Join us

Copyright Mattias Pettersson 2021, Umeå University

Funded PhD position available – machine learning and advanced bioinformatics (especially computer scientists / mathematicians / statisticians welcome!). See projects below to get an idea of the topic

Computer scientist student wanted for master thesis or shorter project. See resources -> FACSanadu. With some lesser work a student can push this project to the end and get a paper out of it!

We are developing new analysis methods for single-cell and CRISPR data. These require increasingly advanced knowledge of Bayesian statistics and Machine learning. For an on-going project we are e.g. looking into a custom formulation of variational autoencoders. However, you will also perform “routine”. Some knowledge of biology needed but can be basic. More importantly, you need proficiency in writing code and an ability to grasp modern mathematics. Our standard language is Python but proficiency in any language, especially R, Java or C, is helpful!

Postdocs positions in general

We are otherwise always welcoming spontaneous applications, in which case we would write a proposal and apply to a funding agency if you are postdoc (e.g. Marie curie, HFSP, and several local Swedish ones). Relevant keywords: T cell culture, virus production, cloning, FACS, CRISPR, single-cell or RNA-seq or ATAC-seq or other omics methods. Knowledge in R and Python beneficial but not the primary requirement

PhD student positions in general

Funding for PhD students is comparatively rare, but some sources exist. To get these we would first need to offer a temporary assistant position until the time is right. Or even better, first do your master thesis with us.

Master thesis projects and unpaid internships

Our group works interdisciplinary, meaning that almost no matter your background, there might be a spot for you. The PI (Johan) is a mechanical engineer, now doing biology, maybe giving you an idea of how broad we are.

We prefer students who wish to spend at least 10 weeks with us. You will otherwise barely be able to learn the skills to run a project! Theoretical projects can be done remotely.

Master thesis project suggestion for physicists / engineers – microscopy/microfluidics

We are looking for a student who wish to build a cell sorter using microfluidics and automated image analysis. This project is suited for a pair of students working together (software and hardware). It will be in collaboration with the group of Magnus Andersson. See this paper for inspiration. This technology will allow us to measure cells in new ways.

Master thesis project in philosophy or statistics – The theory of science

Moving from classical statistical testing to AI, we see that our basis for doing science is radically changed. We no longer have enough data for performing statistically testing. Our models are largely subjective. How do we motivate this, and how do we move past positivism (or modify it)? Broad thinking required.

Master thesis projects for physicists / computer scientists / engineers – AI and bioinformatics

To solve our problems, we are increasingly moving towards the use of variational autoencoders. Several problems are rather disconnected from the biology and rather requires new innovation on the side of algorithms and mathematics. This includes new penalization approaches, latent space formulations and error terms.

Master thesis projects for biologists – bioinformatics

You should have at least touched a programming language before to get the most out of the stay. The simpler tasks involve looking at existing datasets, extracting information that we can include in our T cell model. Slightly more advanced projects will immediately involve multi-omics integration and doing things that essentially have not been done before (it is a new field). While we don’t expect a mathematical wiz, be prepared that you will need to write code that solves or computer at least basic equations (only some linear algebra will take you far).

Master thesis projects for biologists – wet lab

If you are keen on advanced molecular biology, and ideally have 20 weeks of time (hard to get much out of a shorter time – then rather do a dry project), then we have challenges for you! These projects are not for the faint of heart. We expect a fair degree of independent thinking, as you might be doing things no one has ever done before. Our lab develops new assays which always involves a fair amount of trouble shooting. However, this is our pedagogy  – unlike in the previous courses, where everything is streamlined, the thesis project is a chance to work in a sharp situation where not everything goes as planned. Your ability to overcome problems is what will set you apart from the undergrads.

We try to get a senior in our lab to work closely with you. For projects which mainly involve cloning and synthetic biology (less concern for everyone’s health!), you might also get to try and work a bit more independently.

Master thesis projects for biologists – moist!

In modern biology, especially involving proteomics or NGS, you need to be a bit of a jack-of-all-trades. If you are here for 20 weeks then we will attempt to give you a mixed wet-and-dry project. In other words, from data generation to data analysis.

Summer students

If you are studying at the Medical Faculty in Umeå, you can get a stipend to hang out with us over a summer. Check the program Forskaraspiranter, with deadline 1st Feb in 2020 (announced yearly).

Of course, we can consider summer students also funded under other programs or just on their own interest.

The location – MIMS, Umeå, Sweden

Our lab is located at Umeå University, and MIMS, a part of the Nordic EMBL Partnership for Molecular Medicine. This place has long been a centre of excellence for molecular genetics and pathogen research. Our group takes advantage of this, bringing mechanistic knowledge of disease up to modern scale with high-throughput biology. Umeå is a vibrant town, largely due to the students – international as well as from all over Sweden. Some personal favourites include the Swedish cuisine (gastropubs and microbreweries), over 6 dance styles represented, one of Swedens largest ju-jutsu clubs (among other budo), indoor and outdoor climbing, winter sports, sailing club, etc … Accommodation is affordable. Oh, and don’t worry about the language. The local pub even runs their pub quiz in english, as is the case with many other social activities! No lack of auroras in winter. For some news from Sweden, in english, try out The local.