[Thesis Defense] Minimizer-space computation

Title: Minimizer-space computation

Presenter: Barış Ekim
Presenter’s affiliation: CSAIL
Thesis supervisor(s): Prof. Bonnie Berger

Date: May 9, 2025
Time: 09:30AM – 11:30AM
In-person location: 32-G575

Zoom link: https://mit.zoom.us/j/95555831150

Abstract: As the volume of DNA sequencing data increases, the need for algorithmic advances to efficiently handle the data arises. One such concept is minimizers, which are genomic substrings that allow for reduced representations of larger DNA sequences. In this thesis, we introduce minimizer-space computation as a new algorithmic paradigm for DNA sequence analysis. Instead of DNA nucleotides, we consider minimizers as the letters of an extended alphabet in which algorithms operate. We present several techniques on how to efficiently construct these extended alphabets, demonstrate how to develop approaches that use these alphabets and consequently use only a fraction of sequence data, and show how fundamental biological tasks, such as genome assembly and read mapping, can be significantly accelerated over state-of-the-art methods.