Project offers
IBG works in several ways to stimulate students themselves to create, develop and maintain relevant contacts with work-life. One part of this effort is to help you as a student to find suitable projects for research internships, degree projects, etc. In the project database, we publish project offers from academia, corporations and government agencies. We sometimes also announce different career-promoting events of a more general nature.
Some projects are described in English; others in Swedish. The current offers are listed below.
Project offers
Student project: Bioinformatic Pipeline for Monitoring Mutations Affecting Padlock Probe Performance
Published: 2026-10-21
Readily Diagnostics develops diagnostic products based on an isothermal amplification technology called rolling circle amplification, utilising padlock probes. Padlock probes are powerful molecular tools used for highly specific nucleic acid detection. Their performance depends on efficient ligation, which can be influenced by mismatches between the probe and its target sequence. Continuous monitoring of sequence variation is therefore essential for maintaining assay reliability.
This project focuses on developing a bioinformatic workflow for surveillance of mutations occurring in padlock probe target regions. The student will identify suitable genomic databases, develop an automated pipeline for retrieving and analysing sequence data, and implement methods to detect mutations in probe-binding sites. Using experimental data generated in a wet-lab based project, the pipeline will also evaluate the potential impact of identified mutations on probe ligation efficiency. The resulting workflow will support ongoing monitoring of assay performance and provide a framework for future probe design and optimization.
We are looking for a student with a bioinformatic background that can work with us during the spring semester 2027. Project length: 15 to 30 hp.
Contact: Sofia Larsson, sofia.larsson@readily.se
PhD-position: Evolutionary and Ecological Genetics
Published: 2026-10-07
Project description
A central question in evolutionary biology is whether evolution is repeatable, and whether the same genes contribute to repeated phenotypic adaptations. This question has important implications for predicting genetic responses to changing environments. This project aims to integrate mechanistic insights about phenotypic adaptation with genomic data to understand how species evolve adaptations to changes in their environment.
The project will leverage data from a large-scale Evolve-and-Resequence experiment in a cosmopolitan insect pest, the seed beetle Callosobruchus maculatus. This unique system allows us to study the roles of determinism and chance in local adaptation and the evolution of a species’ ecological niche. Extensive phenotypic, RNA-seq, and DNA pool-seq data are available from multiple time points in the experiment, which is still ongoing. Several other C. maculatus strains sampled across its global distribution and closely related seed beetle species are available in the host lab. This provides opportunities for comparative genomics and additional experiments and data collection to further develop the project.
Duties
The PhD project will involve a combination of experimental work and bioinformatic analysis, with emphasis on the latter. The exact balance between tasks may depend on the candidate's interests and the project's development.
PhD students at the Institute of Ecology and Genetics (IEG) have the option to engage in teaching and to develop their pedagogic CV by taking courses. The type and level of teaching will depend on availability and the student's interests but cannot exceed 20% full-time employment. The position and funding is extended by the time the student has engaged in teaching.
The PhD candidate will work with the main supervisor David Berger and with the co-supervisor, SciLifeLab fellow Dr. Gabriela Montejo-Kovacevich, both at IEG.
Qualifications required
To meet the entry requirements for doctoral studies, you must:
- hold a Master’s (second-cycle) degree in Evolutionary Biology, Ecology, Bioinformatics, or a related field, or
- have completed at least 240 credits in higher education with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
- have acquired equivalent knowledge in some other way (e.g. extensive research experience).
Candidates who have not yet completed their degree but are expected to meet the degree requirements before the start date are encouraged to apply.
The ideal applicant should also:
- Have a grasp of key concepts in ecology and evolutionary biology/genetics.
- Have experience with programming and scripting.
- Be highly motivated and curious and thrive in a collaborative environment.
- Be able to take responsibility for carrying out and finishing independent tasks and projects.
- Candidates must be able to express themselves at a high level in spoken as well as written English.
For further information about the position, please contact: Associate Professor, David Berger, david.berger@ebc.uu.se
Master thesis project: Optimization of cultivation media components removal using tangential flow filtration with a Design of Experiment (DOE) based approach
Published: 2026-10-07
We are currently looking for a chemical, biomedical or biochemistry student (or within other relevant fields) who would like to perform their master thesis at GALDERMA for the spring semester of 2027.
As part of your master thesis you will join the Product Science Bioprocess Development team at the GALDERMA site in Uppsala, Sweden. The team has actively worked over several years with developing a novel pharmaceutical product using a manufacturing process involving cell fermentation, cell culture clarification and filtration, along with chromatographic separation techniques.
The aim of this project revolves around optimization of a tangential flow filtration (TFF) step in a protein manufacturing process, with the purpose of removing process-related impurities in the form of residual cultivation media components and small molecules. The focus will be to evaluate the significance, effects and interactions between different process parameters, and statistically predict optimal running conditions.
The DOE design will be constructed using the statistical software JMP, and the experiments will be conducted using an ÄKTAflux system. The project also includes the analysis of generated experimental samples using size exclusion chromatography (SEC), spectrophotometry and nuclear magnetic resonance (NMR) spectroscopy.
If you are interested and would like to apply or have additional questions about the project you are most welcome to contact me:
Sebastiaan Mul, Manager Bioprocess Development Group, Product Sciences, sebastiaan.mul@galderma.com
PhD-position: Modelling phytoplankton succession in lakes
Published: 2026-10-07
Project Description
Phytoplankton form an important foundation of lake food webs and their community composition changes markedly throughout the year in response to physical and chemical changes as well as predation pressures. These changes are in turn moderated by different functional traits between groups, which determine how they respond to environmental conditions. Using models, we can study how environmental changes (such as climate warming, eutrophication, and extreme weather events) influence successional patterns in phytoplankton and identify conditions that create windows of opportunity for specific functional groups. We can then use these models to assess potential future changes. We are seeking a highly-motivated PhD student who is keen to use process-based biogeochemical models to investigate these dynamics. The outcomes of this work will improve our ability to forecast changes in phytoplankton communities, with direct application to lake ecosystem functioning and drinking water provisioning. The position is based at Uppsala University’s Department of Ecology and Genetics, within the Limnology program.
Duties
Your duties will have a strong focus on data handling and process-based, dynamical modelling, but also include teaching, course work, and collaborating in research teams.
Requirements
To meet the entry requirements for doctoral studies, you must
- hold a Master’s (second-cycle) degree in limnology, aquatic ecology, environmental sciences, geoscience, biology, environmental engineering or other relevant subjects at the time of employment, or
- have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
- have acquired substantially equivalent knowledge in some other way.
Candidates who have not yet completed their degree but are expected to meet the degree requirements before the start date are encouraged to apply.
This work lies in the intersection of physics, biogeochemistry, and ecology, and has a strong numerical emphasis. Eligible candidates need to demonstrate skills with advanced numerical approaches (e.g. modelling, statistics, or large-scale data analysis). Some programming experience (for example in R or Python) is required. Candidates must be able to express themselves to a very high degree in spoken as well as written English. In the evaluation of candidates, particular emphasis will be put on personal qualities such as independence, strong motivation and teamwork skills.
For further information about the position, please contact: Jorrit Mesman, jorrit.mesman@ebc.uu.se
Master thesis project: Do hybrid flycatchers experience reduced cognitive abilities?
Published: 2026-10-06
Background: Collared (Ficedula albicollis) and pied (F. hypoleuca) flycatchers naturally hybridize on the Swedish island of Öland, where we study various reproductive barriers to learn more about the process of speciation (Qvarnström et al. 2010). Selection against hybrids is an important post-zygotic reproductive barrier. We have found that hybrid flycatchers have impaired physiological abilities (sterility and reduced survival) due to incompatibilities between the two parental genomes. Whether the reduced survival chances can be explained by, e.g., reduced foraging success due to compromised neural development or impaired cognition remains unknown.
Objective: To investigate whether flycatcher hybrids experience reduced cognitive abilities.
Your Role: You will perform cognition and personality assays on collared and pied flycatchers as well as on their hybrids. This will involve:
- Behavioural assays: Conducting commonly recognized and used cognition and personality assays on individuals near the nest boxes they breed in. Setting up remote video cameras to record assays and measuring behaviours afterwards.
- Data Collection and Analysis: Quantifying behaviours from video recordings of assays and comparing individual behavioural performance across species and with the hybrids.
- Long-term monitoring fieldwork: Participating in long-term breeding data collection by monitoring nest boxes and measuring nestlings.
Requirements:
- You need to be enrolled in a Master's programme (in Sweden or abroad) that insures you while working at Uppsala University and on Öland (Sweden) during the field season. We are also open to ERASMUS traineeships.
- You need to be available for the whole of next field season (1 May to 1 July 2027). Joining us in the field for the full two months is essential.
If you meet these conditions, this project is for you!
Contact: Michaëla Berdougo (michaela.berdougo@ebc.uu.se)
Master thesis project: Effects of phenological mismatch on top-down regulation
Published: 2026-10-06
Background: Tritrophic interactions, such as the tree-caterpillar-bird food chain, play an important role in ecosystems. For example, insectivorous birds, such as flycatchers, may have a role in top-down regulation of caterpillar populations, reducing the insect damage on trees. Climate change is however disrupting these tritrophic interactions, as warmer springs cause trees to bud and caterpillars to hatch earlier, and birds may not be able to adjust to the earlier emergence of caterpillars quickly enough, resulting in phenological mismatches. This may lead to an increase of insects in trees, which may increase defoliation, reduce growth, or lead to tree death. If flycatchers are potentially important agents of top-down regulation, what will happen to tree growth if bird-caterpillar phenological mismatches exist? We hypothesize that years with larger flycatcher-caterpillar mismatch will impose severe consequences on tree growth, due to higher pressure from herbivorous caterpillars that experience lower predation pressure from the mismatched birds.
Objective: To understand the effects of caterpillar-bird phenological mismatch on tree growth over the last 20+ years.
Your Role: You will make use of the long-term flycatcher-caterpillar phenological mismatch data and associate it with tree growth at this population's breeding sites over the last 20+ years. This will involve:
- Field work: Extracting tree cores from oak and hazel trees in the breeding sites of the long-term flycatcher study on Öland, and measuring stem density and basal area of vegetation composition at the studied sites.
- Data Collection and Analysis: Extracting tree growth from the collected tree cores, and statistically linking it with flycatcher-caterpillar phenological mismatch, obtained from the long-term breeding data.
- Long-term monitoring fieldwork: Participating in long-term breeding data collection by monitoring nest boxes and measuring nestlings.
This project offers a rare opportunity to work at the intersection of climate change, trophic interactions, and evolution, using a powerful dataset to answer a pressing ecological question.
Requirements:
- You need to be enrolled in a Master's programme (in Sweden or abroad) that insures you while working at Uppsala University and on Öland (Sweden) during the field season. We are also open to ERASMUS traineeships.
- You need to be available for the whole of next field season (1 May to 1 July 2027). Joining us in the field for the full two months is essential.
If you meet these conditions, this project is for you!
Contact: Michaëla Berdougo (michaela.berdougo@ebc.uu.se)
Master thesis project: Climate Change, Mismatch, and Survival
Published: 2026-10-06
Background: Climate change is disrupting the tritrophic terrestrial tree-caterpillar-bird food chain. In our study system, warmer springs cause trees to bud and caterpillars to hatch earlier. However, migratory birds like our study species, the pied and collared flycatchers, have not advanced their breeding schedules as much. This creates a "phenological mismatch": when the nestlings hatch, the peak abundance of caterpillars they need for food may have already passed.
This mismatch is most severe in warm springs and acts as a powerful agent of natural selection. But there can only be an evolutionary response to selection if there is genetic variation in the traits subject to selection. Why do some nestlings survive these poor conditions while others do not? Understanding the key traits that determine the birds' resilience is thus important to better predict how climate change will affect populations.
Objective: To determine which individual phenotypic traits are key to an individual's resilience to climate-driven trophic mismatches.
Your Role: You will investigate how a nestling's innate physiology influences its ability to survive this mismatch. This will involve:
- Data Analysis & Modelling:
- Analysing high-resolution measurements from nestlings.
- Working with our long-term demographic dataset (survival, breeding dates, etc.) spanning multiple years.
- Quantifying the annual degree of phenological mismatch between birds and caterpillars.
- Using statistical modelling to determine if offspring with certain traits have a survival advantage.
This project offers a rare opportunity to work at the intersection of physiology, climate change, and evolution, using a powerful dataset to answer a pressing ecological question.
Requirements:
- You need to be enrolled in a Master's programme (in Sweden or abroad) that insures you while working at Uppsala University and on Öland (Sweden) during the field season. We are also open to ERASMUS traineeships.
- You need to be available for the whole of next field season (1 May to 1 July 2027). Joining us in the field for the full two months is essential.
If you meet these conditions, this project is for you!
Contact: Michaëla Berdougo (michaela.berdougo@ebc.uu.se)
Master thesis project: Cognition and capacity to perceive olfactory cues
Published: 2026-10-05
Background: Tritrophic interactions, such as the tree-caterpillar-bird food chain, play an important role in ecosystems. For example, insectivorous birds, such as flycatchers, may have a role in controlling caterpillar populations, reducing the insect damage on trees. Climate change is however disrupting these tritrophic interactions, as warmer springs cause trees to bud and caterpillars to hatch earlier, and birds may not be able to adapt to the earlier emergence of caterpillar larvae quickly enough to avoid population decline. Cognition, and more specifically learning, should provide the right mechanisms for the behavioural adaptation needed in changing environments to cope with variation and uncertainty (Ghosh et al. 2023). To fully understand the general ability of birds to act as active biological control agents it is thus important to consider the cognitive processes underlying behaviours.
Objective: To understand whether individual variation in learning, cognition, and behavioural plasticity in flycatchers provides an advantage in detecting insect herbivore-induced emission of biogenic volatile organic compounds (IH-BVOCs) for foraging.
Your Role: You will experimentally test how variation in cognitive abilities influences the birds' ability to identify IH-BVOCs. This will involve:
- Behavioural assays: Conducting commonly recognized and used cognition assays on individuals near nest boxes, and volatile discrimination tasks on the same individuals. Setting up remote video cameras to record assays and measuring behaviour afterwards.
- Chemical Sampling: Maintaining control oak seedlings and experimentally manipulated seedlings that emit higher IH-BVOCs, for use in behavioural assays. Collecting IH-BVOC samples for subsequent chemical analysis.
- Data Collection and Analysis: Quantifying behaviours from assay recordings and linking individual behavioural performance with each individual's accuracy in discriminating seedlings with higher IH-BVOC emission.
- Long-term monitoring fieldwork: Participating in long-term breeding data collection by monitoring nest boxes and measuring nestlings.
Requirements:
- You need to be enrolled in a Master's programme (in Sweden or abroad) that insures you while working at Uppsala University and on Öland (Sweden) during the field season. We are also open to ERASMUS traineeships.
- You need to be available for the whole of next field season (1 May to 1 July 2027). Joining us in the field for the full two months is essential.
If you meet these conditions, this project is for you!
Contact: Michaëla Berdougo (michaela.berdougo@ebc.uu.se)
Master thesis project: Using Olfactory Cues to Find Food
Published: 2026-10-05
Background: While it has been shown that excluding birds from crop fields can lead to increased insect damage (e.g., Garcia et al., 2018), their regulation role in natural settings remains unknown as well as the mechanisms by which birds locate the best feeding spots. Ground-breaking research, including our own, suggests that olfaction may play a crucial role. We have found that genetic variation in olfaction-related genes in collared flycatchers is linked to the amount of caterpillar larvae on their breeding territories. Does this mean that flycatchers actually use olfaction cues to locate trees that are heavily infested with their prey? If true, this means that we have severely underestimated the birds' capacity to detect and respond to local pest outbreaks.
Objective: To directly test the hypothesis that pied and collared flycatchers use insect herbivore-induced emission of biogenic volatile organic compounds (IH-BVOCs) to identify trees with more caterpillars.
Your Role: You will manipulate IH-BVOC emissions from sampled tree branches and observe the change in birds' activity, before and after manipulation. This will involve:
- Field Observation & Monitoring: Manipulating tree branches by adding a component that induces the emission of IH-BVOCs, and setting up remote video cameras to monitor bird visit rates to those tree branches.
- Chemical Sampling: Collecting IH-BVOC samples from experimental branches for subsequent chemical analysis.
- Data Analysis: Statistically linking the chemical profiles of trees with recorded bird foraging activity, obtained from video recordings.
- Long-term monitoring fieldwork: Participating in long-term breeding data collection by monitoring nest boxes and measuring nestlings.
This project offers a unique opportunity to contribute to a cutting-edge field and help answer a fundamental question with implications for both basic and applied ecology.
Requirements:
- You need to be enrolled in a Master's programme (in Sweden or abroad) that insures you while working at Uppsala University and on Öland (Sweden) during the field season. We are also open to ERASMUS traineeships.
- You need to be available for the whole of next field season (1 May to 1 July 2027). Joining us in the field for the full two months is essential.
If you meet these conditions, this project is for you!
Contact: Michaëla Berdougo (michaela.berdougo@ebc.uu.se)
Project offer: Development of fluorescence labelled HSA assays for detection of cellular internalization of receptor bound Affibody® molecules
Published: 2026-10-05
Execution:
Cell binding assays are commonly used to identify molecules that can bind to tumor cell targets. A cell internalization assay measures how much of a ligand, Affibody® molecule, is taken up into cells after binding. If the targeting molecule is a monoclonal antibody, there are several commer-cially available reagents for detection of both bound and internalized antibodies. With Affibody® molecules, an extra staining step with proprietary antibody reagents is currently needed. The pro-ject aims to develop alternative ways of visualizing cell-bound and internalized Affibody® mole-cules by utilizing the strong interaction between the albumin-binding domain (ABD), often incor-porated in Affibody® molecules for half-life extension, and human serum albumin (HSA). If there is time, other alternative staining techniques will also be explored.
Key features included in the project:
- Evaluate different pH sensitive fluorophores and techniques for labeling HSA.
- Perform routine cell culture in a sterile environment.
- Develop and optimize cell staining protocols for different tumor in vitro cell models.
- Develop and optimize acid-wash methods for separating surface-bound and internalized material.
- Analyze stained cells with flow cytometry, in a plate reader and depending on instrument availability, the live cell imaging platform Incucyte®.
- Quality testing of the final new protocol.
Supervisor: Malin Ryner, PhD. If you have any questions, please contact: malin.ryner@affibody.se. Affibody AB, Scheeles väg 2, 171 65 Solna.
Application: If you are interested, send your personal letter and CV to jobs@affibody.se latest October 16th, 2026, and mark your application with EX050.
Career day: CHaSE 2026
Published: 2026-09-30
CHaSE 2026, Friday 23 October, Aula Medica, Solna. Free to attend, open to all universities.
Register: https://luma.com/maqodj4b
Upload your CV: https://chasesthlm.se/chase-cv-upload/
CHaSE is Stockholm's premier career fair in life science and health, run by students since 2014. Companies and organisations of all sizes set up booths to meet you, with mainstage talks, panel discussions and workshops running in parallel throughout the day.
Already confirmed: AstraZeneca and Sanofi, with more announced every week across pharma, biotech, MedTech, healthcare, consulting and clinical R&D, from start-ups to international companies and NGOs.
Whether you are BSc, MSc, PhD or postdoc, and whether you already know what you want or have no idea yet, it is a low-pressure way to see what the industry actually looks like.
Follow @chasesthlm on Instagram or CHaSE Stockholm on LinkedIn for the company announcements.
Student project: Improving diagnostics of Chlamydia psittaci
Published: 2026-09-29
Background
Our laboratory provides service in clinical microbiology, mainly for the health care in Region Uppsala but also some national reference tasks. One of our national reference tasks is diagnostics of Chlamydia psittaci, a species that may cause zoonotic infections in humans, even with severe outcome.
At present >12 different Chlamydia species are defined of which some are zoonotic and cause human infections. The most prevalent species is C. psittaci having birds as natural host. Other species occasionally causing human infections are C. caviae, C. abortus and C. felis. We wish to improve our diagnostics and also genotype detected C. psittaci cases. The aim is to study the transmission from birds to humans and identify C. psittaci genotypes and their linkage to different kind of birds. This will improve the epidemiological understanding of the zoonosis psittacosis. The study has focus on Swedish psittacosis cases but it is also linked to an international multicenter study in Europe.
We will use HRM-PCR, a special kind of PCR based on melt curve analysis, and also gene sequencing.
The project can preferably start in 2026 or at least in early 2027.
Contact person and supervisor: Björn Herrmann
Mail: bjorn.herrmann@medsci.uu.se
PhD-positions: TagTIC Marie Skłodowska-Curie Doctoral Network
Published: 2026-09-07
We are currently recruiting 11 fully funded PhD candidates for the TagTIC Marie Skłodowska-Curie Doctoral Network (Joint Degree for 4 years), focusing on infection-driven gastrointestinal cancers. The projects cover a broad range of topics, including cancer biology, microbiology, immunology, organoids, multi-omics, drug discovery, medicinal chemistry, AI and digital pathology.
We would particularly appreciate reaching motivated candidates who are interested in interdisciplinary and international PhD training at the interface of infection biology and cancer research.
Further information about TagTIC and the individual PhD projects is available at www.tagtic.eu. The projects are scheduled to start in January 2027.
Master’s Thesis Project: Friendly Neighbours? Investigating Mitochondrial Transfer Between Cells
Published: 2026-08-20
This project aims to establish a reliable method for transferring mitochondria between cells and determine whether transferred mitochondria can restore metabolic function in cells lacking functional mitochondria, providing the basis for an exciting new research project investigating mitochondrial compatibility.
The student will work with 143B and mitochondria-deficient 143B Rho cells. The project will address the questions:
- Can mitochondria be transferred efficiently into 143B Rho recipient cells?
- Which mitochondrial transfer method is most effective?
- Can transferred mitochondria restore metabolic function in recipient cells?
- How do recipient cells respond to the introduction of functional mitochondria?
Tasks
The student will undertake experimental laboratory work and associated data analysis. Tasks will include:
- Mammalian cell culture using 143B and 143B Rho cells.
- Experimental planning and optimisation of mitochondrial transfer protocols.
- Isolation and fluorescent labelling of mitochondria from donor cells.
- Comparison of mitochondrial transfer methods, including co-culture and centrifugation-assisted delivery.
- Assessment of mitochondrial transfer using fluorescence microscopy.
- Detection and quantification of transferred mitochondrial DNA using digital PCR.
- Real-time measurements of cellular metabolism using the recipher system.
- Analysis, visualization, and biological interpretation of experimental data.
- Scientific writing and presentation of the findings.
Requirements
We are looking for a motivated Master’s student with:
- A background in cell biology or a related subject.
- An interest in mitochondrial biology, cellular metabolism, physiology, or biomedical research.
- An ability to work carefully and independently in a laboratory environment.
- Good scientific communication and writing skills in English.
Previous experience with mammalian cell culture is preferable.
Practical information
Extent/credits: 45 or 60 hp, with preference for a 60 hp project.
Start date: Spring 2027.
Location: Programme for Physiology and Environmental Toxicology, Evolutionary Biology Centre, Uppsala University.
Supervision: Andrea Cediel Ulloa and John Lees, Uppsala University.
Contact: John Lees, john.lees@ebc.uu.se
To apply, please send a short CV describing your educational background and any relevant laboratory experience. Informal enquiries about the project are also welcome.
Master's Thesis Project: Genetic and Epigenetic Adaptation to Environmental Unpredictability
Published: 2026-08-11
Project aims
The project will investigate whether birds living under contrasting levels of environmental predictability differ in their genetic and epigenetic profiles.
Depending on the duration of the thesis and the student’s interests, the project could address questions such as:
- Do the Atacama and Fray Jorge populations exhibit genetic differentiation?
- Which genomic regions show differential DNA methylation between the environments?
- Are the observed molecular differences associated with genes and biological pathways involved in environmental responses, metabolism, stress regulation, or life-history transitions?
- To what extent are differences in DNA methylation independent of, or associated with, the underlying genetic variation?
Tasks
The student will work primarily with bioinformatic and statistical analyses. Tasks may include:
- Quality control and processing of GBS-MeDIP sequencing data.
- Read alignment and assessment of sequencing coverage.
- Identification and analysis of SNPs and differentially methylated regions.
- Population structure and genetic differentiation analyses.
- Genomic annotation and functional enrichment analysis.
- Integration of genetic, epigenetic, environmental, and phenotypic information.
- Visualization and biological interpretation of the results.
- Scientific writing and presentation of the findings.
Requirements
We are looking for a motivated Master’s student with:
- A strong interest in evolutionary biology, genomics, epigenetics, or adaptation to changing environments.
- Previous experience with bioinformatics, R, UNIX/Linux, or analysis of sequencing data.
- An ability to work independently while participating actively in project discussions.
- Good scientific communication and writing skills in English.
Previous experience with population genomics or DNA methylation analysis is advantageous but not essential.
Practical information
Extent/credits: 30, 45, or 60 hp.
Start date: Autumn 2026 or spring 2027, according to agreement and data availability.
Location: Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University.
Supervision: Fábio Pèrtille and (co) Carlos Guerrero-Bosagna, Uppsala University, in collaboration with Paulina González-Gómez, University of California, Davis.
Contact: Fábio Pèrtille, fabio.pertille@ebc.uu.se
To apply, please send a short statement describing your interest and relevant experience, together with your CV and transcript of records. Informal enquiries about the project are also welcome.
Master thesis project: Root fusion in plants – establishing a model system using strangler figs
Published: 2026-08-06
In nature, natural grafts can form when roots press against each other and create a functional fusion. Such root fusions can for example transfer carbohydrates to support shaded trees. Root fusion is common in forests between trees of the same species, especially in forestry plantations where many individuals are closely related. This is a major problem within forestry because pathogens, such as root rot fungus, can spread using root grafts, so forestry seeks to suppress root grafting.
We would like to study the root fusion (also called root grafting) process further - for this it would be useful to have a lab based model system. Plants of the genus Ficus is promising as a root fusion model system because a subset of Ficus species, the strangler fig trees, create abundant root grafts as they grow.
Project tasks: The master project would be mostly lab based, and involve growing plants, setting up experiments, histology, and imaging. You would establish a model system for studying root fusion in the laboratory, and describe in detail how fusion occurs within a plant individual for one or two species. Imaging would be done initially by confocal microscopy or light microscopy, then you would prepare thin embedded sections using a microtome for detailed morphology analyses such as cell division patterns and vascular differentiation. Fluorescent dyes can be applied and movement of the dye followed. If time allows you could also set up experiments to test other questions, such as to what degree fusion between different individuals and species is affected by how closely related they are, or whether you could produce root fusion in the lab in other species such as Norway spruce or Scots pine. Apart from the lab skills you will also get experience with scientific writing and presentation.
Location: Lab work will be in Charles Melnyk’s lab at SLU Uppsala. Supervision will be by Charles Melnyk (SLU Uppsala; https://melnyklab.com/) and Charlotte Jandér (UU; https://sites.google.com/view/charlottejander/home).
Project length: 30 / 45 / 60 hp.
Start date: According to agreement.
Contact: If interested, please contact charlotte.jander@ebc.uu.se
Master thesis project: The gut microbiota and its metabolites in multiple sclerosis: new routes to predicting disability progression
Publshed: 2026-06-29
Project description
This master project addresses one focused part of our wider MS research programme: expanding the set of reference standards available for studying gut microbiota–derived metabolites in MS. The gut microbiota produces and modifies a wide range of small molecules, including bile acids as well as other microbially derived metabolites, that signal to the host and may influence MS disease progression. Many of the metabolites that appear most relevant to MS are not available commercially as reference standards, which currently prevents us from confidently identifying and quantifying them in patient samples.
To remove this barrier, the project combines organic synthesis with analytical chemistry and translational research.
- Synthesise a selection of novel standards for gut microbiota–derived metabolites relevant to MS (for example bile acids or other microbial metabolites) that are not available commercially.
- Characterise the synthesised compounds by LC-MS, establishing chromatographic and mass-spectrometric properties such as retention behaviour and fragmentation patterns.
- Use the characterised standards to identify and confirm the corresponding metabolites in human samples, supported by our LC-HRMS method.
- Evaluate the role of the identified compounds in MS disease progression.
The project gives hands-on experience across the full workflow, from bench synthesis, through method development on modern high-resolution mass spectrometry instrumentation, to clinical relevance, within a translational research environment, and contributes directly to ongoing studies of MS disease progression.
Suitable student profile
We are looking for a motivated student who is curious about applying chemistry to questions in human health. The ideal candidate has:
- A strong background in chemistry, with a particular emphasis on organic chemistry and practical synthesis experience.
- Some familiarity with analytical chemistry, ideally including chromatography and/or mass spectrometry (training will be provided).
- An interest in metabolomics, the gut microbiota, and biomedical or translational research.
- The ability to work carefully and independently in the laboratory, while collaborating within a multidisciplinary team.
Practical information and how to apply
Extent / credits: 30 / 45 / 60 hp
Start date: After agreement
Location: Department of Medical Sciences, Uppsala University,
Supervisor / contact: Ida Erngren — ida.erngren@uu.se
To apply, please send a short letter of motivation together with your CV and a transcript of records to the contact above. We are happy to answer any questions about the project before you apply.
Master thesis project: Investigation of nucleotide and structural preferences in miRNAs that specify their binding to different Argonautes in Dictyostelium
Published: 2026-05-29
Project overview
The social amoeba, Dictyostelium discoideum is an eukaryotic model organism with the property of aggregative multicellularity. This unicellular organisms upon starvation, initiates a developmental program that enables transition from free-living cells to multicellular structures. Micro(mi)RNAs are key regulators of gene regulation. Caenorhabditis elegans, yet another foundational model organism, is widely studied to understand fundamental biological mechanisms. The core RNA interference (RNAi) machinery—specifically the Argonaute (Ago) protein family—is deeply conserved between C. elegans and D. discoideum, despite the two lineages diverging roughly one billion years ago. However, why the Argonaute select specific miRNAs to repress their target genes, has not been well studied. The current project investigates the preferential selection of microRNAs by Ago protein subfamilies from both model organisms.
Scientific aim
The project aims to build a deep learning-based (DL) classifier model to learn the sequence and structural preferences in microRNAs, that dictate their binding to specific Argonautes in Dictyostelium. With expressed RNAs, stratified into different Ago/Dicer KO conditions, and utilizing relative expression of the miRNA, cellular localization and conserved protein domains, we will build the DL classifier model. Furthermore, publicly available small RNA-seq data (and iPAR-CLIP datasets - to screen for functional miRNAs) from C. elegans, will be used for model inference. The project will aim to identify the nucleotide patterns necessary for D. discoideum miRNAs and their variants (or isomiRs) to bind to specific Ago in the cell. The resulting model will serve as a baseline that can be extended to Argonautes/dicers from other organisms to discover additional rules that may specify miRNA selection.
Requirements
- python programming and bash scripting
- basics of machine learning and deep learning, building models and inference
- basic bioinformatics knowledge will be helpful
- interest in learning about small RNA biology
For more information, contact
Ranjan K Maji, BMC, Uppsala University (ranjan.kumar.maji@icm.uu.se) and Fredrik Söderbom, BMC, Uppsala University (fredrik.soderbom@icm.uu.se)
Master thesis project: Does antiparasitic treatment change the reindeer gut microbiome?
Published: 2026-05-20
Info: Reindeer are semi-domesticated cervid ruminants which roam and forage freely in Sweden. The calves are given Ivermectin (antiparasitic drug) to reduce reindeer bot fly infections. It is still unknown how this treatment affect their intestinal microbiota (the symbiotic bacteria).
In this collaboration between UU and SLU, we have collected fecal samples from reindeer calves before treatment and two times points after treatment. We have evaluated changes in parasite load and now we want to investigate any effect ivermectin might have on the gut microbiota.
Tasks include: Analyze microbiome DNA sequence data in R, interpret results, read scientific papers, and write a thesis about the findings. The findings will be published in a scientific journal. There’s also an opportunity for a short field trip sometime during the winter 2026/2027.
Requirements: An interest in learning about wildlife microbiomes, parasites, and coding in R.
Duration: ~20 weeks (30 hp). Start: Nov 2026 or later.
Contact: Elin Videvall, Animal Ecology, EBC, Uppsala University (elin.videvall@ebc.uu.se) and Peter Halvarsson, Animal Biosciences, SLU Uppsala (peter.halvarsson@slu.se).
Master thesis project: Ultrasound-based staging of mouse embryos for automated developmental classification
Published: 2026-04-20
Scientific aim
This project aims to generate a validated reference atlas of ultrasound images of mouse embryos mapped to precise Theiler stages through ex vivo histological confirmation. In addition to establishing an ultrasound based staging pipeline, the project will address the biological question of developmental heterogeneity within individual pregnancies at defined embryonic ages. It will further identify anatomical landmarks that can be reliably recognized by ultrasound and validated by histology, thereby informing stage specific strategies for precise in utero embryonic manipulation. The resulting dataset will also serve as a standardized resource for future machine learning based automated stage classification.
Research questions
1. What is the range of developmental stages present within individual pregnancies at the same nominal embryonic day and time?
2. Which anatomical structures can be reliably identified by ultrasound at different developmental stages and confirmed by histological analysis?
Expected outcomes
The resulting dataset will be used to train machine learning models that enable automated stage recognition, ultimately supporting real-time decision-making for applications such as automated embryo injection systems.
60 hp project
Contact: Robert Tonoian, robert.tonoian@ki.se
Master’s Thesis Projects (45/60 credits): Molecular Mechanisms of Behavior
Published: 2026-03-26
Are you interested in the interplay between evolutionary biology and animal behavior? We invite students to join our research program for a thesis project exploring molecular mechanisms underlying key phenotypic traits in the guppy (Poecilia reticulata), an important model system in behavioral and evolutionary biology.
What you’ll be doing
Your project will build on extensive groundwork of experimental evolution, behavioral experiments, and molecular work which have produced datasets ready to be analyzed. Your work will be purely computational: analyzing sequence data, building visualizations, and producing results aimed to directly contribute to a scientific manuscript.
You will contribute to developing bioinformatic pipelines combining short- and long-read RNA sequencing to study gene expression and alternative splicing. How to best combine data from multiple technologies is an emerging field, providing the opportunity to contribute to exploratory work at the intersection of bioinformatics and behavioral biology.
Alongside the computational work, there will be a strong emphasis on understanding both animal behavior and bioinformatics methods literature, scientific writing, and communicating results clearly, treated as an integral part of your training throughout the project.
Two available themes
- Development of sexually selected traits: how gene expression and alternative splicing contribute to characters shaped by sexual selection across developmental stages.
- Social cognition: genomic and transcriptomic variation associated with behavioral differences following exposure to different predation pressures.
The project is available immediately.
More information about the lab: albertocorralscience.github.io
Please send a short statement of interest to alberto.corral@ebc.uu.se. Informal inquiries to discuss the projects are also very welcome.
Master’s Thesis Projects: Comparative Life‑History Analysis in Gerridae
Published: 2026-03-18
Are you interested in evolutionary biology, insect ecology, or comparative life‑history strategies?
We invite motivated students to join our research group for a thesis project (can be adapted to 30, 45 or 60 hp) exploring developmental and morphological variation across the insect family Gerridae (water striders).
Project Overview
Water striders (Hemiptera: Gerridae) provide an excellent model system for studying how life‑history traits evolve in relation to habitat, phylogeny, and environmental constraints. This project investigates four central traits: developmental time, fecundity, wing length/morph frequency, and body size.
Student Responsibilities
- Collect and curate trait data (in spring 2026), published studies or already available lab datasets.
- Conduct statistical and comparative analyses.
- Produce visualizations and interpret results in an evolutionary context.
What You Will Learn
- Insect collection, rearing and handling
- Comparative methods and statistical modelling.
- Data synthesis across species.
- Insect morphology and life‑history evolution.
- Scientific writing and presentation skills.
Who Should Apply?
Ideal for students interested in behavioral ecology, evolutionary biology, insect ecology, life‑history theory, or quantitative analysis. Experience with R is helpful but not required.
How to Apply
Please send a short statement of interest to arild.husby@ebc.uu.se.
Master thesis project: Meadow restoration in Kvikkjokk
The Unit of Biotope Monitoring at the Ecology Department of SLU (Ultuna) is seeking a motivated master’s student with an interest in habitat restoration and landscape ecology. The student would work on the restoration of a hay meadow near Kvikkjokk (Norrbotten) after 70 years of abandonment. The site provides a rare opportunity to study vegetation recovery and management needs in a unique biogeographic area.
The project’s objectives are: (a) to develop a long-term management plan for the meadow, (b) to map internal land-use zones within the meadow, (c) to quantify how prolonged abandonment has affected vegetation structure compared to other meadows in the region.
The project starts in summer and it includes one week of fieldwork in late July in Kvikkjokk followed by vegetation, landscape, and species composition analysis. B-level driving licence is required.
Contacts: Giulia Zacchello (giulia.zacchello@slu.se)
Anders Glimskär (anders.glimskar@slu.se)
Master thesis project: Greenhouse gas and oxygen dynamics in littoral zones of lakes
Published: 2026-02-12
Background
Lakes are affected by climate change that can trigger a dangerous feedback loop by increasing the amount of greenhouse gases (GHG, i.e. carbon dioxide (CO2) and methane (CH4)) released by lakes. This research project specifically deals with GHG emissions and oxygen (O2) dynamics in littoral zones of lakes, which are hotspots for lake CH4 emissions but can also take up atmospheric CO2 and act as carbon sinks.
Project aims and description
In this project, the student will determine how emergent macrophytes affect O2 and GHG dynamics over short time scales in a greenhouse experiment and in situ at the lake Erken. The student will then model GHG and O2 dynamics over diurnal cycles using the collected data to estimate net ecosystem productivity, gross productivity and respiration. This master project is connected to two large projects RELITORATE and CLIMIPHY, the student will work in team and have multiple possibilities for interaction
Qualifications
Interest in biogeochemistry. Interest in working in the field and lab but also in modelling. The project will involve spending time on a small boat or docks close to the shore of lakes.
Department: Department of Ecology and Genetics, Uppsala University (limnology unit)
Place: EBC, Uppsala
Start: Spring 2025 or later
Application: charlotte.grasset@ebc.uu.se
Credits: preferably 45-60 but can be discussed
Master thesis project: The fate of organic matter in sediments of constructed wetlands
Published: 2026-02-04
Constructed wetlands accumulate large amounts of organic carbon in their sediments, constituting a strong carbon sink. However, in order to maintain the function of the constructed wetland (e.g. retention of nutrients or contaminants), the sediments need to be removed at regular intervals, typically every 15-20 years. The removed sediment is commonly either piled up on land, moved into a pit, or dewatered prior to putting it on a landfill. However, at present it is unclear what effect these different ways of dealing with removed sediment have on the fate of the sediment organic matter. If the sediment organic matter is degraded and produces the powerful greenhouse gases methane and nitrous oxide, the wetland’s climate footprint will become greater. Conversely, if the removed sediment organic matter is stabilized, or only partially transformed back to carbon dioxide, the wetland is more climate-friendly.
This project will use an experimental approach, and simulate different strategies of handling removed sediment of a constructed wetland at the lab-scale, measuring the emission of the greenhouse gases CO2, CH4 and N2O. Potentially, and depending on the length of the MSc thesis (30, 45 or 60 hp), it might also be possible to do meso-scale outdoor experiments, using larger volumes of sediment exposed to variable weather conditions.
The project will be conducted in collaboration with Water Revival Systems (WRS), an environmental consultancy in Uppsala that is specialized on the design and management of constructed wetlands. The work is embedded in a larger research project called CLIMIPHY.
The start date of the MSc thesis is flexible.
Supervisors: Sebastian Sobek and Charlotte Grasset (UU), and Jenny Näslund (WRS).
Contact: sebastian.sobek@ebc.uu.se
Master thesis project: Interested in a project in bee genomics?
Published: 2026-02-04
A master's project is currently available with the goal of analysing evidence for a newly-discovered cryptic bumble bee species. Our group has performed extensive sampling and whole-genome sequencing of mountain bumblebee populations in the Rocky Mountains USA. Surprisingly, we identified an unexpected genetic cluster, indicative of a previously unrecognised cryptic species. Our results are reported in Christmas et al. 2021, 2022. We have now performed sequencing of additional samples with the aim of identifying specimens that belong to this species and then describing them with the help of experts. This work will contribute to the description of a new species. The master's student will be required to perform processing, phylogenetic and genetic clustering analysis of sequences that we have already generated in order to define which species each specimen belongs to and contribution to writing scientific manuscripts.
In addition, we are always interested to hear from students interested in projects on topics of interest to the lab. A number of projects for master's students are possible which would be suitable for students interested in bioinformatics, lab work, and/or field work. Please visit our web site to learn about our research: www.websterlab.net
For more details, please contact matthew.webster@imbim.uu.se
Master thesis project: Eastern Baltic cod Ecology, Evolution, immunity and microbiome
Published: 2026-01-13
We are offering two exciting Msc thesis:
1. Population genomics and immune gene variation
Project goal: inferring population structure and detecting evolutionary signatures of selection in immune-related genes.
2. The role of microbiome in hypoxia
Project goal: The primary aim of the study was to investigate the effect of prolonged mild hypoxia on activity of cod, using accelerometers on the fish. This type of tag logs activity in three dimensions. The fish were kept at either normoxia or mild hypoxia (4.9 mgO2/L) for 6 weeks (12C, 20 PSU).
This is a unique opportunity to:
- Gain hands-on experience in bioinformatics and evolutionary data analysis
- Apply cutting-edge methods in molecular ecology and conservation genomics
- Contribute to globally relevant research on the evolutionary processes shaping immune systems and microbiome in wild fish populations
We are seeking a motivated student with a strong interest in molecular ecology, conservation biology, and evolutionary genomics. Prior experience in bioinformatics is not required, but would be considered an advantage.
If interested, please contact:
Start date: Flexible, immediately if it desired
Place: EBC, Uppsala University
Project length: 30- 60hp
Master thesis project: Disease ecology and evolution in amphibian species
Published: 2026-01-13
We are offering an exciting MSc thesis projects investigating how anti-fungal treatments affect the skin microbiome and how microbiome changes with infection and temperature. This project offers a unique opportunity to gain practical experience in molecular techniques and ecological data analysis, while contributing to globally relevant research on infection dynamics in wild amphibian populations and the interplay between the amphibian microbiome, infectious diseases and possible treatments. Laboratory and data analysis training will be provided.
Background
Amphibians are undergoing massive population declines due to emerging infectious diseases. Tebuconazole is used to treat amphibians infected with the chytrid fungus Batrachochytrium dendrobatidis (Bd). However, the substance's broader effects remain unknown, particularly how it induces dysbiosis in the skin microbiome.
This project might involve field work, lab work and bioinformatic analyses
Department of Ecology and Genetics, Animal Ecology Program, Cortazar lab
If you are interested, please contact us for more details.
Contact detail: maria.cortazar@ebc.uu.se for further inquiries
Start date: Flexible, can start straight away Place: EBC Uppsala
Project length: 30-60hp