Postdoc in spatial transcriptomic technologies at Department of Veterinary and Animal Sciences

26 May 2023
Job Information

Organisation/Company

University of Copenhagen

Department

Department of Veterinary and Animal Sciences

Research Field

Neurosciences » Neuropsychology

Researcher Profile

First Stage Researcher (R1)

Country

Denmark

Application Deadline

1 Jul 2023 - 12:00 (Europe/Copenhagen)

Type of Contract

Temporary

Job Status

Full-time

Offer Starting Date

1 Sep 2023

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

We are looking for a highly motivated and dynamic researcher for a 21-month position, who holds a PhD and has a background in neuroscience or neurophysiology and single cell/spatial transcriptomics or bioinformatics to commence on the 1st September 2023 or as close to this date as possible.

The position entails molecular profiling of the entorhinal cortex in the murine and porcine brain using smart-seq, bioinformatic analyses of smart-seq datasets and comparing this technology to data obtained from Merfish and multi-electrode arrays. The position also involves a short stay at Harvard University, US with a collaborating group to perform Merfish.

Information on the department can be found at: https://ivh.ku.dk/english

Our research

The Group for Brain Development and Disease is an inclusive and diverse research group that is composed of local and international researchers. The group collaborates with leading experts in a variety of different fields (bioinformaticians, neuroanatomists, neurologists, developmental biologists, nanoengineers and imaging experts) both nationally and internationally. It is expected that all group members thrive on achieving excellence, are an active team member and respect their peers and colleagues, irrespective of their gender or background. The group’s values include providing positive feedback, rewarding excellence, envisioning BIG if starting small, being passionate about research, that growth and learning is in our DNA, and that it’s all about the people. The research group was established in 2017 and has over the last years focused on categorizing the developing entorhinal cortex using single cell RNA sequencing, bioinformatics, MRI, Diffusion Tensor Imaging, immunohistochemistry technologies and most recently, established patch-seq. The group has discovered the genotypes of several cells within the entorhinal cortex and that the entorhinal cortex forms in a sandwich/parallel pattern atypical of the inside out typical formation of the rest of the neocortex. The entorhinal cortex is the brain region in focus for the group, as it is “ground zero” for the emergence of Alzheimer’s disease pathology. Understanding the uniqueness and intricacies of this part of the brain is important for better understanding Alzheimer’s disease, which could lead to novel treatments in the future. For more info see the group’s research page: https://ivh.ku.dk/english/research/pathobiological-sciences/brain-development-and-disease/

Your job

This project is a highly collaborative and interdisciplinary project with researchers based at the Brigham Women’s Hospital/Harvard Uni, US and DeLille University, France. Your tasks will be to work together with a trained electrophysiologist to perform patch-seq on acute brain slices from pigs and mice. You will help to maintain the mouse colony for experiments. You will help to generate cDNA libraries, and process smart-seq datasets using bioinformatic pipelines from single cell nuclei. You will generate probes for Merfish to study gene expression in the entorhinal cortex. As part of the postdoc, you will travel to the US for a short stay to learn and perform Merfish. You will also study extracellular signalling in neural/brain slice cultures from the entorhinal cortex using multi-electrode arrays. You will be expected to write high-quality manuscripts suitable for publishing in excellent journals. You will also be expected to train guest researchers and other new incoming researchers on certain techniques/technologies and run certain events and activities in the group such as the journal club. We strive for excellence, a team-player attitude, a thirst for learning and discovering and a passion for research. We also encourage a small amount of teaching in one or more of our teaching courses, which could include participation in Cell Biology practicals.

Profile
We are looking for a highly motivated and enthusiastic scientist with the following competencies and experience:

Essential experience and skills:

• You have a PhD in Neuroscience, Neurophysiology, Bioinformatics, Molecular Biomedicine or similar.
• You have practical cell culture experience in culturing neural cells or organotypic slices.
• You have practical experience in molecular biology techniques and single cell RNA sequencing (scRNAseq).
• You have practical experience in bioinformatics and handling of single cell data sets and have excellent practical experience in using Seurat, R, Python and diverse single cell tools and packages.
• You have a solid understanding of patch-seq or other single cell transcriptomic approaches.
• You have a solid understanding of bioinformatic pipelines for analysing scRNAseq data.
• You have proficient communication skills and can work in teams.
• You have excellent English skills, both written and spoken.
• You have at least FELASA B certificate or equivalent for handling lab animals.

Desirable experience and skills:

• Have experience in using multi-electrode arrays from Multichannel systems.
• You have practical experience in producing acute brain slices.

Have experience in using a spatial transcriptomic technology.

• Have experience in producing MERFISH probes.
• Have general electrophysiology knowledge.
• You have a high level of knowledge on the entorhinal cortex.
• Have published in a medium to high impact journal as first or co-author.
• Have obtained own research money for travel or research through externally applied for grants.
• Have obtained a research/poster prize for your previous research.

Place of employment

The place of employment is at the Department of Veterinary and Animal Sciences, Faculty of Healthy and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern laboratories, GMO Class 1 and 2 cell labs, bacterial and molecular labs, a confocal microscope, a Leica vibratome and electrophysiology equipment for patch clamping of brain slices.

Terms of employment
The employment as postdoc is a full time and fixed-term position for 21 months. Starting date is 1st September 2023 or as close to this date as possible.

Salary, pension and terms of employment will be in accordance with the agreement between the Danish Ministry of Finance and AC (Danish Confederation of Professional Associations). Currently, the monthly salary starts at 36,300 DKK/ approx. 4,870 Euro (April 2018-level). Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % to your pension fund.

Non-Danish and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years.

The position is covered by the “Memorandum on Job Structure for Academic Staff at the Universities” of June 28, 2013.

Questions
For further information please contact Associate Professor Vanessa Hall; [[email protected] ]; www.sund.ku.dk

Foreign applicants may find this link useful: www.ism.ku.dk  (International Staff Mobility).

Application procedure
Your online application must be submitted in English by clicking ‘Apply now’ below. Furthermore your application must include the following documents/attachments – all in PDF format:

1. Motivated letter of application (max. one page).

2. CV incl. education, work/research experience, language skills and other skills relevant for the position.

3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.

4. List of publications.

Application deadline:  1st July 2023, 23.59pm CET

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held in August 2023.

University of Copenhagen wish to reflect the diversity of society and welcome applications from all qualified candidates regardless of age, disability, gender, nationality, race, religion or sexual orientation. Appointment will be based on merit alone.

Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

Requirements

Research Field

Neurosciences » Neuropsychology

Education Level

PhD or equivalent

Additional Information
Work Location(s)

Number of offers available

1

Company/Institute

University of Copenhagen

Country

Denmark

Geofield

Where to apply

Website

https://candidate.hr-manager.net/ApplicationInit.aspx?cid=1307&ProjectId=159348…

Contact

City

Copenhagen

Website

http://www.ku.dk/english/

STATUS: EXPIRED