Detecting reoccurring patterns of scrambled genes

Abstract: DNA recombination occurs at both evolutionary and developmental levels, and is often studied through model organ- isms such as ciliate species Oxytricha and Stylonychia. These species undergo massive genome rearrangements during their development of a somatic macronucleus from a zygotic micronucleus. We use graphs and words to represent the rearrangement process and we investigate genome-wide the range of scrambled gene architectures that describe the precursor-product relationships. We find that there are two general patterns, reoccurring genome wide, that describe over 90% of the Oxytricha’s scrambled genes. We further investigate the patterns of interleaving genes and find that there are specific star-like graph structures that describe most complex interleaving patterns. Joint work with M. Saito. 

Short bio: Prof. Natasa Jonoska is one of the major experts of molecular computing. Her research interests are in theoretical and computational models of molecular self-assembly and molecular biology, developed beside extensive collaborations with experimentalists in molecular biology and structural DNA nanotechnology. She is a Fellow of the American Association for the Advancement of Science, was named Blaise Pascal Professor for 2015 at the Leiden University,  and has been awarded the Rozenberg Tulip Award in DNA Computing and Molecular Programming by the International Society for Nanoscale Science and Computing. She serves on editorial boards of several journals (including TCS, NC, Computability, Int. J. of Foundations of Computer Science..), as a chair (or a member) of Steering Committee of main conferences in the field (e.g., DNA computing and molecular programming, UCNC, Developments in Language Theory), and has edited several books on these topics. She is the leader of a research group in Discrete and Topological Models for DNA assembly, an attraction pole and inspiration source for many undergraduate, PhD, and post-doc students: some of her recent contributions may be found on http://knot.math.usf.edu/

Contact person: Giuditta Franco