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Doctoral (PhD) student position in Infectious diseases – Karolinska Institutet, Sweden – Nov 2021


Division of Infectious Diseases looking for a Doctoral (PhD) student position within genome-wide bioinformatics/ computational biology skills at Department of Medicine, Karolinska Institutet, Sweden – Nov 2021

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General Info

Position: Doctoral (PhD) student
No. of Positions: 1
Research Field:
Joining Date: ASAP
Contract Period: 4 Years
Salary: According to Standard Norms

Division of Infectious Diseases
Department of Medicine
Karolinska Institute (KI)

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Qualification Details

In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.

It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.

A) General eligibility requirementYou meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

  1. have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
  2. have satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the advanced/second-cycle/master level, or
  3. have acquired substantially equivalent knowledge in some other way in Sweden or abroad.*

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.


B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

- Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Follow the instructions on the web page English language requirements for doctoral education.

Verification of your documents Karolinska Institutet checks the authenticity of your documents. Karolinska Institutet reserves the right to revoke admission if supporting documents are discovered to be fraudulent. Submission of false documents is a violation of Swedish law and is considered grounds for legal action.

(A) and (B) can only be certified by the documentation requirement for doctoral education.

Skills and personal qualities

Mastery of the core concepts of Bioinformatics is expected. These include (a) advanced methods in computational biology towards the machine learning in medical science, (b) knowledge and awareness of the basic principles and concepts of biology, computer science and mathematics, (c) the design and implementation of relational databases, and (e) the construction of predictive mathematical models of biological systems. The PhD student is expected to analysis large amount of omics data mainly transcriptomics and proteomics. Experience of bioinformatics in HIV infection and microbiota is a great assess. The candidate must hold a at least Masters Degree in the field of systembiology.

We seek a highly motivated candidate with a demonstrated record of interest in science. It is highly beneficial if the candidate also have: i) second-cycle background in genetics and/or bioinformatics; ii) Interest and prior experience in transcriptomics and mass-spectrometry based proteomics analysis are essential. Provide github account details; iii) The applicant should have competence in Python, R-programming language and network analysis (e.g. Cytoscape); iv) Experience of analysis of HIV or other viral diseases as well as microbiota; v) The applicant should be able to work well in a multidisciplinary team, as well as having the ability to work independently; vi) the applicant should possess good organizational skills and know how to multitask; vii) Excellent communication skills in both spoken and written English is of utmost importance.

We welcome a creative, hardworking and enthusiastic team-player to our group. The PhD candidate is expected to take part in experimental design, experimentation, presentations, and preparation of publications.

Responsibilities/Job Description

We are looking for an ambitious PhD-student with solid genome-wide bioinformatics/ computational biology skills to join our highly accomplished team. The PhD programme aims towards proteo-transcriptomics studies to execute novel bioinformatics and statistical methods for transcriptomics, proteomics, and multiparametric proteotranscriptomics analysis to identify biomarkers, and their relation to novel antiviral drugs, as well as the importance of the gut microbiota for viral persistence and pathogenesis. The PhD candidate should thus have a strong background in bioinformatics.

In the proposed PHD project we will explore the effect of the microbiome on clinical outcomes in HIV infection.

The aims are:

  • To establish and incorporate the gut microbiome analytic techniques in studies of people living with HIV (PLWH).
  • To study the effect of antiretroviral therapy (ART) on gut microbiome.
  • To study the effect of microbiome on the outcome of COVID vaccines in PLWH
  • To study the changes of gut microbiome as well as proteome/metabolome in patients on long term ART.

How to Apply?

Online Application through "Apply Now" Button from this page

Reference Number: STÖD 2-4850/2021
(If any, use it in the necessary place)

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Documents Required

Your application must contain the following documents:

- A personal letter and a curriculum vitae (Swedish or English)

- Degree projects and previous publications, if any (Swedish or English)

- Any other documentation showing the desirable skills and personal qualities described above (Swedish or English)

- Documents certifying your general eligibility (see A above)

- Documents certifying your specific eligibility (see B above)

About the Department

The Division of Infectious Diseases conducts preclinical, translational, clinical and epidemiological research projects. Its laboratory is located within the newly build facilities at Alfred Nobels Allé 8 (ANA Futura Laboratory), Campus Flemingsberg, Karolinska Institutet. The announced position will be placed in Associate professor Piotr Nowaks research group, which has a focus on pathogenesis, antiretroviral treatment, including HIV drug resistance, with special focus on the role of the microbiome in the pathogenesis. The group is working closely with research groups at the Division of Clinical Microbiology KI and beyond. The day-to-day activities are often integrated. The translational research is a strong component involving basic molecular, virological and immunological investigations with close ties to the HIV Unit at the Department of Infectious Diseases, Karolinska University Hospital. Dr Nowak is involved in several collaborations with focus on HIV, Covid-19 and microbiome. He publish 3-4 well cited (articles per year in renowened journals. Dr Nowaks group consists presently of one post-doc in the laboratory, and several clinical researchers. The new PhD students PhD-project will be bioinformatics on Dr Nowaks project related to HIV and the microbiome and he/she will work in close collaboration with other members of respective teams at the laboratory.

The Department of Medicine, Huddinge, conducts preclinical and clinical research in a variety of areas and undergraduate and graduate education. The department is internationally oriented and consists of seven units with a total of nearly 60 research groups, including three research centres.

About the Employer: Karolinska Institute (KI)

Note or Other details

A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. As a doctoral student you are offered an individual research project, a well-educated supervisor, a vast range of elective courses and the opportunity to work in a leading research group. Karolinska Institutet collaborates with prominent universities from all around the world, which ensures opportunities for international exchanges. You will be employed on a doctoral studentship which means that you receive a contractual salary. Employees also have access to our modern gym for free and receive reimbursements for medical care.

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Contact details

Associate professor Piotr Nowak,

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