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Séminaire ICI : Olgica Milenkovic

Titre du séminaire et oratrice

Coding Techniques for Emerging DNA-Based Storage Systems.

Olgica Milenkovic, University of Illinois, Urbana-Champaign (UIUC).

Date et lieu

Vendredi 10 juillet 2015, 14h.

ENSEA, salle 384.

Abstract

Despite the many advances in traditional data recording techniques, the surge of Big Data platforms and energy conservation issues have imposed new challenges to the storage community in terms of identifying extremely high volume, non-volatile and durable  recording media. The potential for using macromolecules for ultra-dense storage was recognized as early as in the 1960s, when the celebrated physicists Richard Feynman outlined his vision for nanotechnology in the talk “There is plenty of room at the bottom.” Among known macromolecules, DNA is unique in so far that it lends itself to implementations of non-volatile recoding media of outstanding integrity (one can still recover the DNA of species extinct for more than 10,000 years) and extremely high storage capacity (a human cell, with a mass of roughly 3 pgrams, hosts DNA with encoding 6.4 GB of information).

Building upon the rapid growth of biotechnology systems for DNA synthesis and sequencing, we developed and implemented a new DNA-based rewritable and random access memory. Our system is based on DNA editing and new constrained and error-control coding techniques that ensure data reliability, specificity and sensitivity of access, and at the same time, provide exceptionally high data storage capacity. The coding methods involve error-correcting balancing codes and prefix-synchronized codes. As a proof of concept, we encoded in DNA parts of the Wikipedia pages of six universities in the USA, selected specific content blocks and edited portions of the text within various positions in the blocks. For this purpose, we used Overlap-Extension PCR and gBlock methods. We Sanger-sequenced the resulting DNA sequences to verify the accuracy of the process, and detected no errors. The results suggest that DNA media may be used in the near future for both archival and rewritable storage applications.

A Joint Work with Han Mao Kia, Jian Ma, Hussein Tabatabaei Yazdi, Yongbo Yuan, and Huimin Zhao.

Bio

Olgica Milenkovic is a professor of Electrical and Computer Engineering at the University of Illinois, Urbana-Champaign (UIUC), and Research Professor at the Coordinated Science Laboratory. She obtained her Masters Degree in Mathematics in 2001 and PhD in Electrical Engineering in 2002, both from the University of Michigan, Ann Arbor. From 2002 to 2006, she was with the University of Colorado, Boulder, and in 2005 she also served as consultant for the Bell Laboratories. During the years 2006 and 2007 she visited the University of California, San Diego, and then subsequently joined the University of Illinois in 2007. She is a member of the NSF Center for Science of Information and was a long term visitor of the Simons Institute at Berkeley as part of the 2015 Information Theory program.

Prof. Milenkovic heads a group focused on addressing unique interdisciplinary research challenges spanning the areas of algorithm design and computing, bioinformatics, coding theory, machine learning and signal processing. Her scholarly contributions have been recognized by multiple awards, including the NSF Faculty Early Career Development (CAREER) Award, the DARPA Young Faculty Award, the Dean’s Excellence in Research Award, and several best paper awards. In 2013, she was elected a UIUC Center for Advanced Study Associate and Willett Scholar. In 2015, she became Distinguished Lecturer of the Information Theory Society. From 2007 until 2015, she has served as Associate Editor of the IEEE Transactions of Communications, Transactions on Signal Processing and Transactions on Information Theory. In 2009, she was the Guest Editor in Chief of a special issue of the IEEE Transactions on Information Theory on Molecular Biology and Neuroscience. She was co-chair of the Allerton 2013 and 2014 conferences, and TPC co-chair of the 2014 International Symposium on Information Theory.

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