The sequence reconstruction problem and its connection to the DNA storage channel

Prof. Eitan Yaakobi

Faculty of Computer Science
Technion - Israel Institute of Technology


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Abstract:

In the sequence reconstruction problem, a length-n string x yields a collection of noisy copies, where each copy is independently obtained from x by passing through the same channel. The main goal under this paradigm is to determine the required minimum number of copies in order to reconstruct x in the worst case or with high probability. This problem has been studied recently for many channels and additionally has some more variants which have several applications, among them are DNA-based storage systems. DNA-based storage has attracted significant attention due to recent demonstrations of the viability of storing information in macromolecules. Given the trends in cost decreases of DNA synthesis and sequencing, it is estimated that within the next decade DNA storage may become a highly competitive archiving technology. This technology introduces new challenges in finding coding solutions to address various problems associated with the implementation of DNA-based storage systems. This talk will review some of the recent advances in coding methods for several sequence reconstruction problems and their connections to overcoming the unique challenges associated with the synthesis, storage, and sequencing phases of the DNA storage channel.

Biography:

Eitan Yaakobi is an Associate Professor at the Computer Science Department at the Technion --- Israel Institute of Technology. He received the B.A. degrees in computer science and mathematics, and the M.Sc. degree in computer science from the Technion --- Israel Institute of Technology, Haifa, Israel, in 2005 and 2007, respectively, and the Ph.D. degree in electrical engineering from the University of California, San Diego, in 2011. Between 2011-2013, he was a postdoctoral researcher in the department of Electrical Engineering at the California Institute of Technology and the Center of Memories and Recording Research at the University of California, San Diego.
His research interests include information and coding theory with several applications to non-volatile memories, distributed storage, and private information retrieval. In particular, his work has been focused on advancing coding solutions for memories and systems and their applications in state-of-the-art storage systems. He is also working on next generations memories such as racetrack memories and DNA storage systems.