Postdoc in Exploring Micro-scale Microbial Ecology through Oligopaints and Laser Microdissection Technologies at the Globe Institute

We are looking for a highly motivated and dynamic postdoc for an extendable 24-month position on optimising and implementing novel oligopaints and laser microdissection-based technologies to explore microbial interactions at the micro-scale within animal guts, to commence on the 1st of February 2024.

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

Our research
The Center for Evolutionary Hologenomics (CEH) is a Center of Excellence funded by the Danish National Research Foundation to develop and implement state of the art omics and associated computational techniques, to address through experimental and theoretical research. CEH’s main purpose is to address basic scientific questions through interdisciplinary approaches, operating at the intersection of natural sciences, medical sciences and the humanities.

Your job
The postdoc will be involved in two projects that share the common goal of increasing the spatial resolution of animal-associated microbiome analyses to the micron scale, and generating microbiome data at hitherto unseen level of detail. The first project, called 3D’omics, is a multi-partner H2020 project implementing micro-scale metagenomic technologies to reconstruct microbial communities through laser microdissection (Leica LMD7). The second project, called InSituMicroSeq, is a technology-development project aimed at implementing a novel technique based on in situ sequencing (Bucker Vutara VXL) of barcoded probes targeting functional genes. The two projects are coordinated by Assoc. Prof. Antton Alberdi, in collaboration with international partners. This postdoctoral position will be supervised by Assoc. Prof. Antton Alberdi (Section for Hologenomics at UCPH),  Ass. Prof. Urvish Trivedi (Section for Microbiology at UCPH) and Prof. Marc A. Marti-Renom (CNAG and CRG, in Barcelona).

The job of the postdoc will be to develop, generate, analyse and compare two different types of micro-scale (microns) microbial data. The technology for micro-scale metagenomic data generation and analysis is already advanced, so the postdoc will primarily generate and analyse data using existing protocols and infrastructure. In contrast, the technology for in situ sequencing of barcoded probes targeting functional genes will require further development, including visits to Barcelona to conduct part of the analysis.

The range of technologies and infrastructure the postdoc will implement include cryosectioning (using Leica CM3050S), laser microdissection (using Leica LMD7), DNA sequencing library preparation (using Covaris LE220 and Tecan DreamPrep workstation), conventional DNA sequencing (using Illumina NovaSeqX and PacBio Sequel IIe), high-resolution imaging (using ZEISS LSM800), and in-situ sequencing (using Bucker Vutara VXL). The postdoc will receive counsel and support by fellow researchers already employing such instruments.

The postdoc will be part of a larger team including two more postdocs and two research assistants with expertise in laser microdissection, imaging and metagenomics, who will interact on a daily basis and collaborate to ensure quality and quantity of scientific output is maximised. The postdoc is expected to participate in the coordination meetings of the H2020 project, spend short periods of time in Barcelona, lead high-impact papers and present scientific results in international conferences.

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 Biology, Biochemistry, Biotechnology or similar.
• You are highly experienced in laboratory procedures related to microbial research, including confocal microscopy imaging, image processing, probe design, and microbial (meta)genomics.
• You have proven experience managing, creating and optimising laboratory procedures.
• You have proven experience in leading high-impact publications.
• You have an active interest in microbe-microbe and animal-microbe interactions.
• You have proficient communication skills and ability to work in teams.
• You have excellent English skills written and spoken.

Desirable experience and skills:

• Experience in probe design for multiplexing.

Place of employment
The place of employment is at the Section for Hologenomics, Øster Farimagsgade 5, building 7, floor 2, 1353 Copenhagen K.

About Globe Institute
The Globe Institute is part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute’s main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities. Information on the institute can be found at: https://www.globe.ku.dk/.

The Globe Institute is committed to creating an inclusive and diverse environment where employees and students can belong and thrive. See website for more information. All qualified applicants will receive full consideration. Candidates who, through their research, teaching, and/or service, contribute to diversity and competencies of our Institute are encouraged to apply. The University of Copenhagen strives to offer a family friendly and flexible working environment with a sustainable balance between work- and private life, including parental leave schemes (up to 47 weeks for both parents) and up to six weeks of paid holidays per year. Researchers that have not been tax liable in Denmark for the last 10 years can apply for a special (reduced) tax scheme. The university offers a variety of services for international researchers and accompanying families.

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 2 years. The starting date is on February 1st 2024 or at the earliest available opportunity thereafter.

Salary, pension, and other conditions of employment are set in accordance with the Agreement between the Ministry of Taxation and AC (Danish Confederation of Professional Associations) or other relevant organisation. Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % to your pension fund.

Foreign 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 Job Structure for Academic Staff at Universities 2020.

Questions
For further information please contact Antton Alberdi (antton.alberdi@sund.ku.dk), Urvish Trivedi (urvish.trivedi@bio.ku.dk) and/or Marc A Marti-Renom (martirenom@crg.eu).

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.

Deadline for applications: October 31st, 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 https://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.

The University of Copenhagen wishes to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.