@article{volkel_tomek_keung_tuck_2022, title={DINOS: Data INspired Oligo Synthesis for DNA Data Storage}, volume={18}, ISSN={["1550-4840"]}, url={http://dx.doi.org/10.1145/3510853}, DOI={10.1145/3510853}, abstractNote={As interest in DNA-based information storage grows, the costs of synthesis have been identified as a key bottleneck. A potential direction is to tune synthesis for data. Data strands tend to be composed of a small set of recurring code word sequences, and they contain longer sequences of repeated data. To exploit these properties, we propose a new framework called DINOS. DINOS consists of three key parts: (i) The first is a hierarchical strand assembly algorithm, inspired by gene assembly techniques that can assemble arbitrary data strands from a small set of primitive blocks. (ii) The assembly algorithm relies on our novel formulation for how to construct primitive blocks, spanning a variety of useful configurations from a set of code words and overhangs. Each primitive block is a code word flanked by a pair of overhangs that are created by a cyclic pairing process that keeps the number of primitive blocks small. Using these primitive blocks, any data strand of arbitrary length can be assembled, theoretically. We show a minimal system for a binary code with as few as six primitive blocks, and we generalize our processes to support an arbitrary set of overhangs and code words. (iii) We exploit our hierarchical assembly approach to identify redundant sequences and coalesce the reactions that create them to make assembly more efficient.}, number={3}, journal={ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS}, publisher={Association for Computing Machinery (ACM)}, author={Volkel, Kevin and Tomek, Kyle J. and Keung, Albert J. and Tuck, James M.}, year={2022}, month={Jul} }
 @article{tomek_volkel_indermaur_tuck_keung_2021, title={Promiscuous molecules for smarter file operations in DNA-based data storage}, volume={12}, ISSN={["2041-1723"]}, url={https://doi.org/10.1038/s41467-021-23669-w}, DOI={10.1038/s41467-021-23669-w}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Tomek, Kyle J. and Volkel, Kevin and Indermaur, Elaine W. and Tuck, James M. and Keung, Albert J.}, year={2021}, month={Jun} }
 @article{tomek_volkel_simpson_hass_indermaur_tuck_keung_2019, title={Driving the Scalability of DNA-Based Information Storage Systems}, volume={8}, ISSN={["2161-5063"]}, DOI={10.1021/acssynbio.9b00100}, abstractNote={The extreme density of DNA presents a compelling advantage over current storage media; however, to reach practical capacities, new systems for organizing and accessing information are needed. Here, we use chemical handles to selectively extract unique files from a complex database of DNA mimicking 5 TB of data and design and implement a nested file address system that increases the theoretical maximum capacity of DNA storage systems by five orders of magnitude. These advancements enable the development and future scaling of DNA-based data storage systems with modern capacities and file access capabilities.}, number={6}, journal={ACS SYNTHETIC BIOLOGY}, author={Tomek, Kyle J. and Volkel, Kevin and Simpson, Alexander and Hass, Austin G. and Indermaur, Elaine W. and Tuck, James M. and Keung, Albert J.}, year={2019}, month={Jun}, pages={1241–1248} }