Umeå University is one of Sweden’s largest institutions of higher education with over 36,000 students and 4,100 faculty and staff. We are characterised by world-leading research in several scientific fields and a multitude of educations ranked highly in international comparison. Umeå University is also the site of the pioneering discovery of the CRISPR-Cas9 genetic scissors – a revolution in genetic engineering that has been awarded the 2020 Nobel Prize in Chemistry. We welcome your application!

The Integrated Science Lab (IceLab) (icelab.se) jointly with several departments at Umeå University and SLU offer three postdoctoral scholarships that will be affiliated with one of six possible multidisciplinary projects.

The ideal postdocs will have expertise in mathematical, machine learning, computational modeling, systems biology, molecular biology or an interest in obtaining experience in these areas. Further, postdocs should have a deep interest in scientific collaboration between researchers using theoretical and empirical approaches.

The six projects are:

Light variability as a driver of organismal resilience to environmental change
Deciphering infection-related epigenetic dynamics to explain the variability of human susceptibility to infections with respiratory pathogens.
Modelling ecological sustainability and economic viability of multi-trophic farming for Nordic latitudes
Dissection of the cell shape acquisition mechanisms in plants
Resolving microbial genomes in complex communities at the single-cell level
Outer membrane tethering in Gram-negative bacteria.

Detailed information on each project is given below.

The IceLab Multidisciplinary Postdoctoral Program

The under-explored terrain between traditional disciplines is full of fascinating and impactful research questions. At IceLab, we promote and facilitate transdisciplinary collaborations – with a focus on cutting-edge research that integrates theoretical, computational, and empirical work.

We will welcome you to IceLab with genuine support by creative researchers working on a panel of interdisciplinary problems. You will participate in both professionally and personally rewarding and entertaining activities aimed at training a new kind of researcher. A multidisciplinary team of researchers with complementary expertise will supervise each postdoc.

The two-year postdoc fellowships are financed by the Kempe foundations and are part of the IceLab Multidisciplinary Postdoctoral Program. A fellowship amounts to 2 years funding: 336 000 SEK per year. The scholarships are tax-free. Application deadline September 21, 2023. Start winter/spring 2024 (exact start date according to agreement).

Formal qualifications

To qualify as a postdoctoral scholarship holder, the postdoctoral fellow is required to have completed a doctoral degree or a foreign degree deemed equivalent to a doctoral degree. This qualification requirements must be fulfilled no later than at the time of the decision about scholarship recipient.

Priority should be given to candidates who completed their doctoral degree, according to what is stipulated in the paragraph above, no later than three years prior to the decision date for the scholarship recipient. If there are special reasons, candidates who completed their doctoral degree prior to that may also be eligible. Special reasons include absence due to illness, parental leave, appointments of trust in trade union organizations, military service, or similar circumstances, as well as clinical practice or other forms of appointment/assignment relevant to the subject area.

Candidates should have experience in computational, machine learning, quantitative modeling, systems biology, molecular biology or an interest in learning those skills. Personal qualities such as collaboration, communication, strong drive and motivation, critical thinking abilities, creativity and analytical skills are essential. You should be able to take on the research independently and as part of a team. Good knowledge of oral and written English is required.

Application

A full application should include:

A cover letter clearly stating which project or projects you are particularly interested in and summarizing your qualifications, your scientific interests, and your motives for applying (max 2 pages),
A curriculum vitae (CV) with publication list,
Certified copy of doctoral degree certificate,
Certified copies of other diplomas, list of completed academic courses and grades,
Copy of doctoral thesis,
Copies of relevant publications,
Contact information for at least two reference persons,
Other documents that the applicant wishes to claim.

Submit your application as a PDF marked with the reference number FS 2.1.6-1347-23, both in the file name and in the subject field of the email, to medel@diarie.umu.se. The application can be written in English or Swedish. Application deadline is 21 September 2023.

We look forward to receiving your application.

Project descriptions, specific qualifications, and contact information

(1) Light variability as a driver of organismal resilience to environmental change

Marine photosynthesis supports almost all ocean life, especially in the coastal zone. The underwater light environment is therefore of critical importance for ocean health. Unfortunately, climate change and human activity are causing significant changes in light availability. The impact of this on photosynthesis remains poorly understood, especially in coastal habitats with high structural complexity. In this project, the postdoctoral fellow will focus on light harvesting in red coralline algae – morphologically complex seaweeds that create reef structures in coastal seas all around the world, but face extinction because of climate change and human pressures. The fellow will have the opportunity to investigate coralline algal light harvesting from both a theoretical and experimental perspective, using (1) multiphysics modelling to reconstruct 3D light environments that account for the organism-scale morphological complexity and (2) single-cell spectroscopy to measure cell-scale light dynamics; support and training will be provided as required, depending on the candidate’s incoming expertise. Combining these results with our previous photophysiology knowledge will allow us to predict spatial variability in light harvesting from cell to habitat scales. This will provide important new insight into environmental resilience – which can subsequently be used to inform marine conservation and ocean sustainability strategies.

This postdoc will be housed in IceLab and hosted by the Department of Ecology & Environmental Science and the Department of Physics, supervised by a multidisciplinary team with complementing expertise in algal ecology & biogeochemistry, photonics & multiphysics modelling of light-matter interactions, as well as optics and biophysics.

Specific Qualifications for Project 1

To qualify for the fellowship, the candidate should have a PhD degree, or a foreign degree that is deemed equivalent, in theoretical biophysics, experimental physics, or numerical biological modelling. The ideal candidate has skills in multiphysics modelling (finite element method), biophysical modelling and / or optical spectroscopies (including frequency and time domain fluorescence, Raman spectroscopies). Importantly, the candidate will be interested in pursuing research that addresses climate change and sustainable development challenges at the intersection of physics and (plant) biology.

Contact Information Project 1

Heidi Burdett, Department of Ecology & Environmental Science, Umeå University, heidi.burdett@umu.se

Nicolò Maccaferri, Department of Physics, Umeå University, nicolo.maccaferri@umu.se

Magnus Andersson, IceLab and Department of Physics, Umeå University, magnus.andersson@umu.se

(2) Deciphering infection-related epigenetic dynamics to explain the variability of human susceptibility to infections with respiratory pathogens

This project explores the epigenetic effects of tuberculosis (TB) and COVID-19, two major pandemics of our time with highly variable infection susceptibility. We know these infections leave epigenetic marks, but the origin, dynamics, and impact on disease susceptibility, severity, and the potential for long-term effects like long-COVID-19 syndrome remain unknown. Our extensive longitudinal biobanks offer a unique chance to study these knowledge gaps. We hypothesize that dynamic epigenetic changes early in infections help control disease in healthy individuals, and deviations can lead to susceptibility or long-term effects. We will use machine learning to analyze epigenome data from unique clinical materials to predict outcomes and understand epigenetic shifts. Deep autoencoders and higher-order network models will help us decode complex epigenetic dynamics.

This postdoc will be housed in IceLab and hosted by the departments of Clinical Microbiology and Physics, supervised by a multidisciplinary team, including Johan Normark and Martin Rosvall at Umeå University and Anna Smed Sörensen at Karolinska Institute with complementing expertise in machine learning, infectious diseases, and immunology. The postdoctoral fellow will work in a translational environment involving dynamic interaction with colleagues from diverse research fields.

Specific Qualifications for Project 2

To qualify for the fellowship, the candidate should have a PhD degree, or a foreign degree that is deemed equivalent, in one of the following fields: computing science, physics, or related field. The ideal candidate has a machine learning profile and excellent skills in modern computer programming languages, such as C++, Python, or R, and experience from analyzing large experimental and clinical data sets.

Contact Information Project 2

Johan Normark, Department of Clinical Microbiology, Umeå University, johan.normark@umu.se

Martin Rosvall, IceLab and Department of Physics, Umeå University, martin.rosvall@umu.se

Anna Smed Sörensen, Department of Medicine Solna, Karolinska Institutet, anna.smed.sorensen@ki.se

(3) Modelling ecological sustainability and economic viability of multi-trophic farming for Nordic latitudes

Energy-intensive industries in northern Sweden produce enormous amounts of heat (<65°C). Today, this low-grade heat is released unused into the environment. Supported by a multi-disciplinary consortium of scientists, our aim is to channel low-grade waste energy from these industries into the local production of tropical food in an integrated multi-organism farming system that includes fish, plants, insects, and microorganisms in separate compartments that are linked through the transfer of water, nutrients and energy. The multi-organism, circular farming aims at fully closing the nutrient loop to enable an environmentally sustainable, local production of tropical food.

We have gained much empirical knowledge about the functioning of individual components of the multi-organism farming system. Yet, the full integration of these components into a circular food production system requires a quantitative description of their interplay, which is a prerequisite for the scaling, steering, and optimizing of processes from both an environmental and economic perspective. We therefore propose to develop mathematical models of a full-scale farming system that we will use to explore its dynamical behaviour under different environmental and economic scenarios.

We envision that the dynamics inside the individual growing compartments can be described with model formulations borrowed from ecology that are parameterized and validated against data. The adaptive scaling and steering of inputs, outputs and flows through the network will be treated as an optimization problem in environmental engineering under dynamic economic constraints. The integrated model will subsequently be used to analyze potential synergies and conflicts between ecological sustainability and economic viability, with the goal to dimension a facility that is not only ecologically sustainable but also feasible from an economic perspective. The integrated model should also allow us to analyze how sensitive different system configurations are to changes in external conditions, world prices, etc. This will provide projections of risks and economic viability, an aspect that has often been raised by municipalities and investors so far.

This postdoc will be housed in IceLab and be hosted by the Department of Plant Physiology, Umeå Plant Science Centre, the Department of Mathematics and Mathematical Statistics, and the Department of Ecology and Environmental Science. The postdoc will be supervised by a multidisciplinary team with complementing expertise in multi-trophic farming and the mathematical modelling of ecological as well as socio-economic systems.

Specific Qualifications for Project 3

To qualify for the fellowship, the candidate should have a PhD degree, or a foreign degree that is deemed equivalent, in one of the following (or related) fields: Applied mathematics, Mathematical Biology, Physics, Biophysics, Plant Sciences, Theoretical Ecology, Environmental Economics.

The ideal candidate has strong skills in building and implementing mathematical models. Experience in modelling dynamic systems and solving numerical optimization problems is of advantage.

The applicant needs additionally to have excellent skills in modern computer programming languages such as Python, C#, C++, MATLAB or R.

Contact Information Project 3

Olivier Keech, Department of Plant Physiology and UPSC, Umeå University, olivier.keech@umu.se

Sebastian Diehl, Department of Ecology and Environmental Science, IceLab, Umeå University, sebastian.diehl@umu.se

Jonas Westin, Department of Mathematics and Mathematical Statistics, Umeå University, jonas.westin@umu.se

(4) Dissection of the cell shape acquisition mechanisms in plants

All living organisms experience mechanical stress as they grow and develop. In plants, physical stress can emerge from variable external threats, such as high temperatures, drought, pollution, or physical damage by herbivores. Plants have developed an extensive flexibility, allowing them to modify their development by morphological adjustments to cope with their surrounding environment. Plant leaves are the primary site of photosynthesis and gas exchange, and they are also the first point of contact for external stimuli. These external factors can damage the leaves and affect their ability to function properly.

Understanding how the leaf morphology can change to help mitigate the effects of stress is thus essential for bringing further our knowledge on plant development. The outermost single cell layer, the epidermis acts as an important physical barrier to protect plants from the external environment. A tight control of epidermal cell fate and shape is essential to ensure plant survival.

The aim of this project is to better understand cuticle-mediated cell shape acquisition in plants and to a large extent the overall regulation of tissue morphogenesis with the integration of extracellular layer signaling mechanisms. By combining atomic force microscopy and enhanced optical spectroscopy, we target to reveal the intrinsic mechanical forces originating from the cuticle layer that potentially coordinate the determination of epidermal pavement cell shapes and build an in-silico model to unveil which factors are dominantly coordinating this regulation. To reach this goal, we will investigate the link between the cuticle mechanochemical properties and cell shape during cellular morphology acquisition using a multidisciplinary approach, including genetics, cell biology, Raman spectroscopy, and physics-based simulation.

The postdoctoral researcher will be hosted in IceLab, supervised by a multidisciplinary team with complementing expertise in plant development, cell biology, optical spectroscopy, and computational physics.

Specific Qualifications for Project 4

To qualify for the fellowship, the candidate should have a PhD degree, or a foreign degree that is deemed equivalent in physiology, plant development, molecular biology or biophysics.

Ideally, the candidate should be an expert either in plant development with a strong biophysics background or in optical spectroscopy and willing to expand her/his/their skills in plant development biology. The candidate should also be able to communicate with the theoretical team led by Martin Servin and give them input to implement the hardcore simulation part.

Contact Information Project 4

Stéphanie Robert, SLU, Department of Forest Genetics and Plant Physiology, UPSC, stephanie.robert@slu.se

Nicolò Maccaferri, Department of Physics, Umeå University, nicolo.maccaferri@umu.se

Martin Servin, Department of Physics, Umeå University, martin.servin@umu.se

(5) Resolving microbial genomes in complex communities at the single-cell level

A fundamental question in microbiome research involves determining which organisms are part of a given microbial community. Despite major breakthroughs in shotgun metagenomic sequencing (SMS) and bioinformatic analysis methods, determining “who is there” in a microbial community remains extremely challenging: de novo assembly of sequencing reads generated via SMS typically results in a collection of contigs that cannot be grouped into strain-level genomes. Here, the postdoc will develop a high-throughput method, which can reconstruct whole microbial genomes from microbiome samples at the single-cell level. Following prototyping, the method will be used to characterize clinical oral microbiome samples collected from a cohort of Swedish patients, with the goal of understanding why some humans develop chronic oral infections, while others do not.

This postdoc will be housed in IceLab and hosted by the Departments of Clinical Microbiology, Molecular Biology, and Odontology and supervised by a multidisciplinary team with complementing expertise in microbiology, single-cell technology development, bioinformatics, computer science, and oral infection biology.

Specific Qualifications for Project 5

To qualify for the fellowship, the candidate should have a PhD degree (or a foreign degree that is deemed equivalent), preferably in (micro)biology, molecular biology, (bio)chemistry, bioinformatics, engineering, physics, computer science, or a related field; candidates from other fields with high-throughput (meta)genomic and/or single-cell sequencing experience (e.g., sequencing library preparation, analysis of Illumina or long-read sequencing data; see below) are also strongly encouraged to apply.

The project includes both generation and analysis of single-cell metagenomic data; as such, we are ideally looking for someone with “moist lab” experience (i.e., a mix of wet lab and computational skills). However, we strongly welcome applications from highly skilled, motivated wet or dry lab scientists who are willing to collaborate with our research groups to learn new skills.

The ideal candidate has:

(i) Proficiency in written and spoken English.(ii) A desire to work in a diverse, inclusive, interdisciplinary, and highly collaborative environment.

We welcome applications from candidates with combinations of any of the following skills:

(i) Experience working with DNA or RNA in any form, especially within the context of advanced cloning methods and/or preparing DNA/RNA for high-throughput sequencing.(ii) Experience working with bacterial or eukaryotic cells and associated methods (e.g., flow cytometry).(iii) Experience developing or optimizing protocols for high-throughput sequencing.(iv) Experience using single-cell instruments and/or robotics for wet lab automation.(v) Experience analyzing Illumina or long-read sequencing data, preferably single-cell data derived from any organism or (meta)genomic/(meta)transcriptomic data derived from microbes.(vi) Proficiency in Bash shell scripting and a relevant programming language (e.g., Python, R, C, or Java).(vii) Knowledge of statistics and machine learning methods.(viii) Knowledge of data structures and algorithms.

Contact Information Project 5

Laura Carroll, Department of Clinical Microbiology, MIMS, IceLab affiliate, Umeå University, laura.carroll@umu.se

Johan Henriksson, Department of Molecular Biology, MIMS, IceLab affiliate, Umeå University, johan.henriksson@umu.se

(6) Outer membrane tethering in Gram-negative bacteria

Bacteria are enveloped by a multilayered structure that offers structural support and shields against environmental challenges. Gram-negative bacteria possess a double membrane envelope, enclosing the periplasmic space containing the peptidoglycan cell wall. While it is known that the integrity of the cell envelope relies on covalent bonds between the peptidoglycan and outer membrane proteins, the specific proteins involved and the enzymatic mechanisms responsible for these interactions remain largely unexplored across species.

In this project, our focus is to unravel the mechanism by which Gram-negative bacteria establish the connection between the outer membrane and the peptidoglycan. We aim to identify the key structural and enzymatic proteins involved in this critical reaction. To achieve this, we will employ high-throughput proteomics (at the Mateus lab) to analyze purified sacculi (i.e., peptidoglycan) obtained from a diverse collection of phylogenetically distinct species (at the Cava lab). Through this comprehensive approach, we will uncover proteins that are covalently linked to the peptidoglycan. Subsequently, using computational methods, we will prioritize these candidates for further mechanistic and physiological investigations. The data generated from this study holds exceptional potential in terms of discovering novel targets for the development of effective antimicrobials.

This postdoc will be housed in IceLab and hosted by the departments of Chemistry and Molecular Biology, supervised by a multidisciplinary team with complementing expertise in proteomics, bacterial genetics and physiology, and systems biology.

Specific Qualifications for Project 6

To qualify for the fellowship, the candidate should have a PhD degree, or a foreign degree that is deemed equivalent, in one of the following fields: microbiology, molecular biology, or biochemistry.

The ideal candidate has experience in microbiology, molecular biology and/or biochemistry. It is of added value if the candidate postdoc has previous experience with cell wall biology, proteomics, or data analysis skills. If the candidate does not have these skills, they should be open to developing them.

Contact Information Project 6

André Mateus, Department of Chemistry, The laboratory of Molecular Infection Medicine Sweden (MIMS, EMBL Nordic partner institute), Umeå University, andre.mateus@umu.se

Felipe Cava, Department of Molecular Biology, MIMS, SciLifeLab and IceLab Affiliate, Umeå University, felipe.cava@umu.se