Open position: Postdoctor in machine learning for single-cell data analysis

Johan Henriksson, group leader at MIMS and the Dept. of Molecular Biology, in close collaboration with Tommy Löfstedt, group leader at the Dept. of Computing Science, are looking for a postdoc.

Project description

Gene isoforms play key roles in disease etiology and outcome. Despite that gene isoforms are involved in most biological processes, they are commonly ignored because we lack tools to understand them. In this project we will build new large-scale machine learning tools to extract gene isoform information from commonly existing single-cell RNA-seq data.

The approach we consider is based on variational autoencoders and sequence models. The challenges lie in the data being extremely large, sparse, and noisy. The project will open doors into the currently most rapidly expanding field in biology.

Application deadline: 1 December 2022

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Open position: PostDoc Project in In vivo efficacy and mode of action of novel antimicrobials acting against intracellular bacteria

The Sixt lab at MIMS is looking for a postdoc to join the group and advance them at the field of Chlamydia research. 

Project: The extensive use of broad-spectrum antibiotics is a major aggravator of the alarming spread of antimicrobial resistances. Moreover, it impacts patient health negatively by its devastating collateral effects on the microbiota. Hence, there is an urgent need for more selective treatment options. Using an innovative antimicrobial discovery approach, we have recently identified a set of compounds displaying narrow-spectrum activity against Chlamydia, a group of obligate intracellular bacteria that every year causes millions of cases of urogenital, ocular, and respiratory infections. The purpose of this project is to determine in vivo efficacy and selectivity of our most potent compounds, and to determine their molecular targets and mode of interference with the intracellular growth and development of the pathogen.

Applications are possible from now until a suitable candidate was found. Starting date: preferentially between late 2022 and early 2023 (can be negotiated).

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Open position: Postdoc opportunities in the Henriksson lab

Picture: Johan Henriksson, MIMS group leader. Credit: Mattias Petterson. 

The Henriksson lab is seeking two postdoctoral scientists to work on Project 1) in CAR T cells and CRISPR screening methods development, or on Project 2) in machine learning for single-cell data analysis. You will be based in the lab of Johan Henriksson (www.henlab.org). The Henriksson lab is based at the Department of Molecular Biology and is part of The Laboratory of Molecular Infection Medicine Sweden (MIMS), which is the Swedish node within the Nordic EMBL Partnership for Molecular Medicine.

Applications are reviewed as they come in. 

Read more: Open position: Postdoc opportunities in the Henriksson lab

Master student thesis projects in the Henriksson lab

Master thesis projects available in advanced molecular biology protocol development, of relevance for CAR T cells and malaria high-throughput screening! Hard working students who are prepared to roll up their sleeves and move out of their comfort zone are most welcome to apply :)

We are developing several protocols to improve the efficiency of pooled CRISPR or barseq screens, where extracting more information about each cell will boost the statistics. This is especially important when the cells are few (primary cells) or the expansion is uneven (in vivo screens). The project may also be combined with bioinformatics (python, R or java) based on student interests.

Keywords: Cloning, sequencing, inverse PCR, padlock probes, UMIs, mate pairing, HiC, ATACseq, RNAseq, CRISPR, cell culture, lentiviruses, bioinformatics

Illustration by Johan Henriksson. 

Read more: Master student thesis projects in the Henriksson lab

Students are welcome

If you are interested to do an internship in a research group at MIMS and you know which group and topic should it be, please contact This email address is being protected from spambots. You need JavaScript enabled to view it. (project coordinator at MIMS) and she will get in touch with the selected group leader. To see the research groups and their topics, go to https://www.mims.umu.se/groups.html .