-MS analysis, by using the analytical instrumentation at Chemical Ecology, Department of Plant Protection Biology, Swedish University of Agricultural Sciences (SLU) on Campus Alnarp.

Course leader

Björn Bohman
Swedish University of Agricultural Sciences
Campus Alnarp
E-mail: bjorn [dot] bohman [at] slu [dot] se (bjorn[dot]bohman[at]slu[dot]se)

Course period

27–31 October 2025

Course code

PLS0062

This course covers modern mass spectrometry with a particular focus on the analysis of low molecular weight analytes. The emphasis is on understanding the fundamental processes involved, the instrumentation used, including different ionisation sources and mass analysers, and interpretation of generated data. For accurate quantitative or qualitative analysis, mass spectrometry is today combined with different chromatographic techniques.

Mass spectrometry for small molecules includes an overview of mass spectrometric techniques that can be used for analysis of low molecular weight analytes in both the gas and liquid phases. Gas chromatography in combination with chemical ionisation and electron ionisation, and liquid chromatography in combination with electrospray ionisation, atmospheric pressure chemical ionisation and atmospheric pressure photo ionisation will be covered. 

Different types of mass analysers will also be discussed, including the quadrupole, the 3d and linear ion traps, the time of flight, the orbitrap, and the Fourier transform ion cyclotron resonance mass analysers, and their combinations. Interpretation of mass spectra and data treatment will also be covered, together with practical aspects of mass spectrometry method development. 

The course leader gives theoretical and practical knowledge on how mass spectrometry can be used in qualitative and quantitative analyses of small molecules. Mass spectrometers with different designs and their advantages and shortcomings in different applications will be covered. 

We will pay great attention to data interpretation. Practical parts include analysis of own or supplied samples by chromatography and mass spectrometry, with subsequent data analysis and identification of sample components.

Course leader

Peter Spégel
Centre for Analysis and Synthesis (CAS)
Department of Chemistry
Lund University
E-mail: peter [dot] spegel [at] chem [dot] lu [dot] se (peter[dot]spegel[at]chem[dot]lu[dot]se)

Course period

17–21 November 2025

Course code

NKE005F

Flow cytometry is a high-throughput technique for counting and studying microscopic particles in suspension by passing them through a laser and an electronic detection apparatus. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of up to thousands of particles per second. 

Flow cytometry is used for single-cell analysis of cell populations and monitoring of population phenotypic heterogeneity, as well as for preparative sorting of individual cells and subpopulations. Flow cytometry has important applications in many fields, including fundamental and applied microbiology, bioprocess monitoring, protein engineering, plant biology and marine biology.

In the course, we will cover the most important applications of microbial flow cytometry and provide a clear view of what kind of information can be obtained, as well as how to analyse and interpret the data. The focus of the course will be on getting practical experience of flow cytometry for single-cell analysis and cell sorting of microorganisms.

Course leader

Magnus Carlquist
Applied Microbiology
Department of Chemistry, Faculty of Engineering
Lund University
Telephone: +46 46 222 98 75
Email: magnus [dot] carlquist [at] tmb [dot] lth [dot] se (magnus[dot]carlquist[at]tmb[dot]lth[dot]se)

Course period

10–14 November 2025

Course code

KMB020F

Visualisation and understanding of cellular structures and their composition are of great importance in biological research, and also for applications of bio-based materials. The course gives an overview and hands-on training on common low- and high-resolution microscopy methods. A short introduction and hands-on training of optical and electron microscopy, as well as fluorescence and confocal laser scanning microscopy, is included. As a new method, micro-computed tonography (micro-CT) is introduced.

The course is applicable to any type of biological material. Sample preparation for different types of microscopy is discussed. Special emphasis is given on how to handle plant material for microscopy. Participants can use their own material to a certain extent during training sessions. Case studies highlight how microscopy methods can be applied in research. The course is completed with a round-table discussion where the participants discuss given case studies and possible applications of microscopy in their own projects.

The course is located partly at Lund University, Department of Biology, and partly at the Swedish University of Agricultural Sciences (SLU) campus Alnarp, Department of Plant Protection Biology.

Course leader

Salla Marttila
Swedish University of Agricultural Sciences (SLU)
Telephone: +46 40 41 55 22
E-mail: salla [dot] marttila [at] slu [dot] se

Co-leader

Ola Gustafsson
Lund University
The microscopy platform at the Department of Biology

Course period

24–28 November 2025

Course code

PLS0085

In this course, the participants will get hands-on experience of protein production and purification using bacterial and insect cell-based expression systems (baculovirus expression vector system (BEVS)). The course presents methods to express genes, which have products that are known, unknown or not well characterised, and to analyse the gene products. Theories behind the methods are discussed, and experiments are performed. 

The methods to be presented include

• optimisation of recombinant gene expression in Escherichia coli and in the BEVS
• affinity purification of tagged proteins
• using proteases for the removal of protein fusion tags
• generation and analysis of gene fusions
• molecular cloning
• metabolic engineering
• seleno-methionine incorporation for MAD phasing
• 2H-, 13C-, 15N-metabolic labelling for NMR studies
• production of perdueterated proteins for neutron-scattering experiments. 

Strategies for improving production of "difficult" proteins will be presented. The lectures will cover the current status of cell-based protein production systems and theoretical aspects of the methodology. The course will be held in collaboration with the Lund Protein Production Platform, LP3 (http://www.lu.se/lp3). Study format: lectures (ca 20%), student presentations (ca 5%), and laboratory exercises (ca 75%).

Course leader

Claes von Wachenfeldt
Department of Biology
Faculty of Science
Lund University
Telephone: +46 46 222 34 56
E-mail: Claes [dot] von_Wachenfeldt [at] biol [dot] lu [dot] se

Course period

8–12 December 2025

Course code

NABI009

This course gives an introduction to how to use protein mass spectrometry as a tool in protein science. Practical parts include protein and peptide sample preparation and sample deposition with different techniques, prefractionation of complex peptide samples by nanoLC and solid phase extraction with reversed phase chromatography. 

Manual and automated MS-data acquisition is conducted, for intact protein mass in linear mode, for peptide mass in reflector mode, and for peptide sequence information using MSMS. Also included is basic data analysis, using Mascot-searches for protein identification, assessment of PTMs and high-resolution MS/MS data to determine amino acid sequence. At the end of the course, the students have the possibility to analyse their own samples.

Course leader

Katja Bernfur
Department of Biochemistry and Structural Biology
Faculty of Science
Lund University
Telephone: +46 46 222 93 82; (0)731-571366
E-mail: Katja [dot] Bernfur [at] biochemistry [dot] lu [dot] se (Katja[dot]Bernfur[at]biochemistry[dot]lu[dot]se)

Course period

6–10 October 2025

Course code

NAKE007

Optical techniques are used to obtain information about the structure, interactions and dynamics of proteins. It is therefore the aim of the course to provide the necessary knowledge to collect “good and reliable” data, to understand preprocessing routines, and eventually to analyse the data. The course will cover the 4 main techniques found in protein spectroscopy: UV absorbance, Fluorescence, Circular Dichroism and Vibrational Spectroscopy.

The content included is

• short description of the techniques and what they can do
• short description of advanced usages of the techniques and analysis (accessories and software)
• short description and tutorial on data analysis, especially secondary structure estimation and conformational transitions
• lab practicals with all 4 techniques on standard proteins and on students' own proteins (data collection and analysis)

Course leader

Cedric Dicko
Pure and Applied Biochemistry
Department of Chemistry
Lund University
Telephone: + 46 (0)46 222 82 62
E-mail: cedric [dot] dicko [at] tbiokem [dot] lth [dot] se (cedric[dot]dicko[at]tbiokem[dot]lth[dot]se)

Course period

22–26 September 2025

Course code

KBK001F

Dates of the next course to be announced (1.5 ECTS).

This course’s aim is to provide a basic introduction to R, preparing students for using R in their own research. The course will use a combination of brief lectures and tutorials where the students will work on prepared problems. The last day of the course will include an open problems session where students are encouraged to bring their own data or analysis problems.

We will cover:

• basic R commands,
• basic data manipulation in R (different data structures),
• import and export of data,
• plotting commands (basic plotting and ggplot),
• functions for data summary and manipulation (for example, computing means, variances, maxima,
  minima, and apply-functions) and
• time permitting – basic statistics.

Course leader: Johan Lindström

Dates of the course to be announced (1.3 ECTS).

This four-day course introduces the fundamental principles of building phylogenies using molecular data, as well as the latest techniques and programs in this field. The aims of this course are to introduce the theory and practice of phylogenetic inference from molecular data and to introduce some of the most used methods and computer programs. 

The emphasis will be on model-based methods using maximum likelihood and Bayesian inference, with a focus on DNA sequences as data. We will introduce programs such as IQTREE, MrBayes, as well as BEAST for timing of divergence analyses. 

The course will consist of lectures, demonstrations of computer programs, and independent projects on fully analysing an example dataset (either your own or given by the lecturer). The course is aimed at PhD students but is also suitable for researchers at any stage, including motivated MSc students.  

Course leaders: Jadranka Rota & Niklas Wahlberg

Dates of the course to be announced (3 ECTS).

The aim of this course is to teach students how to develop and perform systematic reviews and meta-analyses. These are valuable techniques for identifying broad-scale patterns and trends in published literature. The course will provide practical training in how to perform systematic reviews and meta-analyses to a publishable standard, as well as how to assess the quality of other systematic reviews and meta-analyses.

This course will introduce key aspects of research data management through a combination of lectures and hands-on exercises. It is particularly suited for researchers looking to adopt a more systematic and reproducible approach to analysing and managing their research data. This course will be taught by NBIS with a number of places on the course reserved for IBIO students. The registration is closed.

Modern high-throughput technologies generate complex biological data that requires powerful yet accessible tools for analysis. This 3-day beginner-level workshop will introduce participants to data integration and multivariate analysis using the R package mixOmics. You will have the opportunity to analyse your own data under the guidance and advice of instructors.

Register no later than 26 August (Office form)

On 1 September, you will get an email to tell you whether you have a place on the course or not. 

Course leader: Kim-Anh Lê Cao, University of Melbourne

This five-day course will introduce the fundamental principles of phylogenetic comparative methods and their practical application through lectures and hands-on exercises in R. The course will cover topics such as plotting traits on phylogenies, character evolution modelling, ancestral state reconstruction and analysing data using linear phylogenetic models. 

Course leader: Charlie Cornwallis

This two-day course will train learners in the theory and application of codon-based tests for detecting the signals of natural selection. 

Course leader: Emily O’Connor