PhD student in Computational Mathematics

The Department of Mathematics at Stockholm University has with its long tradition of excellent research a prominent place in Scandinavian mathematics. The department consists of three divisions: Mathematics, Mathematical Statistics and Computational Mathematics. The research at the Division of Computational Mathematics covers many different areas in numerical analysis, symbolic computations, computer science, computational biology and computational statistics. More information about us, please visit: Department of Mathematics.

Project description

We seek to recruit a PhD student for the following project:

Computational methods for complex SV detection using sequencing data

Main supervisor: Kristoffer Sahlin, ksahlin@math.su.se.

Co-supervisor: Adam Ameur, adam.ameur@igp.uu.se.

In the Department of mathematics at Stockholm University, we are announcing the position as DDLS PhD student in data driven cell and molecular biology. Data driven cell and molecular biology covers research that fundamentally transforms our knowledge about how cells function by peering into their molecular components in time and space, from single molecules to native tissue environments. 

The project aims to design data-driven algorithms to detect complex structural variants in humans using long DNA sequencing reads. 

A structural variant (SV) is a large-scale alteration in the genome that involves rearranged, deleted, or inserted DNA segments with respect to the reference genome. A combination of SV events in a genomic region characterizes a complex SV. Complex SVs play an important role in many diseases. The data used to detect and examine SVs are whole genome sequencing reads (or simply reads). The reads mapping over and around variation sites can be used to classify the SV. Previous sequencing technologies often produced relatively short reads, making it impossible for reads to span over large and complex SVs. However, recent advancements in long-read sequencing technologies now offer the potential of a cheap and powerful method for understanding complex genomic alterations. While sequencing technologies have made a leap forward, work is still needed on the computational side to fully use the technology. 

This is an interdisciplinary project. The project concerns algorithm design, implementations of algorithms, and simulated and biological data analysis. The student is expected to learn a bit of relevant molecular biology to efficiently interact in the interdisciplinary project. We seek candidates with a strong computer science, mathematics, statistics, or bioinformatics background and strong programming skills. Some previous knowledge or experience working with biological sequencing data is beneficial but not necessary. 

Feel free to email me if you have any question when preparing your application. 

About the DDLS PhD student program

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. 2    The program is funded with a total of 3.7 billion SEK (about 290 MUSD) 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 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! 

Keywords: Bioinformatics, computational biology, algorithms, data structures, sequencing data

Qualification requirements

In order to be admitted to postgraduate education, the applicant must have the general and specific entry requirements. The qualification requirements must be met by the deadline for applications.

You meet general entry requirements if you have completed a second-cycle degree, or completed courses equivalent to at least 240 higher education credits, of which 60 credits must be in the second cycle, or have otherwise acquired equivalent knowledge in Sweden or elsewhere.

In order to meet the specific entry requirements, the general syllabus for doctoral studies in the field of Computational Mathematics stipulates that applicants must have completed courses equivalent to at least 60 credits in a mathematical subject and at least 30 credits in either numerical analysis or computer 

Selection

The selection among the eligible candidates will be based on their capacity to benefit from the training. The following criteria will be used to assess this capacity: the candidates’ documented knowledge in the relevant field of research, written and oral proficiency in English, the capacity for analytical thinking, the ability to collaborate, as well as creativity, initiative, and independence. The assessment will be based on previous studies and grades, the quality of degree projects, references, relevant experience, the candidate’s written motivation for applying for the position and, for select applicants, interviews. Please note that applicants may be called to an interview on a short notice. Tentatively, interviews will be held around the middle of May.

Admission Regulations for Doctoral Studies at Stockholm University.

About the employment

We offer a fixed-term employment as a doctoral student according to Chapter 5 of the Higher Education Ordinance (1993:100). The period of employment may not be longer than what corresponds to full-time doctoral education for four years. As a doctoral student, you should primarily devote yourself to your own doctoral education, but the employment may include work with education, research and administration to a limited extent (maximum 20 %).

A new employment as a doctoral student is for a maximum of one year, the employment is then renewed for a maximum of two years at a time.

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

Contact

For more information, please contact the director of PhD studies Chun-Biu Li, cbli@math.su.se, or the division head Lars Arvestad, arve@math.su.se.

Application

Apply for the PhD student position at Stockholm University's recruitment system. Attach a personal letter and CV as well as the attachments requested in the application form. 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.

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