PhD fellowship in metagenomics focusing on next generation sequencing and bioinformatic analysis of the early life microbiome

The Department of Biology, Faculty of Science at University of Copenhagen (UCPH) is seeking to hire two enthusiastic and talented PhD fellows to contribute towards a better understanding of the longitudinal development of the early life human gut microbiome and the microbial interactions occurring therein.

The proposed positions are part of the research projects: Collaborative investigation on gut-brain interactions in childhood and Social Networking in the Gut Microbiome funded by the Novo Nordisk Foundation and the Independent Research Fund Denmark.

In recent years, we have begun to understand the important role of the human microbiome in the development of chronic inflammatory disorders. We have recently described, how an adequate microbial maturation process during the first year of life can protect children from developing asthma and allergy. In the proposed PhD projects, we want to understand the mechanistic implications of this finding and how other health outcomes in childhood are affected by the early life microbiome.

The projects will leverage the COPSAC birth cohort with its longitudinal microbiota material and clinical phenotyping including symptoms, but also their general health, epigenetics, metabolomics, and immunological profiles.

As part of the department’s work on the COPSAC cohort, we will investigate which role the early life microbiota has in development of such diseases. The main tasks in these projects will be to lead the metagenomic sequencing of microbiome samples and the following bioinformatic analysis of metagenome sequencing data and integration of data from clinical examinations of the COPSACcohort.

The positions are for a 3-year period, commencing on 15th of February 2023, or as soon as possible thereafter.

The scientific environment
The positions are available at the Section of Microbiology, headed by Professor Søren Johannes Sørensen. The Section offers a highly diverse and inclusive environment consisting of  around 35 researchers that specialize in microbial community interactions, mobile genetic elements, horizontal gene transfer, and the early life human microbiome. The group has gained international reputation in applying a combination of bioinformatics and molecular biology approaches to address research questions of ecological, clinical, and biotechnological interest, which lie at the intersection of computational biology, genomics, and bacterial evolution.

We offer creative and stimulating working conditions in a dynamic and international research environment. The Section will provide state-of-the-art expertise, mentoring, sequencing, necessary data storage, molecular microbiology laboratories and equipment. It will also contribute with highly experienced financial, legal, administrative and IP management support and facilities.

See more: https://www1.bio.ku.dk/english/research/microbiology/

Your principal supervisor will be Professor Søren Sørensen. Department of Biology, Section of Microbiology, Email: [email protected], Direct Phone: +45 5182 7007 and your Co-supervisor will be Assistant professor Urvish Trivedi, Department of Biology, Section of Microbiology, Email: [email protected].

Job description
Your key tasks as a PhD at SCIENCE are:

● Manage and carry through your research projects.

● Collaborate closely with partners in international research projects.

● Disseminate your research and write scientific articles.

● Complete approximately 30 ECTS in PhD courses

● Take part in mentoring activities and teaching at the Department.

● Research stay abroad at an international institution (up to the candidate).

Key criteria for the assessment of applicants

Educational qualifications:
● BSc in Bioinformatics, Biotechnology, or a related Biological Sciences field

● MSc in Microbiology, Bioinformatics, Biotechnology, or a related Biological Sciences field. (Only candidates with a MSc equivalent to a Danish Master degree (180 ETCS) will be considered qualified for the position).

Required qualifications:
● Documented experience working with computational biology and bioinformatics

● Experience in working with metagenomic datasets (including sequence assembly, functional annotation, strain-level analysis)

● Knowledge of statistical analysis, including multivariate analysis, statistical learning, and temporal analyses

● Theoretical background in the ecology of microbes and/or in host-associated microbiomes

● Hands on experience with next generation sequencing techniques and model organisms

● Ability to work with command line tools. Coding skills using common languages such as Python, R, and bash

● Proficiency in English, in oral and writing

● Excellent communication skills and collaborative mentality

● Excited to be part of a team but are also comfortable working independently

● Curious and willingness to work across disciplines

● Rational and creative mind-set promoting teamwork and solutions

Desired:
● Interest in working with sequencing techniques, particularly metagenomics.

● Interest in supervision of BSc and MSc level students.

● Interest in participating in international meetings and scientific activities.

● Competitive research output/experience documented.

● Motivation to engage in outreach activities and Science communication.

● Likes the occasional social gatherings together with colleagues.

The PhD programme
A three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

Qualifications needed
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. (cell) biology, molecular biomedicine, biochemistry, nanoscience, biotechnology or human biology. For information of eligibility of completed programmes, see General assessments for specific countries — Uddannelses- og Forskningsministeriet (ufm.dk)

Terms of employment
Employment as PhD fellow is full time and for maximum 3 years. Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure

Questions
Further information on the Department is linked at https://www.science.ku.dk/english/about-the-faculty/organisation/ .

Inquiries about the position can be made to Professor Søren Johannes Sørensen ([email protected]) and Assistant Professor Urvish Trivedi, Email: [email protected]

General information about the PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/ .

If you consider applying from abroad, you may find useful information on how it is to work in Denmark and at UCPH in these links: http://ism.ku.dk , https://www.nyidanmark.dk/en-us/frontpage.htm and https://www.workindenmark.dk/

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Application and Assessment Procedure
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include

● Curriculum vitae.

● Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.

● Motivation letter specifying project related experience.

● Complete publication list, if any

● If available, separate reprints of 2-3 particularly relevant papers.

The deadline for applications is 4 November 2022, 23:59 GMT +1.

The further process

 After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above-mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/

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.