Research assistant

The group of Kristoffer Sahlin, part of the Department of Mathematics, seeks a research assistant for algorithm development for DNA sequencing data. Our research interests broadly span algorithm development and analysis of sequence data. We have ongoing projects on method development for rapid sequence mapping and sequence similarity searches, various computational problems in transcriptomic analysis, and collaborative projects in genomics and metagenomics. We are located in Stockholm at the Science for Life Laboratory.

For more information about us, please visit: www.su.se/english/profiles/krsa3529-1.475542.

Main responsibilities

Your tasks will consist of algorithm development and programming in a low-level language such as C++, or Rust. You will conduct benchmarking experiments, perform data analysis, and write a report on the study. Brief information regarding the project follows below.

DNA and RNA play an essential role in determining the state and condition of cells and tissue and, therefore, hold key information to study diseases, traits, and evolution. We can now generate large-scale DNA and RNA sequencing data at low cost. However, the computational methods to extract information from the data could be improved in terms of accuracy, runtime, and memory usage in many applications. We have previously published a tool, strobealign, for rapid short-read mapping, which follows a seed-filter-extend approach. A key step in read mapping is the seeding step. The successful applicant will investigate alternative methods for the seeding and filtering steps in strobealign

Qualification requirements

We are looking for you who have an education in Computer Science with a focus on algorithms and data structures. It is beneficial if you have developed efficient algorithms for analyzing sequencing data.

The ideal applicant has:

Strong skills in C++ or Rust
Experience with implementing algorithms for sequencing data
Experience with analyzing sequencing data
Good communication skills

About the employment

This is a part-time employment for a six-month period. Stockholm University applies individual salary setting. The applicant should start in spring 2025, with a preference for March 2025.

We offer

With us, you will experience the dynamic interaction between higher education and research that makes Stockholm University an exciting and creative environment. You will work in an international environment and get favourable conditions. The university is located in the National City Park with good transport links to the city.

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

Contact

Further information about the position can be obtained from Kristoffer Sahlin, ksahlin@math.su.se.

Application

Apply for the position at Stockholm University's recruitment system. It is the responsibility of the applicant to ensure that the application is complete and that it is submitted before the deadline.

The instructions for applicants are available at: How to apply for a position.