PhD position in microbial bioinformatics

Reference number PAR 2024/609

The University of Gothenburg tackles society's challenges with diverse knowledge students and 6 600 employees make the university a large and inspiring place to work and study. Strong research and attractive study programmes attract researchers and students from around the world. With new knowledge and new perspectives, the University contributes to a better future.

The Department of Chemistry and Molecular Biology conducts high-quality research and education in chemical sciences and molecular life sciences. Our research and education focuses on a deep understanding of chemical and biological processes in cells and in the environment.

We address important societal issues such as antibiotic resistance, cancer, brain diseases, environmental problems and climate change. In this way, we contribute to achieving the UN's global goals for sustainable development in the areas of good health and well-being, sustainable energy for all, sustainable cities and communities, and combating climate change.

The department is an international environment with interdisciplinary collaborations in both research and education, and contributes strongly to the University of Gothenburg's top ranking in life science

The department is responsible for postgraduate education in the subject area Natural Sciences with a focus on chemistry, biophysics, biology and educational science. In addition, the department hosts educational programs in molecular biology, genomics and systems biology, chemistry, organic chemistry and pharmaceutical chemistry, as well as prescription education. The department collaborates with various societal actors such as schools, business and authorities. The Department of Chemistry and Molecular Biology has around 200 employees. We are located in central premises in Natrium on Campus Medicinareberget in Gothenburg.

Helicobacter pylori is a bacterium that chronically colonizes the stomach of almost half the world's population and that can cause ulcers and gastric cancer. H. pylori's resistance to antibiotics is rapidly increasing and more knowledge is needed in terms of virulence and colonization mechanisms and the bacterial interaction with the gastric mucosa. The group of Kaisa Thorell is studying H. pylori and host-microbe interaction focusing on bioinformatic analysis of bacterial omics data. We study large datasets of for example whole genome sequences of bacteria from different parts of the world and with different level of disease association and also work with characterization of bacterial isolates and their interaction with human cells using RNA-seq, proteomics, glycomics, and other large scale data analyses. Dr Thorell was recently appointed as a fellow within the Swedish Data Driven Life Science (DDLS) program and the project will be performed within the DDLS framework.

The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative that focuses on data- driven research, within fields essential for improving the people ́s lives, detecting and treating diseases, protecting biodiversity and creating sustainability. The programme will train the next generation of life scientists and create a strong computational and data science base. The program aims to strengthen national collaborations between universities, bridge the research communities of life sciences and data sciences, and create partnerships with industry, healthcare and other national and international actors. Read more:

The focus of the position will be to characterize an ancient ecospecies of H. pylori that we recently identified in regions of high gastric cancer risk (Tourrette, ...Thorell, Falush. BioRxiv, These bacteria will be investigated from different aspects, with a focus on bioinformatics analysis of among others RNA-seq, proteomics, and comparative and functional genomics. Depending on the candidate's interest and background one can also take part in the experimental characterization. Lastly, application and development of pan genome analysis in bacteria will be part of the project. There is also room for the candidate to shape the project.

The position is funded as a part of the Swedish Data Driven Life Science (DDLS) initiative (see below) and the candidate will be a part of the DDLS network and the DDLS research school.

General description of the DDLS program

Data-driven life sciences (DDLS) use data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. SciLifeLab and Wallenberg's national program for data-driven life science (DDLS) aim to recruit and train the next generation of researchers in data-driven life science and create globally leading competence in computational and data science for life science in Sweden. The program has SEK 3.1 billion in funding (approx. USD 290 million) over 12 years from Knut and Alice Wallenberg's foundation.

The DDLS research school is a national initiative that will train scientists with high competence within the DDLS research areas. The aim is to meet the future needs within data-driven life sciences in R&D, industry, health care and society at large. The research school further aims to provide PhD students with a common ground in data-driven life science, cutting edge knowledge and skills, offer state of the art training, mentors, collaborations nationally and internationally. The research school will be launched in 2024.

Within the DDLS program, there will be 185 PhDs (whereof 45 industrial) and 135 postdocs (whereof 45 industrial) and additionally the PhDs and postdocs included in the DDLS fellows funding package leading to a total of over 300 attendees. The research school will have an annual intake and starts in 2024 with the recruitment of the first PhD students.

Vision and Aim of the Research School

The research school aims to train future researchers with a high competence within the DDLS area. The research school will meet the future needs within data-driven life sciences in R&D, industry, health care and society at large.

The focus is to create a collaborative network and an environment in which synergy between education, research and innovation is reflected and strongly integrated into graduate education. To provide PhD students with a context, knowledge and skills necessary to perform cutting-edge research within the field of DDLS and with a direct impact on the societal challenges we are facing.

Education at third-cycle level comprises four years of full-time study, and leads to a doctoral degree.

As part of your employment as a doctoral student, you may have departmental duties corresponding to up to 20 % of full-time employment, distributed throughout your study period. Departmental duties usually consist of teaching at first- and second-cycle levels, but may also include research and administration.

To be eligible for third-cycle studies, the applicant must meet both the general and specific entry requirements: A person meets the general entry requirements for third-cycle courses and study programs if he or she:

• has been awarded a second-cycle qualification,
• has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second-cycle, or
• has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

To meet the specific entry requirements for third-cycle studies, applicants must: (i) have a second-cycle (advanced-level) degree in a relevant* subject area in the natural sciences, or (ii) have completed studies for at least 60 higher education credits at a second-cycle level in relevant subject areas in the natural sciences, or (iii) have completed a corresponding program of relevance to the planned third-cycle program, in Sweden or in another country, or have equivalent qualifications.

*Relevant for the planned third-cycle education

The specific entry requirements also include an acceptable command of spoken and written English. Guidelines for assessing English proficiency may include a minimum score of 550 on the TOEFL test (or 213 on the TOEFL-CBT, or 79 on the TOEFL-iBT).

The selection of applicants who meet the basic and specific eligibility requirements will be based on the ability to assimilate the education at third-cycle level.

You should have an MSc degree in molecular biology, biomedicine, bioinformatics, or other subject relevant for the position.

Given the data-driven nature of the project, formal training in bioinformatics, molecular evolution, and statistic are merits, as well as documented previous experience in bioinformatics analysis, including command line analysis.

Skills in programming and analysis and visualization of large-scale data using for example R is a strong merit, as well as a keen interest in machine-learning and other AI methods.

Previous experience and interest in microbiology is meriting.

The working language is English and excellent communication skills in English orally and in writing are required. We are looking for a candidate that is highly motivated, organized, and inquisitive, and interested in academic research. You should like to work in teams and contribute positively to the development of the research environment.

Type of employment: Fixed-term employment, four years full time

Extent: 100 %

Location: Department of Chemistry and Molecular Biology, Gothenburg

First day of employment: As soon as possible based on agreement

University applies local agreement on salaries of graduate students.

Once you have been admitted for education at third-cycle level, you will be employed as a doctoral student at the University of Gothenburg.

The provisions for employment as a doctoral student can be found in ordinance SFS1993:100.

Initial employment as a doctoral student may apply for a maximum of one year, and may be renewed by a maximum of two years at a time.

A doctoral student may be employed as a doctoral student for a maximum of eight years, but the total period of employment may not be longer than the equivalent of full-time education at third-cycle level for four years.

The University applies a local agreement on salaries for doctoral students.

In order to apply for a position at the University of Gothenburg, you have to register an account in our online recruitment system. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the job advertisement, and that it is submitted before the deadline.

You must include the following, in PDF format

• Personal letter
• CV
• Diploma and transcripts showing that you meet with the general entry requirement
• Proof of completion of English 6 course or the acquired equivalent knowledge through previous studies
• Two references (name, e-mail, telephone number, relation

If your degree has not been verified by a Swedish authority you need to provide contact details to the issuing university, registrar or similar, that can verify the degree at our request.

You can apply to be admitted for education at third-cycle level via the University of Gothenburg's recruitment portal.

It is your responsibility to ensure that the application is complete as per the vacancy notice, and that the University receives it by the final application deadline.

Applications must be received by:

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The University works actively to achieve a working environment with equal conditions, and values the qualities that diversity brings to its operations.

Salaries are set individually at the University.

In accordance with the National Archives of Sweden's regulations, the University must archive application documents for two years after the appointment is filled. If you request that your documents are returned, they will be returned to you once the two years have passed. Otherwise, they will be destroyed.

In connection to this recruitment, we have already decided which recruitment channels we should use. We therefore decline further contact with vendors, recruitment and staffing companies.