PhD student position in population genomics

The Department of Organismal Biology teach about, and explores the evolution, development and function on the organismal level. We study the deepest branches of the tree of life with the help of bioinformatics and experimental molecular techniques. Research about how chemicals of anthropogenic origin interact with cellular functions and cause long-lasting adverse health effects in humans and wildlife is also performed. For more information see www.iob.uu.se

Data-driven life science (DDLS) uses 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. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.3 billion SEK over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

In 2025 the DDLS Research School will be expanded with the recruitment of 19 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic research areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see https://www.scilifelab.se/data-driven/ddls-research-school/

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

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Project description
At Department of Organismal Biology, Uppsala University, we are announcing the position as DDLS PhD student in Data driven evolution and biodiversity. Data driven evolution and biodiversity concerns research that takes advantage of the massive data streams offered by techniques such as high-throughput sequencing of genomes and biomes, continuous recording of video and audio in the wild, high-throughput imaging of biological specimens, and large-scale remote monitoring of organisms or habitats. 

The project focuses on trying to disentangle population structure among archaic and modern humans over time. The project will investigate these processes using large-scale population genomic data from modern-day and prehistoric humans. The PhD position is part of the The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS). The successful candidate will work in Maximilian Larena’s research group, and co-supervised by Prof. Mattias Jakobsson and Prof. Carina Schlebusch. The research program consists of an international team of researchers (senior scientists, post-doctoral fellows, graduate students and research engineers) with different areas of expertise. The research program is multidisciplinary with competence in computational biology, population genomics and ancient DNA, and associated with the Swedish Research Council’s excellence center for the Human Past (https://centerforthehumanpast.se/). The research environment is international with English being the working language. See the Larena lab web-pages for more information and recent publications: https://www.larenalab.com

Duties
The PhD research project will focus on population genomic studies and the analysis of archaic ancestry in present-day and prehistoric humans across the globe. The duties will involve large-scale analyses of genomic datasets, from present-day and prehistoric individuals, to make inferences about demographic history, migration and admixture patterns, and signals of adaptation. The project will include computational analysis of archaic introgression and its functional implications across diverse worldwide populations. The specific project/s will be developed together with the successful candidate.

Requirements
To meet the entry requirements for doctoral studies, you must

• Hold a Master’s (second-cycle) degree in molecular biology/genetics or other orientation that the employer deems equivalent., or
• Have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• Have acquired substantially equivalent knowledge in some other way.

We are looking for a person with good knowledge and experience in bioinformatics and good knowledge of laboratory work, with experience of working with palaeogenomics. Great importance to be placed on personal qualities such as:

• Good analytic skills, good collaboration and communication skills.
• Ability to work independently and to drive projects based on personal initiatives.
• Good skills in organization and planning work and projects. Responsible.
• Good English writing (and speaking) skills.

Additional qualifications
Experience in the analyses of large-scale human population genomic data. Experience in using standardized tools for end-to-end processing of next-generation sequencing data, from raw data to variant discovery (e.g., GATK pipeline). Experience with programming languages (e.g. bash, Python, and R). Experience in using bioinformatic tools to identify archaic ancestry in populations.  Experience in analyzing adaptive archaic introgression and conducting selection analysis. Familiarity with AI-based tools for variant effect prediction. Good knowledge of human prehistory and human evolution. Good knowledge of statistics. Training in bioinformatics, genomics, molecular genetics is advantageous.

How to apply
The application should include 1) a letter of intent describing yourself, your research interests and why you want to do a PhD, 2) a short description of your education, especially in population genetics/genomics, statistics, bioinformatics, and other related areas, 3) a CV, 4) a copy of your master degree diploma, 5) the names and contact information (address, email address and phone number) of at least two reference persons, 6) relevant publications (including master thesis).

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date 1 October 2025. Placement: Uppsala

For further information about the position, please contact:  Dr. Maximilian Larena, +46 18-471 2624, maximilian.larena@ebc.uu.se

Please submit your application by 15 May 2024, UFV-PA 2025/1166.

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