Projekterbjudanden

Master thesis project: Longitudinal microbiota of Scandinavian wolverines

Published: 2026-04-09

This project is a longitudinal study on wild wolverine gut microbiota. The data originates from fecal samples collected in the wild from the same individual across multiple years. We are interested in studying the microbiota dynamics across time and whether we can identify an individualized, stable microbiota. You will be working in a lab group researching microbiota in a diverse set of host species and learn about current research within wild animal microbiomes.

Tasks include: Basic molecular lab methods like DNA extractions, PCR and gel electrophoresis. Bioinformatics and data analysis in R. Reading scientific papers and writing a thesis about the findings. The results will be published in a scientific journal. No specific experience is required but we appreciate someone who likes working collaboratively on projects and is interested in learning more about the subject!

Duration: 30-40 weeks (45-60 hp).

Start: Flexible, Autumn 2026

For more information, please contact Elin Videvall and Charlotte Enkvist,

Department of Ecology and Genetics, Animal Ecology Program, EBC, Uppsala University (elin.videvall@ebc.uu.se / charlotte.enkvist@ebc.uu.se)

Read more in this PDF. pdf, 235 kB.

Master thesis project: Genetic and molecular characterization of candidate gene(s) in edited osteosarcoma cell lines.

Published: 2026-04-08

We, in Kerstin Lindblad-Toh’s group, are open for master’s students interested in research, who would like to join us for a thesis project focusing on understanding the role of a candidate cancer driver gene in osteosarcoma development.

Osteosarcoma is the most common primary bone cancer, with a peak incidence in adolescents and young adults. The disease is aggressive and usually presents complex genetic profiles. We have previously identified a candidate gene in osteosarcoma development and generated CRISPR knock out cell models to study the gene’s effects in carcinogenesis. You will be contributing to the next step of the project, which comprises the characterization of the generated lines using cell-based assays and targeted evaluation of selected pathways involved in the gene’s function.

Learning outcomes:
In our group, you will have the opportunity to perform molecular and cell biology techniques as:

• Mammalian cell culture.
• DNA, RNA and protein extraction and quantification techniques as PCR, RT-qPCR and WB.
• Cell-based assays as cell proliferation, apoptosis and invasion.
• Genotyping of cell lines using sanger sequencing.

You will participate in project planning, journal clubs and group meetings. In our group, you will also learn how to study cancer biology with a multidisciplinary perspective including comparative genomics, in silico analyses, and in vitro modelling.

More information about our research at: https://lindbladtohlab.org.

Your profile:
We are looking for a motivated MSc student, with strong interest in genetics and cancer biology, who wants to improve their expertise in wet-lab techniques and cell culture. Prior experience in cell culture is an advantage, but not a requirement.

Start time: July – September 2026.

Number of credits: Ideally 30 to 45 hp.

If the position sounds interesting, contact Carolina Maya González for further information (Carolina.maya.gonzalez@imbim.uu.se).

Examensarbete: Rovfågeldöd vid Ellevios luftledningar – risk och åtgärdsplan

Publicerad: 2026-04-07

Vi söker dig som vill göra ditt examensarbete hos Ellevio hösten 2026. För rätt kandidat kan det även finnas möjlighet att starta redan under våren.

Beskrivning av examensarbetet
Luftledningar för lokalnät (LN) kan utgöra en risk för fåglar med brett vingspann. Stora rovfåglar och ugglor kan kortsluta ledningarna om de sitter på eller flyger mellan spänningssatta ledningar. Dessa arter är viktiga för ekosystemet och vår biologiska mångfald – och flera av dem är dessutom utrotningshotade. Därför är det viktigt att elnätsföretag kartlägger riskerna och vidtar lämpliga åtgärder.

Nu vill vi utöka undersökningen till hela Ellevios kvarvarande luftledningsnät (LN) och:

• Inventera och mappa luftledningar mot platser där rödlistade rovfåglar och ugglor rör sig, med fokus på berguv och kungsörn, genom GIS-data från Artdatabanken och kontakt med lokala ornitologiska föreningar.
• Samköra data med avbrottsstatistik och rapporter om eldöd.
• Identifiera riskområden och kartlägga om Ellevio har:
  • Planerade kablifieringsprojekt i närtid
  • Installerad fågelskyddsutrustning
• För riskområden utan skydd eller planerade kablifieringar, sammanställa en handlingsplan för åtgärder.
• Formulera ett mål som beskriver hur och när Ellevio kan eliminera risken för eldöd.

Din profil
Examensarbetet anses lämpligt för dig som läser Masterprogram i biologi gärna med inriktning på ekologi/naturvård, naturvårdsbiologi, miljö och hållbarhet eller liknande. Grundläggande kunskap i GIS krävs. Har du dessutom intresse för fåglar, arters tillstånd och hållbar infrastruktur ser vi det som meriterande.

Du behärskar också svenska och engelska obehindrat i såväl tal som skrift. Arbetet är lämpat både för dig som vill skriva det på egen hand och för er som planerar att skriva i par.

Du visar ditt intresse genom att klicka på "Ansök" och besvara frågorna i ansökningsformuläret. I din intresseanmälan vill vi gärna att du berättar kort om varför du är intresserad av att göra ditt examensarbete hos Ellevio, vilken utbildning du går, samt delar med dig av dina tankar och idéer kring det aktuella examensarbetet.

Länk till mer information och ansökan.

Kontakt
Mana Ashja
Handledare
mana.ashja@ellevio.se

Gabriella Boumadi
Rekryterare
gabriella.boumadi@ellevio.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

1. Development of sexually selected traits: how gene expression and alternative splicing contribute to characters shaped by sexual selection across developmental stages.
2. 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.

Read more in this PDF. pdf, 145 kB.

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.

Read more in this PDF. pdf, 490 kB.

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)

Course: Shinkishi Hatai International Marine Biology Course 3rd–9th July, 2026

Published: 2026-02-13

The Research Center for Marine Biology (RCMB), Tohoku University will hold the Shinkishi Hatai International Marine Biology Course (SHIMBC) on 3rd–9th July 2026. The details of the course are available on our website:
http://www.biology.tohoku.ac.jp/lab-www/asamushi/shimbc2026.html

The course is designed for undergraduate and graduate students with an interest in marinebiology, imparting experiences in basic practices. Not only international students but also some Japanese students will participate in this course, presenting a significant opportunity to enhance
scientific and intercultural exchange among students. We regard this course as a unique opportunity for participants to learn about marine biology and specific techniques. Experience with handling marine organisms is not necessary, but priority for acceptance is given to students with much interest in marine developmental biology and coastal ecology.

Overview:
A marine biology station is the ideal environment to observe live marine organisms and to begin studying marine biology. The marine biology course held at our marine biology station, RCMB, situated on the coast of Mutsu Bay, provides hands-on experience in handling marine organisms and explores the diversity and ecology of coastal invertebrates. The course will be comprised of basic and advanced projects. The basic project will introduce the participants to two fields, developmental
biology of ascidians and coastal ecology. In the latter advanced project, participants will conduct a supervised project led by instructors, and their findings will be presented on the last day.

Qualifications:
The course is open to undergraduate and graduate students (approx. 15 in total) from any institute, who major in or have an interest in marine biology or related fields. If the number of applicants exceeds our hosting capacity, we may have to decline certain applications. Experience in
handling marine animals is not necessary, but priority for acceptance will be given to students with much interest in marine developmental biology and coastal ecology. Accommodation and meals are available at a reasonable rate at the center’s dormitory (for details see the center’s website: For Users). We are unable to support your travel expenses.

Read more in this PDF. pdf, 130 kB.

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

Read more in this PDF. pdf, 226 kB.

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

Stipendium: Landshypotek Banks uppsatsstipendium

Publicerad: 2026-02-04

Nu kan du söka Landshypoteks uppsatsstipendium

Du kanske redan är mitt i uppsatsskrivandet om något som kan bidra till ökad kunskap inom svenskt jord- och skogsbruk. Då kan det vara en god idé att under våren söka Landshypotek Banks uppsatsstipendium för de gröna näringarnas framtid.

Syftet med stipendiet är att uppmärksamma och uppmuntra den yngre generationens intresse för svenskt lantbruk. Stipendiet riktar sig till dig som är högskolestudent med intresse för de gröna näringarna.

Prissumman på 10 000 kronor går till en student som med sin uppsats bidragit med nya idéer, perspektiv och kunskap som kan utveckla svenskt lantbruk.

Sista dag för ansökan är 15 juni 2026.

För mer information om stipendiet och dess kriterier: https://www.landshypotek.se/stipendium#false

Uppsatser skickas till stipendium@landshypotek.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

Read more in this PDF. pdf, 189 kB.

Internship / Volunteer Opportunity: Science Project Supervisors at the Erken Laboratory Summer Research School (17th June – 3rd July 2026)

Published: 2026-01-27

The Erken Laboratory, a field station and research laboratory belonging to Uppsala University and located outside Norrtälje, Sweden, invites applications for several internship/volunteer positions as Project Supervisors at our Summer Research School for upper secondary (high school) students in natural sciences.

About the Role
As a Project Supervisor, you will supervise and coordinate small groups of high school students who are conducting their final diploma projects within natural science disciplines such as biology, chemistry, microbiology, or related fields. Your role will involve guiding students through scientific thinking, project planning, data collection, and presentation of results in a supportive and educational environment.

In addition to academic supervision, Project Supervisors are expected to contribute to the daily life at the field station, including assisting with meal preparation and participating in a small number of organized evening activities together with the students.

Dates and Format

• Main period: 17 June – 3 July 2026 (Weekdays)
• Work is primarily on-site at the Erken Laboratory during this period
• Some occasional preparatory sessions may take place remotely prior to 17 June
• Limited remote work during the main period may be possible, but on-site presence is essential

What We Offer

• Free accommodation and meals at the field station during the on-site period
• Hands-on experience in:

• Project management and supervision
• Scientific mentoring and education
• Working with young students in a research-oriented setting
• A strong merit for students interested in academic, educational, or science-related careers
• The chance to live and work in a beautiful summer environment by Lake Erken, with opportunities for swimming, fishing, hiking, and outdoor recreation

Who Should Apply

• Master’s students in natural sciences or related fields (PhD students are also welcome to apply)
• Both Swedish and international students are welcome to apply
• Previous experience in supervision or teaching is an asset but not required
• Ability to work independently, communicate clearly, and engage with high school students

Availability for the full period stated above is required, with some possibility for distance work.

For any questions or more info contact Pia Larsson at Pia.larsson@ebc.uu.se

Read more in this PDF. pdf, 1 MB.

Scholarship: Swedish Chamber of Commerce for the Netherlands Sustainability
Scholarship 2026

Pulished: 2026-01-23

The scholarship supports master’s students in Sweden and the Netherlands who are writing sustainability-related theses with potential business applications, providing up to €4,000 to support their research activities.

Criteria:

• 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.

More information is available here:
https://swedishchamber.nl/the-swedish-chamber-of-commerce-sustainability-scholarship-powered-by-saab/

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:

• maria.cortazar@ebc.uu.se
• anssi.laurila@ebc.uu.se

Start date: Flexible, immediately if it desired

Place: EBC, Uppsala University

Project length: 30- 60hp

Read more in this PDF pdf, 424 kB.

Summary pdf, 429 kB.

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

Read more in this PDF. pdf, 159 kB.

Summary pdf, 611 kB.

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/

Read more in this PDF. pdf, 141 kB.

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.

Read more in this PDF. pdf, 102 kB.

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).

Read more about the position and how to apply here.

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

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:

1. 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.
2. 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

Read more in this PDF. pdf, 88 kB.

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

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

Read more in this PDF. pdf, 335 kB.

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

Read more in this PDF. pdf, 97 kB.

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

Read more in this PDF. pdf, 299 kB.

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

More information is available here.

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

1. Practical skills in R programming, including data cleaning, visualization, and statistical modelling
2. Training in network analysis, error simulation, and behavioural data interpretation
3. Experience linking precision livestock farming (PLF) technologies with animal behaviour research
4. 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.

Contact
Hector Marina, Researcher
HBIO, Quantitative Genetics and Breeding
hector.marina@slu.se

More information is available here.

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

More information is available here.

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:

1. Participate and plan in the design of the research plan
2. Sample malaise and pitfall traps during eight weeks in the summer of 2026 at Kobbefjord Research Station, Greeenland
3. Identify captured arthropods
4. Analyze diel patterns across Arctic arthropod taxa using R
5. Write a report on your findings
6. Publish your findings (optional but encouraged)

Who you are:

1. MSc student in biology, preferably with a specialization in ecology
2. Eligible for a 60ECTS master’s thesis
3. Available for fieldwork abroad June-August 2026
4. Experience of fieldwork in remote settings
5. Interested in insect ecology and identification
6. Possess basic statistical skills with experience in R

Send your application, or reach out with questions, to Viktor Gårdman, viktor.gardman@slu.se

Read more in this PDF. pdf, 3 MB.

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

Read more in this PDF. pdf, 4 MB.