Doctoral (PhD) student position in multi-omics studies in HIV-associated immune-aging - Hiring in process/Finished, not possible to apply

A doctoral student is admitted to third-cycle/doctoral education. A doctoral education consists of supervised research, combined with courses and other educational activities. An individual study plan is established for each doctoral student. For a doctoral degree, the equivalent of four years of full-time doctoral education is required.

Research group
The Neogi group lab work towards unraveling the mechanism of immune-aging in people living with HIV (PLHIV) on successful therapy and understanding the mechanisms of natural immune control in HIV-1 infection using multi-omics system biology approach amalgamating with in vitro and ex vivo experimental assays. Our group aims to understand the genetic, cellular, and molecular mechanisms of immune aging in PLHIV on successful long-term treatment. We are applying high-throughput multi-omics technologies (e.g., epigenomics, transcriptomics, proteomics, and metabolomics), along with in vitro and ex vivo experimental methods that help bridge the gap between genotype and phenotype and to understand how it regulates immune-aging and age-related diseases in PLHIV. Our studies can, therefore, provide possibilities to therapeutically target the immune-aging process through metabolic interference, thus allowing more individualized care. The research group has both bioinformatics team as well as experimental team with four doctoral students, three bioinformaticians, two postdocs and one assistant professor.

The doctoral student project and the duties of the doctoral student
The present Ph.D. positions aims towards benchmarking proteo-transcriptomics studies to develop and execute novel bioinformatics and statistical methods for transcriptomics, proteomics, and multiparametric proteotranscriptomics analysis to identify the biomarkers and map the intercellular pathway of immune-aging in PLHIV.

The intended learning objectives for this Ph.D. program aims to demonstrate mastery of the core concepts of Bioinformatics more specific towards the integrative omics. 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 projects have major component in omics studies (75%) with 25% of laboratory work. The student is expected to analysis large amount of omics data mainly transcriptomics and proteomics and perform laboratory analysis like sample preparations of the omics studies.

Eligibility requirements for doctoral education
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 requirement

You 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.

Skills and personal qualities

• The applicant should have second-cycle background in genetics and/or bioinformatics.
• Interest and prior experience in transcriptomics and mass-spectrometry based proteomics analysis are essential. Provide github account details.
• The applicant should have strong competence in Python, R-programming language and network analysis (e.g. Cytoscape). Preferences will be given who have experience in protein structure analysis.
• Internship in animal models (omics as well as lab experiments) will be added advantage.
• The applicant should be able to work well in a multidisciplinary team, as well as having the ability to work independently.
• The applicant should possess good organizational skills and know how to multitask.

Terms and conditions
The doctoral student will be employed on a doctoral studentship maximum 4 years full-time.

Application process
Submit your application and supporting documents through the Varbi recruitment system. Use the button in the top right corner and follow the instructions.

Your application should 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)

Selection
A selection will be made among eligible applicants on the basis of the ability to benefit from doctoral education. The qualifications of the applicants will be evaluated on an overall basis.

KI uses the following bases of assessment:

• Documented subject knowledge of relevance to the area of research
• Analytical skill
• Other documented knowledge or experience that may be relevant to doctoral studies in the subject.

All applicants will be informed when the recruitment is completed.