The Department of Biochemistry and Biophysics is one of the biggest departments at the Faculty of Life Sciences at Stockholm University with about 300 employees. The research spans a wide area and is in many of the projects of the absolute highest world class. The department is unique in Sweden and also in the world due to its interdisciplinary character and spans a very broad area including neuroscience, cell biology, biochemistry, biophysics and theory. For more information about our business, see our website www.dbb.su.se.


Project description

We are looking for a highly motivated postdoctoral researcher to conduct advanced bioinformatics analysis, including deep learning to elucidate cell intrinsic mechanisms of ageing and neurodegeneration in Parkinson’s Disease and amyotrophic lateral sclerosis (ALS) in the laboratory of professor Eva Hedlund.

During the past decade we have combined pluripotent stem cells, human tissues and mouse models with advanced RNA sequencing methods to elucidate mechanisms of neuronal vulnerability and resilience in ALS, Parkinson’s Disease (PD) and spinal muscular atrophy (SMA). We have identified multiple mechanisms which render certain neurons resilient and which can be modulated in vulnerable neurons to make them less prone to degeneration (Allodi et al, Scientific Reports, 2016, Nichterwitz et al, Nature Communications, 2016; Nijssen et al, Stem Cell Reports, 2018; Nizzardo et al, Acta Neuropathologica, 2020; Nichterwitz, Genome Research, 2020; Aguila, Front Mol Neurosci, 2021).

With the current project we are aiming to address how different neurons cope with the normal ageing process as well as mutation-induced age-accelerating processes leading to neurodegenerative diseases such as PD or ALS. The project builds on large, unique data set of RNA sequencing data generated from neurons isolated from human tissues and derived from induced pluripotent stem cells in the Hedlund lab. Applicants should know advanced AI topics (e.g., Bayesian and probabilistic machine learning, deep learning, sequence models), up-to-date knowledge about novel paradigms and methods in ML, especially DL, advanced programming skills in Python (and their related data processing, machine learning, deep learning, and visualisation libraries) and SQL and/or NoSQL technologies.

 

Candidates with a deep interest in neurodegeneration and skills in machine learning are encouraged to apply.

 


Selected Recent Relevant Publications from the Hedlund laboratory:

Aguila J, Cheng S et al (2021) Spatial RNA sequencing identifies robust markers of vulnerable and resistant human midbrain dopamine neurons and their expression in Parkinson's Disease. Front Mol Neurosci 14:699562

Nichterwitz S et al (2020) LCM-seq reveals unique transcriptional adaptation mechanisms and protective pathways of resistant neurons in spinal muscular atrophy. Genome Research 30:1083-1096.

Nizzardo M et al (2020) Synaptotagmin 13 is neuroprotective across motor neuron diseases. Acta Neuropathologica 139(5):837-853. # equal contribution, co-corresponding authors.

Allodi I et al (2019) Modeling motor neuron resilience in ALS using stem cells. Stem Cell Reports 12(6):1329-1341.

Nijssen J et al (2018) Axon-seq decodes the motor axon transcriptome and its modulation in response to ALS. Stem Cell Reports 11(6):1565-157

Nichterwitz S, Chen G et al (2016) Laser-capture microscopy coupled with Smart-seq2 (LCM-seq) for precise spatial transcriptome profiling. Nature Communications 7:12139

 

Qualification requirements

A postdoctoral fellowship can be given to a candidate during a two-year period within five years after dissertation.

 

Assessment criteria

In the appointment process, special attention will be given to research skills in machine learning. Previous original publications as a first author are a strong merit.

Skills in advanced bioinformatics analyses including machine learning are also a strong merit.

 

Terms

This is a postdoctoral fellowship for two years, with the possibility of extension with an employment.

Start date: March 1st 2022 or as per agreement.


Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

 

Contact

Further information about the position can be obtained from Professor Eva Hedlund, eva.hedlund@dbb.su.se



Application

Please send your application (CV and personal letter) to my.jegenberg@dbb.su.se