Special Seminar: Leena Salmela "Algorithm Engineering for Biological Sequence Analysis"
Algorithm Engineering for Biological Sequence Analysis
High-throughput sequencing has become part of the standard toolkit for modern biological and medical research. Sequencing produces reads which are subsequences randomly sampled from the DNA or RNA sequence. A long standing computational problem in DNA sequencing is genome assembly which is the problem of reconstructing a previously unsequenced genome from a set of sequencing reads. In this talk I will give an overview of the current status of genome assembly methods. As an example of the impact of method development in this field, I will show how careful algorithm engineering and use of state-of-the-art data structures can give significant performance improvements in correction of sequencing errors which is the first phase of genome assembly methods. Finally, I will discuss our ongoing efforts to improve genome assembly with auxiliary long range data such as optical maps and genetic linkage maps. I will conclude by presenting future challenges in processing sequencing data from portable sequencing devices.
Leena Salmela did her doctoral thesis in search algorithms for sequences and obtained her doctoral degree in 2009 at Helsinki University of Technology (now Aalto University). After her doctoral studies she has worked as a postdoctoral researcher in University of Helsinki where her research focus has shifted to bioinformatics. Currently she holds the research post as Academy Research Fellow. Leena Salmela has successfully applied her expertise in algorithms research to real bioinformatics problems. She has worked on genome assembly where the genome of an organism is reconstructed from randomly sampled sequencing reads from the genome. She has published several important results in many subproblems of genome assembly including correction of sequencing errors, scaffolding and gap filling. Together with her collaborators she has sequenced and assembled the genome of the Glanville fritillary butterfly which is the first large genome sequenced in Finland. Currently she works on new methods for reconstructing chromosome wide genome assemblies by integrating auxiliary long range data such as genetic linkage maps and optical mapping data to genome assembly algorithms. Leena Salmela has a strong track record of developing and publishing high quality implementations of her algorithmic discoveries. Software developed by her has been used in numerous biological projects ranging from transcriptomics to genome assembly.