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
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
Master thesis project: Roles of fungal symbionts in tree-killing bark beetles
Published: 2026-01-13
Project information: Bark beetles are typically found in close association with a diverse community of fungal symbionts, yet it is unclear why these insects depend on these microbes for tree colonization and reproduction.
Objectives: This project aims to test 1) whether bark beetles can reproduce without fungi, 2) if not, which services fungi provide to bark beetles, with a focus on nutrition supplementation, and 3) whether adult beetles show any behavioural response to individual fungi in the community, which suggests that bark beetles may actively select among fungal partners.
Your role: The prospective student will
- Manipulate fungal symbionts of beetles using exclusion and reinoculation experiments,
- Measure beetle fitness (developmental time, survival and reproductive output) and
- Analyze the nutritional profile of the fungus (sterols, B vitamins and amino acids; in collaboration with analytical service platforms)
- Perform olfactory-based choice experiments using bark beetles and fungi.
This project offers an opportunity to work on an unsolved fundamental question in bark beetle biology—why bark beetles need microbes to survive and reproduce in conifers.
Required knowledge: Basic laboratory skills. Interested candidates will receive proper training on the system during the thesis. Prospective students are expected to have a general interest in insect-microbe interactions. The project is intended for master’s students (either 45 or 60 credits). The direction of the thesis and the project goals can be adjusted based on the student's interests.
Start date: Any time from March 2026
Contact info: Dineshkumar Kandasamy, Researcher (main supervisor), email:dineshkumar.kandasamy@biol.lu.se.
https://portal.research.lu.se/sv/persons/dineshkumar-kandasamy/
PhD-position: Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna
Published: 2026-01-12
We are seeking students with a keen interest in interdisciplinary teamwork and science that nurtures the precise, personalized, predictive and preventive medicine of the future. We are highly interdisciplinary and looking for medics, biologists, chemists, bioinformaticians, computer scientists, engineers, physicists, mathematicians, and candidates with a degree in a similar subject to apply now.
The deadline for applications is 30th January 2026. A pdf with full details of the opportunity can be found here.
Interested students can apply quickly and easily via our online recruitment platform.
We also have an online open day on Wednesday, 14th January 2026 that interested students can sign-up for here.
Contact: : Matthew Spencer, MSpencer@cemm.oeaw.ac.at
PhD-position: Translational Cancer Immunology – Cologne, Germany
Published: 2026-01-12
The Schlößer laboratory at the Center for Molecular Medicine Cologne works on translationally relevant mechanisms of immune evasion in solid cancers. The specific project focuses on B cells, which represent an important component of the tumor microenvironment and affect naturally occurring anti-tumor immune responses as well as cancer immunotherapies. While the production of antibodies is well characterized in the context of infectious diseases and cancer, many aspects of antigen-presenting B-cell functions need further investigation. We aim to elucidate the role of antigen-presenting B cells and B-cell mediated T-cell responses in immunosurveillance of gastric cancer.
Your Tasks:
- Characterization and phenotyping of induced tumor-specific T-cell responses
- B-cell receptor and T-cell receptor sequencing
- Comparison of immunopeptidome derived from different antigens and processed by different sources of antigen-presenting cells
- In vitro cytotoxicity experiments and testing the influence of specific drugs on the antigen-presenting capacity
Your Profile
- Excellent MSc degree in biology, biotechnology, or a related field
- Strong interest in translational research in immuno-oncology
- Expertise in at least one of the following fields: Complex in-vitro cell culture experiments, immunological assays and/or flow cytometry
- Applicants should be highly motivated, independent and have strong communication skills
- Knowledge of immunological processes is a plus but not a prerequisite
We offer
- A friendly and motivated work environment in a long-standing team of experienced biologists
- Close relation with clinicians and a focus on translationally relevant research questions
- Support and training in several cutting-edge immune assays in a positive environment
- A joint graduate school of the medical faculty and the faculty of natural sciences (IPMM)
The position is available from 01.03.2026 or later and is to be filled for three years with the possibility of an extension.
Please send your application to: hans.schloesser@uk-koeln.de
More information: https://www.cmmc-uni-koeln.de/research/research-areas-projects/research-area-b/schloesser-assoc-rg-45
Master thesis project: Bioinformatics, Epigenetics, and Neuroimmunology
Published: 2026-01-12
Project Background
Multiple Sclerosis (MS) is a chronic inflammatory disease characterized by immune mediated damage to myelin and neurons in the central nervous system (CNS). This damage leads to a wide range of neurological symptoms, including sensory and motor deficits, cognitive impairment, and fatigue. Despite extensive research, the molecular mechanisms underlying MS susceptibility, disease progression, and clinical heterogeneity remain incompletely understood. Consequently, clinically actionable biomarkers for early diagnosis, prognosis, and treatment stratification are still limited, posing challenges for effective disease management.
Small non-coding RNAs (sncRNAs) have emerged as promising molecular biomarkers due to their stability and high-throughput detection. Our group has been leveraging these properties to investigate sncRNA profiles in MS, with the aim of advancing precision medicine approaches. This project builds on our ongoing work using some of the world’s most well-characterized clinical MS cohorts, including STOPMS and MultipleMS with long-term clinical follow-up data.
Project Description
The overarching aim of this Master’s project is to identify and characterize sncRNA signatures associated with MS. Specifically, the student will:
- Compare sncRNA expression patterns among MS patients, healthy controls (HC), and non-inflammatory neurological disease controls (NINDC)
- Identify candidate sncRNAs with potential as early diagnostic and prognostic biomarkers
- Compare sncRNA profiles with clinical parameters, with a particular focus on long-term outcomes such as disease severity and progression
- Infer biological processes and molecular pathways associated with MS by integrating sncRNA profiles using established analytical strategies
Training and Skills
The student will gain hands-on experience in:
- Processing and analysis of small RNA sequencing (Small-RNome) data, including:
- QC, trimming, filtering, alignment, deduplication and annotation
- Normalization, PCA, clustering, differential expression, pathway, network and visualization
- Working in a high-performance computing (HPC) environment
- Bioinformatics and data analyses using R, Bash, and Python
- Translational neuroimmunology research using real-world clinical data
Join Us
Please contact Dr. Maria Needhamsen, Head of the Bioinformatics Team (maria.needhamsen@ki.se), with your CV and motivation letter.
PhD-position: Lake Ice Transitions and Their Impact on the Global Carbon Cycle
Published: 2025-11-28
Do you want to explore how changes in lake ice cover influence the global carbon cycle? Are you looking for an employer who values your professional development and offers a supportive workplace We welcome you to apply for a PhD student position at Uppsala University which will be placed within the Limnology program at the Department of Ecology and Genetics.
Project description
We are seeking a highly motivated PhD student to join our research project on exploring how rapid transitions from ice-covered to open-water states in lakes affect the carbon transformation efficiency in lakes and the emission of greenhouse gases. The project addresses a critical gap in our understanding of lake ice dynamics and their role in the global carbon cycle, using advanced ice core analysis, sensor technologies, and modeling approaches. The position includes close collaboration with Gothenburg University as well as national and international networks such as SITES (https://www.fieldsites.se/) and GLEON (https://gleon.org/). As part of the laboratory work the PhD student will spend approximately 6 weeks each year at the University of Gothenburg’s ice laboratory, where the student will receive specialized training in lake-ice microstructure analysis and analyze the field samples.
Requirements
To be eligible for a PhD-student position, the applicant must hold a master degree (or equivalent) in limnology, aquatic ecology, environmental sciences, geoscience, environmental engineering or other relevant subjects at the time of employment. Eligible candidates need to demonstrate skills in handling large datasets and basic statistics. For the project some experience in practical work such as laboratory and field work or equivalent is required, as well as the willingness to work in cold winter climate and to collaborate with Gothenburg University. 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.
Additional desired qualifications
Car driving license (EU class B).
Master thesis project: Immune gene evolution in reptiles
Published: 2025-11-25
Selection by parasites is a strong evolutionary force that leaves traceable signatures in the genomes of their host species. Several families of immune genes, such as the major histocompatibility complex (MHC), Toll-like receptors (TLRs) and cathelicidins, have expanded and diversified as a consequence of host-parasite co-evolution. These multi-copy genes are difficult to identify during automated genome annotations, leaving loci undetected or mis-identified, which hampers studies on the diversity and evolutionary dynamics of these functionally important genes.
The goal of this project is to characterise immune gene families in the sand lizard genome and study their evolution across squamate reptiles. Project scope is flexible and can be tailored towards student’s interest and skills; can be a project work course or a master’s thesis project.
Aims include:
- Comparative studies of immune gene evolution in squamates by leveraging publicly available reference genomes.
- Diversity and evolution of immune genes in the Swedish sand lizard using available whole genome re-sequencing data. There is the possibility to integrate the immunogenetic diversity with parasite infection.
This is a bioinformatic project that does not involve lab or field work.
Department of Ecology and Genetics, Animal Ecology Program, Lillie lab
Place: EBC Uppsala
Start: Flexible; can start immediately
Project length: 30-60 hp
Contact Mette Lillie (mette.lillie@ebc.uu.se) for further inquiries.
Master thesis project: Cognition and regulation of insect populations
Published: 2025-11-25
Background: Tritrophic interactions, such as the tree-caterpillar-bird food chain, play an important role in the 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 behavioral plasticity in flycatchers have an advantage in foraging and detecting trees with more caterpillar.
Your Role: You will experimentally test how variation in cognitive abilities influence the birds’ ability to identify trees with heavy caterpillar infestations. This will involve:
- Field Observation & Monitoring: Conducting systematic observations and setting up remote video cameras to monitor bird visitation rates to individual trees.
- Behavioural assays: Conduct commonly recognized and used cognition assays to individuals near nestboxes and in aviaries.
- Chemical Sampling: Collecting branch samples for subsequent chemical analysis of IH-BVOCs.
- Data Collection and Analysis: Quantify behaviours from assays recordings and link individual behavioural performance with individuals foraging in trees infested with more caterpillars.
Fieldwork & Data Collection: Participating in long-term data collection by monitoring nest boxes.
Contact:
Michaëla Berdougo (PhD student) – michaela.berdougo@ebc.uu.se
Ana Gomes (PostDoc) – ana.gomes@ebc.uu.se
Anna Qvarnström - anna.qvarnstrom@ebc.uu.se
Master thesis project: Climate Change, Mismatch, and Survival
Published: 2025-11-25
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? We hypothesize that an individual's innate metabolic rate is a key trait that determines their resilience.
Objective: To determine if an individual's metabolic rate is a key trait determining its 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 metabolic rate 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 metabolic traits have a survival advantage.
- Fieldwork & Data Collection: Participating in long-term data collection by monitoring nest boxes.
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.
Contact:
Michaëla Berdougo (PhD student) – michaela.berdougo@ebc.uu.se
Ana Gomes (PostDoc) – ana.gomes@ebc.uu.se
Anna Qvarnström - anna.qvarnstrom@ebc.uu.se
Master thesis project: Using Olfactory Cues to Find Food
Published: 2025-11-25
Background: The ability of birds to regulate insect populations is debated but can be a powerful ecosystem service. Many mechanisms behind the foraging efficiency of birds are still being discovered. 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 biogenetic volatile organic compounds (IH-BVOCs) to identify trees with more caterpillars.
Your Role: You will measure IH-BVOC emissions from sampled tree branches and correlate these with direct bird activity. This will involve:
- Field Observation & Monitoring: Conducting systematic observations and setting up remote video cameras to monitor bird visitation rates to individual trees.
- Chemical Sampling: Collecting branch samples for subsequent chemical analysis of IH-BVOCs.
- Data Analysis: Statistically linking the chemical profiles of trees with recorded bird foraging activity.
- Fieldwork & Data Collection: Participating in long-term data collection by monitoring nest boxes.
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.
Contact:
Michaëla Berdougo (PhD student) – michaela.berdougo@ebc.uu.se
Ana Gomes (PostDoc) – ana.gomes@ebc.uu.se
Anna Qvarnström - anna.qvarnstrom@ebc.uu.se
PhD-postions: University of Exeter
Published: 2025-11-18
- Microbiome-Disease Interactions in European Badgers
- AMR Dynamics in Gamebirds in the UK
https://bpb-eu-w2.wpmucdn.com/blogs.bristol.ac.uk/dist/f/373/files/2025/11/swbio-26-project-34.pdf
- AMR Dynamics in Wild Baboons
https://bpb-eu-w2.wpmucdn.com/blogs.bristol.ac.uk/dist/f/373/files/2025/11/swbio-26-projectAP-7.pdf
- AMR Dynamics in Migratory Birds
Projects 1-3 are BBSRC funded and have an application deadline of 3rd December. Project 4 is NERC and has a more relaxed deadline of 8th January.
Contact: Xav Harrison
Associate Professor of Ecology
Centre for Ecology & Conservation, University of Exeter
E: x.harrison@exeter.ac.uk
W: https://xavharrison.github.io
Master thesis project: Iron Metabolism and Genetic Disorders
Published: 2025-11-13
We are a research group at the Universitat Internacional de Catalunya (UIC) in Barcelona seeking motivated students interested in carrying out their Undergraduate’s Thesis (TFG) or Master’s Thesis (TFM) with us during the 2025–2026 academic year, with the possibility to continue afterwards with a PhD project in our group.
We are looking for undergraduate or Master’s students with:
- A good academic record (minimum GPA of 7.5/10 or 2.5/4 in the Bachelor’s degree).
- Genuine motivation for biomedical research.
- Interest in molecular biology, genetics, RNA Biology, hematology, or iron metabolism.
Available Master’s Thesis Topics:
- New Genes in Iron Metabolism – IRP/IRE Regulatory System: Cutting-edge research on novel mRNAs containing Iron Responsive Elements (IREs) regulated by Iron Regulatory Proteins (IRPs). The project involves international collaborations (EMBL, Oxford, USA) and hands-on experience with mouse and zebrafish models, offering a unique opportunity to contribute to translational discoveries.
- New Diseases, New Genes, and Novel Mutations in Hereditary Hematological and Iron-Related Disorders: Translational research at the forefront of human genetics, focused on the discovery of new diseases and mutations in hereditary hematological and iron-related disorders. The project includes international collaborations (EMBL, Oxford, USA) and hands-on experience with animal models.
Application Requirements:
Please send the following documents:
- Your updated CV
- Your final undergraduate GPA (0–10 Spanish scale).
To learn more about our group and research lines, visit:
https://researchgroups.uic.es/ironmetabolism/
We look forward to receiving your applications and remain at your disposal for any questions.
Contact:
Dr. Mayka Sánchez
Iron Metabolism Research Group
Universitat Internacional de Catalunya (UIC)
msanchezfe@uic.es
Master thesis project: Women's mental health
Published: 2025-11-10
We are looking for a person with a genuine interest in mental health and experience in handling large datasets and/or strong knowledge of biostatistics. The Department of Women’s and Children’s Health is an international and multidisciplinary institution, and our research group focuses on women’s health. Hormonal fluctuations can lead to mood changes that significantly influence the daily lives and well-being of women of reproductive age. In this project, we integrate psychological, biological, and neuroimaging data to explore how these factors interact, with the overall aim of advancing our mechanistic understanding of women’s mental health.
More information: https://www.scilifelab.se/researchers/erika-comasco/
Department: https://www.uu.se/kontakt-och-organisation/organisation?query=X41%3A32
Contact: Ella Schleimann-Jensen, ella.schleimann-jensen@uu.se
Scholarship: Swedish Chamber of Commerce for the Netherlands Sustainability Scholarship 2026
Published: 2025-11-06
This scholarship supports and empowers the next generation of sustainability leaders in Sweden and the Netherlands, offering funding for master’s students conducting sustainability-related theses. It aims to strengthen academic and business collaboration between the two countries while promoting knowledge exchange and innovation in sustainable development.
The scholarship provides up to €4,000 per year to support research activities that contribute to the student’s academic project.
Critera:
- Open to master’s students (120 ECTS) enrolled at a university in Sweden or the Netherlands, aged between 21 and 36 years.
- Applicants must hold Swedish or Dutch citizenship.
- The master’s thesis must focus on sustainability and include potential business applications.
- Applicants should be in the process of planning or writing their thesis and demonstrate how the scholarship will contribute to their research — for example, funding travel, conference participation, company visits, or materials directly related to the project. The thesis must also have relevance to both Sweden and the Netherlands.
- During Q3 or Q4 2026, the Swedish Chamber of Commerce for the Netherlands will host an event where the selected scholar will present their finalized work, either online or in person.
- Students who already receive financial support from another company for their research are not eligible to apply.
Applications for the 2026 scholarship are now open.
More information is available at: https://swedishchamber.nl/the-swedish-chamber-of-commerce-sustainability-scholarship-powered-by-saab/
Master thesis project: Seasonal Changes Inside Lichens: What Really Happens?
Published: 2025-11-04
Your Tasks
- Extract DNA from lichens collected across different seasons.
- Design genotype-specific primers.
- Perform digital PCR to quantify photobiont genotypes from summer to winter.
- Analyze data in R.
Why Join This Project?
- Gain hands-on experience in DNA extraction and digital PCR.
- Explore a novel ecological question in symbiosis research.
- Contribute to a scientific publication.
Who Are We Looking For?
A motivated student with interest in molecular ecology and bioinformatics, attention to detail in lab work, and willingness to learn new techniques. Prior experience with DNA extraction, and PCR is important. Experience with statistical analyses R is a plus.
If interested, please contact:
ioana.brannstrom@ebc.uu.se
Master thesis project: Improving taxonomic reporting thresholds in clinical metagenomics diagnostics
Published: 2025-11-04
Project Description
This master project will include a clinical metagenomics dataset that has been previously analysed with nf-core/taxprofiler [3]. The primary aim is to investigate and define optimal thresholds for reporting bacterial and viral taxa based on what have been reported on current literature ([4,5,6]). Once relevant thresholds have been identified, then those will be implemented in gms/metaval pipeline to automatically filter background noise. The student will validate this approach by running gms/metaval to assess its accuracy in reducing false positives and improving clinical interpretability of metagenomics results.
In this project, the student will learn or improve skills in bioinformatics tool development, Nextflow pipeline development, and open-source collaboration. Additionally, the student will gain insights into the challenges associated with metagenomics analysis.
Start time
Upon agreement
You can read more about our research in this link.
Contact
Sofia Stamouli, sofia.stamouli@scilifelab.se
Master thesis project: PacBio or Nanopore? Decoding the Best Long-Read Strategy for Amplicons
Published: 2025-11-03
We are offering an exciting MSc thesis project that compares PacBio and Nanopore long-read sequencing for amplicons—and gives you the chance to improve existing pipelines or even design a new one.
What will you do?
- Work with PacBio and Nanopore long-read amplicons generated from the same PCR library of photobionts living in lichens.
- Use established pipelines (e.g., DADA2) to create consensus sequences.
- Assign species identities using BLAST and other bioinformatic tools.
- Compare results from both sequencing methods.
- Develop or optimize a pipeline for Nanopore data based on your findings.
Why is this unique?
- Gain hands-on experience in bioinformatics and evolutionary data analysis.
- Apply cutting-edge methods in molecular ecology.
- Contribute to a scientific article.
If interested, please contact:
ioana.brannstrom@ebc.uu.se
Master thesis project: Optimising Interpolation Methods for Missing Positioning Data in Dairy Cattle
Published: 2025-10-22
Project description
This project will focus on:
- Cleaning and processing positioning data from sensor-equipped dairy cows
- Testing different interpolation algorithms to reconstruct missing data
- Developing and evaluating combinations of methods to improve accuracy
- Assessing the impact of improved interpolation on behavioural and movement metrics
Learning Outcomes
- Practical experience in R programming for data cleaning, interpolation, and validation
- Skills in evaluating algorithm performance and statistical accuracy
- Understanding of how positioning technologies support animal welfare and health monitoring
- Insights into the design of next-generation tools for precision livestock farming
Specifications
- Prior experience with R or another programming language is an advantage, but not required. As the analysis will be performed using a custom-developed R package, full supervision will be provided.
- Suitable for students in animal science, veterinary medicine, data science, or related fields with an interest in smart farming technologies and animal behaviour.
Contact
Hector Marina, Researcher
HBIO, Quantitative Genetics and Breeding
hector.marina@slu.se
Master thesis project: Simulating Errors in PLF Data for Cattle Social Networks and Home Range
Published: 2025-10-22
Project description
This is a data-driven project involving:
- Cleaning and analysis of positioning data from sensor-equipped cows
- Simulation of different types and levels of positioning errors
- Construction and analysis of social networks
- Statistical modelling of network structures and home ranges
Learning Outcomes
- Practical skills in R programming, including data cleaning, visualization, and statistical modelling
- Training in network analysis, error simulation, and behavioural data interpretation
- Experience linking precision livestock farming (PLF) technologies with animal behaviour research
- Insights into the robustness of behavioural metrics under varying data quality conditions
Specifications
- Experience with R will be beneficial, but not mandatory. A custom-developed R package for data manipulation and analysis will be provided, along with full supervision and guidance.
- Suitable for students in animal science, veterinary medicine, or related fields with an interest in animal behaviour and smart farming technologies.
ContactPerson
Hector Marina, Researcher
HBIO, Quantitative Genetics and Breeding
hector.marina@slu.se
Master thesis project: Tracking Cow Friendships and analysing variations in the social role over time
Published: 2025-10-22
Project description
This is a data-driven project involving:
- Cleaning and analysis of longitudinal data from sensor-equipped cows
- Mapping and visualisation of contact networks over time
- Statistical modelling of the relationship between social metrics.
- Depending on interest and background, students may also learn and apply dynamic network modelling.
Learning Outcomes
- Gain practical skills in R programming, with applications in data cleaning, visualization, and statistical modelling
- Mathematical skills in network analysis, and time-series modelling.
- Experience linking behavioural ecology with animal physiology
- Insights into real-world applications for smart farming technologies
Specifications
Experience with R will be beneficial, but not mandatory as the candidate will use a custom-developed R package for data manipulation and analysis and receive full guidance throughout the data analysis process.
Suitable for students in animal science or veterinary medicine.
Contact
Hector Marina, Researcher
HBIO, Quantitative Genetics and Breeding
hector.marina@slu.se
Master thesis project: Insect ecology at Kobbefjord in Greenland
Published: 2025-10-17
Background
Insects all across the world exhibit diel rhythm - changes in activity across the day. Yet, when we sample arthropods, we tend to sample across several days and then infer the total biomass as available food for predators regardless of their activity patterns. Understanding the drivers behind fluctuations of arthropod abundances across the day, and the true active community at any given time, is vital to assess what cues drive the activity of insects and map the co-occurrence patterns of predators and prey on a detailed level. Here, the low-Arctic offers an interesting study system as the early summer offers almost 24 hours of sunlight, and the late summer has dark nights.
Objective
In this project, you will sample arthropod communities at short intervals using Malaise traps and pitfall traps at a low Arctic field station in Greenland. The aim is to investigate whether the active arthropod communities differ between different times of the day, how this is affected by sunlight hours, and how weather influences these patterns.
Who are we?
The project is led by PhD student Viktor Gårdman, who is associated with Greenland Institute of Natural Resources and SLU Uppsala. He will guide the fieldwork on site and accompany you during your entire stay in Greenland. The main supervisor of the project will be Prof. Tomas Roslin (SLU Uppsala, University of Helsinki), who has worked with insect ecology for over 30 years in Greenland and across the Arctic realm.
What you’ll do:
- Participate and plan in the design of the research plan
- Sample malaise and pitfall traps during eight weeks in the summer of 2026 at Kobbefjord Research Station, Greeenland
- Identify captured arthropods
- Analyze diel patterns across Arctic arthropod taxa using R
- Write a report on your findings
- Publish your findings (optional but encouraged)
Who you are:
- MSc student in biology, preferably with a specialization in ecology
- Eligible for a 60ECTS master’s thesis
- Available for fieldwork abroad June-August 2026
- Experience of fieldwork in remote settings
- Interested in insect ecology and identification
- Possess basic statistical skills with experience in R
Send your application, or reach out with questions, to Viktor Gårdman, viktor.gardman@slu.se
Master thesis project: Universitat Internacional de Catalunya (UIC)
Published: 2025-10-16
Available Master’s Thesis Topics:
New Genes in Iron Metabolism – IRP/IRE Regulatory System
Cutting-edge research on novel mRNAs containing an Iron Responsive Element (IRE) and post-transcriptionally regulated by Iron Regulatory Proteins (IRPs). The project includes international collaborations with prestigious centres (EMBL, Oxford, USA) and provides hands-on experience with mouse and zebrafish models, offering a unique opportunity to contribute to translational discoveries.
Projects: AIRON RTI2018-101735-B-I00, ARETHA-PID2021-122436OB-I00
Selected Publications: PMID: 33596641 (2021); PMID: 33062942 (2020); 28774878 (2017); 21940823 (2011); 17417656 (2007); 17703216 (2007); 16760464 (2006)
New Diseases, New Genes, and Novel Mutations in Hereditary Hematological and Iron-Related Disorders . Translational research at the forefront of human genetics focused on the discovery of new diseases and novel mutations in hereditary hematological and iron-related disorders. The project includes international collaborations with prestigious centres (EMBL, Oxford, USA) and offers hands-on experience with mouse and zebrafish models, providing a unique opportunity to contribute to clinically relevant discoveries. Projects: AIRON RTI2018-101735-B-I00, ARETHA-PID2021-122436OB-I00. Selected Publications: PMID: 40195342 (2025); PMID: 39081172 (2024); Discovery of a new gene in CDAIII: PMID: 36200420 (2023); 35457224 (2022); 34946929 (2021); 34064225 (2021); 33596641 (2021); 32235485 (2020); 30678075 (2019); 30026338 (2018); 29269865 (2017); 26029709 (2015); 25156943 (2014); 23421845 (2013), and more
At this stage, we are collecting applications, and we kindly ask interested candidates to send us:
- Their updated CV
- Their final overall grade from their undergraduate degree (on the 0–10 Spanish grading scale, with 10 being the maximum)
You can learn more about our group, our projects, and our strong translational focus by visiting our website: https://researchgroups.uic.es/ironmetabolism/
Master Thesis: Antibody purification and analysis
Published: 2025-10-14
At Cytiva, we are developing chromatography resins for processing biopharmaceuticals, such as antibodies. The purification of antibodies is divided into a capture and one to two polishing steps. The capture step is affinity chromatography that aims to isolate the target antibody from the cell culture suspension. In the following polishing step(s), the aim is to remove process and product-related impurities such as aggregated, fragmented or chemically modified Ab species as well as residual host-cell proteins (HCPs) and DNA. The polishing resin can vary; however, ion-exchange chromatography is commonly used. A variety of analytical techniques at each purification step are employed to ensure product purity and verify effective removal of impurities.
What you’ll do
Lab work aiming to evaluate separation performance of chromatography resins on Ab-related test material. This includes sample analysis using different detection methods, for example HPLC-SEC/RPC, MALS, electrophoresis or fluorometric assay. Depending on resources and the applicants’ interests, the project focus can be either on optimization of a polishing process using start material with different impurity profiles or development of analytical method(s) for evaluation of purification performance.
Who you are
- Master’s student in Science or Engineering with a focus on chemistry, biochemistry, or biotechnology.
- Eligible for master thesis work between January 2026 – June 2026.
- Background in chromatography is advantageous.
- You like to work independently and with a structured approach.
Contact: Annika Söderholm, annika.soderholm@cytiva.com
Master thesis project: Development and optimization of orthogonal analytical methods for viral vectors (AAV)
Published: 2025-10-07
This master's thesis focuses on the development and optimization of analytical methods for adeno-associated virus (AAV) viral vectors, with a particular emphasis on comparing newly developed methods with existing orthogonal analytical techniques.
Within the Viral Vector Application team at the Genomic Medicine OpCo, we are actively developing purification solutions for AAV, plasmids, and other viral vector entities used in both research and manufacturing. These vectors serve as delivery vehicles for DNA in cell and gene therapy applications. Our goal is to support customers by providing purification products that enable the production of high-purity viral vectors suitable for use as final drug substances.
To ensure product quality, we utilize a comprehensive toolbox of analytical methods to assess parameters such as purity, concentration, and impurities. Accurate determination of AAV concentration during the purification process is critical. This thesis project will involve hands-on work with analytical instruments and techniques for characterizing AAV.
Who you are
Education in Molecular Biology/Biology/Biotechnology/Biochemistry/Chemistry in the level of master thesis work (Examensarbete). The thesis work could preferably be 30 hp starting in January 2026.
For questions, please contact hiring manager Anna Jansson, anna.jansson@cytiva.com
Master thesis project: Investigating Innovative Methods for Purification of Viral Vectors
Published: 2025-10-07
Master Thesis Project: Investigating Innovative Methods for Purification of Viral Vectors
As part of the Viral Vector Application team within the Genomic Medicine OpCo, we are actively developing purification strategies for AAV and other viral vector types used in both research and manufacturing. These vectors are essential delivery vehicles for DNA in cell and gene therapy applications. Importantly, plasmids play a critical role in the production of viral vectors.
Our goal is to support customers by providing purification solutions that enable the production of high-purity viral vectors and plasmids, suitable for use for final drug substances.
This thesis will investigate novel purification methods, including AAV capture techniques and plasmid capture approaches, and compare them to existing solutions. You will work with ÄKTA chromatography systems and columns, applying various chromatography and analytical methods. The project is highly lab-focused and requires a solid foundation in chromatography, as well as a systematic and analytical mindset.
Who you are
Education in MolecularBiology/Biology/Biotechnology/Biochemistry/Chemistry in the level of master thesis work (Examensarbete). The thesis work could preferably be 30 hp starting in January 2026.
For questions, please contact hiring manager Anna Jansson, anna.jansson@cytiva.com
Degree project: Rapid evolution in butterflies
We are looking for a student to contribute to an exciting project investigating rapid evolution in Heliconius butterflies introduced to the Cook Islands as a biocontrol agent. The role involves photographing butterfly wings from different timepoints and islands, and using geometric morphometric tools to test whether wing size or colour patterns have changed since their release in 2016. You will help digitise specimens, standardise imaging conditions, and analyse shape and colour variation using R. The project offers hands-on experience in evolutionary biology, image analysis, and statistical methods, and would suit someone interested in adaptation, biocontrol, or tropical biodiversity.
Note that this is a short project.
Contact:
Dr Gabriela Montejo-Kovacevich
gabriela.montejo-kovacevich@scilifelab.uu.se
Master thesis project: Population Genomics of Cod
Published: 2025-10-03
Are you curious about population genomics and immune gene variation in marine species?
We are offering an exciting MSc thesis project that explores how immune genetic variation is distributed in Baltic and Atlantic cod, and investigates genomic differences between these populations.
The project will involve bioinformatic analysis of whole genomes from 96 individuals, with the goal of inferring population structure and detecting evolutionary signatures of selection in immune-related genes.
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 in wild 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:
maria.cortazar@ebc.uu.se
anssi.laurila@ebc.uu.se
Start date: As soon as possible
Degree project: Removal low and high molecular weight species by size exclusion chromatography and evaluation of associated process parameters by DOE
Published: 2025-09-29
We are currently looking for a chemical, biomedical or biochemistry student who would like to perform their master thesis at Galderma for the spring semester of 2026.
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 cultivation and the associated downstream protein purification steps. The aim of this project involves the study of the removal of high and low molecular weight species using size exclusion chromatography (SEC) as well as evaluating the effects and interaction between the associated process parameters using a design of experiment (DOE) approach.
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
Principal Scientist Drug Substance, MS&T
D +46 (0)18 489 17 62
M +46 (0)76 181 17 62
sebastiaan.mul@galderma.com
Master thesis project: Seasonal effects on the Przewalski's horse gut microbiome
Published: 2025-09-26
Tasks include: Analyse microbiome DNA sequence data, interpret results, reading scientific papers, and write a thesis about the findings. The results will be published in a scientific journal.
Requirements: An interest in learning about wildlife microbiomes and coding in R.
Duration: ~20 weeks (30 hp)
Start: Anytime.
For more information, please contact Elin Videvall at Animal Ecology, EBC, Uppsala University, elin.videvall@ebc.uu.se
Degree project: Computational modelling of resilience to heat stress in dairy cattle
Goal
The aim of this project is to develop methods for quantifying the genetic basis of resilience to heat stress in dairy cattle. This includes several possible goals that a student may pursue in the project:
- Develop and evaluate a methodology for detecting and quantifying recovery following heat stress perturbation, thereby establishing recovery as a resilience indicator in dairy cattle.
- Develop and evaluate a methodology for calculating resilience indicators specific to heat stress, and investigate their usefulness for estimating genetic parameters for resilience to heat stress.
- Evaluate the usefulness of high-resolution daily milk yield data compared to sparse test data for estimating genetic parameters for resilience to heat stress.
Project Description
This project will use simulation to generate lactation curves and introduce perturbations during heat waves. It will build on general mathematical models to quantify cow’s response to heat stress. These simulations will be based on established parametric milk curve equations and plausible parameter values based on literature and real data. Additionally, using the quantitative genetic simulator AlphaSimR, the project will simulate genetic values for the cows, allowing us to estimate the genetic component of the resilience indicator.
The project is suitable for students in Animal Science and Bioinformatics, who are interested in computational work and dairy cattle.
Contact
Martin Johnsson, Researcher
HBIO, Quantitative Genetics and Breeding
martin.johnsson@slu.se
Pablo Dominguez Castaño, Postdoc
HBIO, Quantitative Genetics and Breeding
pablo.dominguez@slu.se
More information is available here.
Master thesis project: Chytrid fungus and Ranavirosis
Are you interested in disease ecology and evolution in amphibian species? We are offering an exciting MSc thesis project investigating the occurrence of Chytrid fungus and Ranavirosis for the first time in Sweden.
This project will focus on testing for Bd infection and developing molecular techniques to detect Ranavirus from wild skin swab and tissue specimens. Additionally, the project will involve analyzing the skin microbiome using a 16S metabarcoding approach.
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 and infectious diseases.
We are looking for a motivated student with an interest in molecular ecology, conservation biology, disease dynamics in wild populations.
Laboratory and data analysis training will be provided!
If you are interested, please contact us for more details.
Contact detail: maria.cortazar@ebc.uu.se and/or Jacob.hoglund@ebc.uu.se
Project start as early as possible.
Master thesis project: Bat Diet, Food Web Ecology and Biodiversity
Are you interested in bats, biodiversity, and molecular ecology? We are offering an exciting master’s thesis project investigating the diet of wild bats in Färnebofjärden National Park, Sweden, an area where the mosquito control agent Bacillus thuringiensis israelensis (Bti) has been used for over 20 years.
The project focuses on analysing bat diet using DNA metabarcoding of faecal samples to uncover how insecticide use affects food webs at the top predator level. This unique study provides hands-on experience in molecular methods, ecological data analysis, and the opportunity to contribute to an internationally relevant question about the indirect effects of pesticides on ecosystems.
We are looking for a motivated student with an interest in molecular ecology, conservation biology, or trophic interactions to start in January 2026. Laboratory and data analysis training will be provided.
Project start: January 2026
For more information and to apply, please contact: hana.merchant@ebc.uu.se or frank.johansson@ebc.uu.se
Master thesis project: Characterization of the lung microbiome in Multiple Sclerosis.
Project Description
Multiple Sclerosis (MS) is an autoimmune disease of the central nervous system with complex etiology involving both genetic and environmental factors. Cigarette smoking is the strongest known environmental risk factor, linked not only to increased susceptibility but also to a more aggressive disease course. Emerging evidence suggests that the lung may play a previously underappreciated role in MS, as environmental exposures and airway immune activation have both been implicated in disease development.
The project aims to establish a detailed map of lung microbiome changes in MS, and to identify potential microbial contributors to immune modulation in the respiratory tract, and to determine how cigarette smoking influences microbial diversity and composition.
We are looking for a highly motivated student that will help us analyse, explore and integrate datasets and clinical data we have collected and generated from bronchoalveolar lavages (BAL) of a cohort of MS-patients and healthy individuals.
Qualifications:
- Experience with Python or R
- Background in bioinformatics, molecular and cell biology, microbiology, biotechnology, or similar subject area
- Interest in working with clinical data
Project scope:
- Process and analyse lung microbiome 16S rRNA sequencing data.
- Characterise microbial diversity and composition.
- Integrate data with other immune-mediated or exposure-driven lung microbiome datasets.
- Link microbial variation to collected clinical and molecular data.
Please contact me for more details.
Master thesis project: Microbiome diversity in the Swedish sand lizard
The symbiotic relationships between eukaryotic hosts and their associated microbes are essential for maintaining organism health, from their vital roles in digestion and nutrient uptake, to key roles in immune defence and regulation. In a healthy organism, host-microbe interactions are balanced, buffering against biological or environmental disturbances to maintain homeostasis and function. When this balance is disrupted, however, for instance due to habitat degradation and environmental stress, it can lead to impaired function and increased susceptibility to disease.
The aim of this project is to characterize microbiome diversity and composition in sand lizards using established molecular methods and available samples. Collaborators in this project include Elin Videvall, Maria Cortazar-Chinarro, Charlotte Enkvist, Seraina Bracamonte and Mats Olsson (U.Gothenburg).
The project involves both molecular laboratory procedures and bioinformatic and statistical analyses. Multiple projects may be available, as well as the possibility to integrate microbiome data with available genomic datasets and parasite information.
Department of Ecology and Genetics, Animal Ecology Program, Lillie lab
Place: EBC Uppsala
Start: Flexible; can start immediately
Project length: 45-60 hp
Contact Mette Lillie (mette.lillie@ebc.uu.se) for further inquiries.
Internships and degree projects in Toxicology at SLU
The Molecular Toxicology Group at the Department of Animal Biosciences (HBIO), SLU Uppsala, offers a range of degree projects and internships for Bachelor’s and Master’s students. Our research focuses on the identification of toxic compounds from the food chain and the environment, and on elucidating their mechanisms of action, with expertise spanning general toxicology, environmental risk assessment, and cellular and molecular methods.
Projects for 2025/26 cover diverse research areas:
- New Approach Methods (NAMs) for thyroid hormone interference, integrating external biotransformation systems into in vitro assays.
- Toxicological assessment of rare earth elements (REEs), examining acute effects in zebrafish embryos and aquatic invertebrates.
- CRISPR–Cas-mediated transgenesis in zebrafish cell lines, developing ecologically relevant reporter gene assays for high-throughput screening.
- In addition to laboratory-based research, bibliographic degree projects are available on toxicity pathways and transgenic reporter systems in ecotoxicology, using curated literature resources.
Opportunities are offered for various study formats, including Examensarbete (15, 30, or 45 hp), bibliographic projects, and research internships. Project start dates are flexible, and longer research periods combining thesis and internship work are encouraged.
These projects provide training in experimental design, laboratory techniques, data interpretation, and scientific writing, with guidance from experienced researchers. Prior laboratory experience is advantageous but not mandatory.
For more information or to discuss potential projects, please refer to the attached PDF and feel free to contact Sebastian Lungu-Mitea (sebastian.lungu@slu.se).
Master thesis project: Do bacteria that feed on plastics while growing without oxygen exist? And are bioplastics safer in terms of microplastics release into the environment?
In this master thesis project, you will join a research project about investigting the fate of (bio-)plastics in oxygen-free environments, such as biogas- and biofertilizer production facilities. It includes analyzing the potential presence of plastic-degrading microorganisms in these systems via DNA-sequencing techniques and checking whether bioplastics break down completely or leave behind microplastics using advanced chemical analyses. This project is also part of a bigger EU-project with academic and industrial partners in Sweden and abroad (INCLUE; webpage: https://inclue.eu).
The start date for the thesis is flexible, but autumn 2025 or spring 2026 would work well for us. We would also be happy to host you for a longer period than one semester, for example by combining the thesis project (examensarbete) with a research internship course (forskningspraktik).
If you have any questions or would like to discuss this opportunity further with us, please feel free to reach out via email (martine.fischbach@slu.se and maria.westerholm@slu.se).
We are looking forward to hearing from you.
Master thesis project: Disentangling interactions between microbes and their mobile genetic elements
Qualifications:
- Open to students of biology / bioinformatics
- Interest in resolving complex questions
- Working knowledge of basic biology, genomics and bioinformatics analyses
- Experience in programming with Python and R
- (Optional) experience with Linux and high-performance computing
In our lab, we are studying viruses and plasmids that interact with microbes (specifically bacteria) in freshwater lakes. Viruses that infect bacteria are generally known as phages. Phages affect the gene flow and genomic diversity of their host and play an important role in bacterial evolution. Our work focuses on decoding how mobile genetic elements maintain the diversity among lake microbes and how that affects the whole ecosystem. Through your project, you will contribute to our work on understanding the role of mobile genetic elements and their interactions with their microbial hosts.
What you will do?
- Extract the sequences corresponding to mobile genetic elements from sequenced metagenomes and metatranscriptomes
- Assign MGEs to their respective microbial host
- Annotate the function of genes within mobile genetic elements and discuss their impact on interactions of MGEs with their host microbe
- Assess the prevalence and abundance of these MGEs in different environments using publicly available metagenomes
Check our webpage to learn more about ongoing research in our lab: https://www.bionomics-mmlab.com/
Supervisor: Maliheh Mehrshad, Dept. Of Aquatic Sciences and Assessment, SLU.
Maliheh.Mehrshad@slu.se
Master thesis project: Machine-Learning for Physics-Based Force Fields
Prequisites:
- Open to students of chemistry / biochemistry / biophysics / biology / bioinformatics
- Working knowledge of biochemistry / organic chemistry
- Experience in programming Python
- (Optional) experience with Linux and high-performance computing
Description:
Intermolecular interactions are crucial for understanding, for example, hydrogen bonds. Oxygen and nitrogen atoms have a negative partial charge and these attract polar hydrogen atoms that have a positive partial charge. Quantum chemistry methods describe these interactions well, because they explicitly include the electrons but these calculations are very costly. For large systems, e.g. biomolecules such as proteins, approximations are needed and indeed effective models (force fields) have been developed under a long time, but those have limited accuracy and they heavily rely on compensation of errors.
In this project you will contribute to developing models based on extensive quantum chemistry calculations to train a physics-based force field that does not rely on compensation of errors. More in detail, you will
- Perform many quantum chemistry calculations of compound dimers, where the compounds are small molecules, for instance urea, water, acetate and so on. Calculations will use the symmetry adapted perturbation theory (SAPT) which decomposes the interaction energy into four terms, electrostatics, induction, exchange and dispersion. The results are stored in a database.
- Use a machine learning software called the Alexandria Chemistry Toolkit to train models that reproduce the SAPT results.
- Evaluate the models using molecular dynamics simulations.
Supervisor: David van der Spoel, Dept. Of Cell and Molecular Biology, UU.
david.vanderspoel@icm.uu.se
http://folding.bmc.uu.se
Master thesis project: Parasite diversity in the Swedish sand lizard
Parasites have a strong impact on the health of their host and reduce its fitness and survival. In combination with additional stressors, parasites can pose a substantial threat to species of conservation concern. Parasites themselves, however, are sensitive to host demographics, which may benefit some parasite species while driving others to extinction. The aim of this project is to characterize and quantify blood parasite infections across Swedish sand lizard populations using established molecular methods and available samples.
The project involves both molecular laboratory procedures and bioinformatic and statistical analyses. It could be suitable for research training, project work or degree project.
Department of Ecology and Genetics, Animal Ecology Program, Lillie lab
Place: EBC Uppsala
Start: Flexible; can start immediately
Project length: 30-60 hp
Contact Seraina Bracamonte (seraina.bracamonte@ebc.uu.se) for further enquiries.
Master thesis project: Integrative epigenomics in mouse and human embryonic stem cells
We make use of cutting edge epigenome mapping strategies including quantitative MINUTE-ChIP, CUT&Tag, ATAC-seq, single cell omics. We are developing additional technologies, e.g. to map the coincidence of epigenomic features. We are interested in the underpinnings of pluripotency, lineage commitment and cancer.
We are looking for a highly motivated student that will help us analyse, explore and integrate datasets we have collected, generate reproducible code and prepare figures for manuscripts. Excellent programming skills and knowledge in next-gen sequencing analysis are a requirement.
The scope of the thesis will be a subset of the following:
- to perform cell culture based experiments with pluripotent stem cells
- to perform MINUTE-ChIP, CUT&Tag, ATAC-seq
- to use standard NGS suites to process primary data and extract relevant information (bowtie2, samtools, picard, deep tools) based on bach scripting
- Perform custom analyses, e.g. genome-wide correlation, peak overlap analysis to correlate datasets (R and other packages).
- Develop custom data aggregation, transformation and visualizations with R
Please contact me for more details.
Contact
simon.elsasser@scilifelab.se
Tel 0852481227
www.elsaesserlab.org