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Project Description

Doctoral Field: Biotechnology

This project aims to develop robust methods for assessing identification and quantification errors in shotgun proteomics. We will construct probabilistic models to characterize errors in the identification of peptides and proteins from mass spectrometry data. Furthermore, we will extend these models to quantify how identification errors propagate to quantification at the protein level. By evaluating existing methods and proposing new approaches, the project intends to improve the reliability of proteomics data analysis and thereby strengthen subsequent biological interpretation.

The project will use improved probabilistic regression models to estimate error rates for identification and quantification in proteomics data. These error rates will be modeled using hierarchical Bayesian networks to capture dependencies between peptides and proteins. We will implement and test the models on reference datasets and compare their performance with existing methods. Additionally, we will develop scalable computational tools to integrate the models into current proteomics workflows, thereby ensuring practical applicability.

Supervision: Lukas Käll is proposed to supervise the doctoral student. Decision is made upon admission.

Admission Requirements

To be admitted to doctoral studies (Chapter 7, Section 39 of the Higher Education Ordinance), the applicant must have basic eligibility:

• Mobility Rules – Candidates must not have been resident or had their main activity (work, studies, etc.) in Sweden for more than 12 months during the 3 years immediately preceding the recruitment date.
• completed an advanced level degree, or
• completed course requirements of at least 240 higher education credits, of which at least 60 higher education credits at advanced level, or
• acquired in some other way, within or outside the country, knowledge essentially corresponding to the above.

In addition to the above, there is also a mandatory requirement for English equivalent to English B/6.

Selection

To succeed in your doctoral studies at KTH, you need to be goal-oriented and persistent in your work. In the selection of applicants, the ability to:

• independently drive your work forward,
• collaborate with others,
• have a professional attitude, and
• analyze and work with complex issues.

After meeting the eligibility requirements, great weight will be placed on personal qualities.

Final Degree: Doctorate

Information on Admission and Employment

Only those admitted to doctoral studies may be employed as doctoral students. The total employment period may not be longer than what corresponds to full-time doctoral education over four years. An employed doctoral student may, to a limited extent (max 20%), perform certain tasks within, for example, education and administration. A new employment as a doctoral student is valid for at most one year; the employment may thereafter be renewed for at most two years at a time.

As a doctoral student, you are entitled to KTH's employment benefits and have a monthly salary according to KTH's agreement for doctoral salaries. Read more about Doctoral Studies at KTH | KTH | Sweden

Compensation – In addition to the base salary mentioned in the link above, a mobility allowance and potentially a family allowance are included in all positions within the Marie Curie program. For more information, read here. Base salary and additional allowances are stated before tax.

Union Representatives

Contact details for union representatives.

Doctoral Student Section (Student Union of the Royal Institute of Technology)

Contact details for the doctoral student section.

Application

You apply via KTH's recruitment system. As an applicant, you are primarily responsible for ensuring your application is complete when submitted.

The application must contain the following:

• Copies of degree certificates and transcripts from previous university studies and certificates of fulfilled language requirements (see above). Translations to English or Swedish if the original document is not issued in one of these languages. Copies of originals must be certified.
• CV with relevant professional experience and skills.
• Cover letter with a brief account of why you wish to pursue doctoral studies, your academic interests, and how they relate to your previous studies and future goals (Max 2 pages).
• Representative publications or technical reports. For longer documents, please attach a summary (abstract) and a web link to the full text.

The application must be received by KTH no later than the last day of application at midnight, CET/CEST (Central European Time/Central European Summer Time).

Other

For information on the processing of personal data in connection with recruitment.

An employment at KTH may be classified as security-sensitive. If this applies to this specific position, a security clearance check will be conducted on the applicant in accordance with the Security Protection Act (2018:585) with consent. In these cases, a condition for employment is that the applicant is approved after the security clearance check.

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