Ph.D. Scholarship: Streaming Algorithms for Whole Genome Assembly

High throughput sequencing has revolutionized the field of genomics. Current sequencing technologies are relatively cost effective, but rely on storing all data on disk and processing them in bulk. The future of genetic sequencing will require technologies and algorithms where the DNA sequences are analyzed ‘on the fly’ without storing the intermediate results, such as short sequence reads.

Project outline

This project will investigate streaming methods for whole genome assembly, capable of working with data as it is being generated, while limiting the running time and memory usage. The principle objective of the research is to develop such algorithms as well as understanding the theoretical limitations of what can be done in such a setting.

Ideal candidate and requirements

We are seeking a student with dedication, drive and good theoretical background in algorithmic development. The project requires implementation of software, so good programming skills are a benefit. A background in bioinformatics is a plus, but not necessary for this project.

The student will join the Department of Computer Science in the Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, under the supervision of Pall Melsted.

Qualifications

The applicant must have completed a M.Sc. degree in Computer Science, Bioinformatics, Mathematics or related fields from a University approved by the University of Iceland’s Graduate School. Those with an advanced degree including at least a 60 ECTS credits thesis project will be given precedence.

Terms of employment

The project is funded for 3 years by The Icelandic Research Fund. The PhD study should be completed within four years of full time study.

Application

You should send a letter of intent (maximum two pages) explaining your interest in working on this project, why you want to pursue a Ph.D., what you hope to gain and learn during your PhD studies and what makes you suitable for this project. You should also send a CV, transcripts of university diplomas, courses taken at bachelor and masters level, degree project thesis. Additionally, you must have two people familiar with the your work send letters of recommendation. Applications should be sent before March 15th, 2015, to pmelsted@hi.is. We will continue to review applications received after that time on a rolling basis until the position is filled.

University of Iceland

The University of Iceland strives to work against workplace discrimination and to offer equal opportunities to everyone.

For further information contact: Pall Melsted pmelsted@hi.is