• Calendar

May 27, Tuesday
12:00 – 14:00

Speaker BIO: Dr. Swidan was a fellow in the Technion Excellence program and finished his B.A. in Mathematics at the Technion with Summa Cum Laude. He got his PhD in computer science (bioinformatics) from the Technion. Dr. Swidan was the first post doc to join the newly established Janelia Farms Research campus of the Howard Hughes Medical Institute. Currently, he is the CEO and founder of Olymons (TM), Blessing Machines with Vision (TM), and a fellow in the Edmond J. Safra bioinformatic program at Tel-Aviv University. His research work includes the following topics: image processing and computer vision, combinatorial algorithms and their applications to computational molecular biology, genome rearrangement, comparative genomics, phylogenetic inference, string algorithms, graph algorithms, and patten matching algorithms. Title: Reconstructing repeat-annotated phylogenetic trees Abstract: A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals and repeats. These biological findings are formalized here in a new mathematical model, called repeat-annotated phylogenetic trees (RAPT). We show that, under RAPT, the evolutionary process - including both the tree-topology as well as internal node genome orders - is uniquely determined, a property of major significance both in theory and in practice. Furthermore, the repeats are employed to provide linear-time algorithms for reconstructing both the genomic orders and the phylogeny, which are NP-hard problems under the classical model of sorting by reversals (SBR). For that, a new data structure - namely set-tries - is presented, and is shown to support efficient linear-time insert and find operations. Joint work with Michal Ziv-Ukelson and Ron Pinter. The presentation is self contained.