University of Illinois

Other

Imperial College Innovations Limited

Olgica Milenkovic

S M Hossein Tabatabaei Yazdi

Huimin Zhao

Ryan Christopher Gabrys

Alvaro Gonzalo Hernandez

Charles M Schroeder

SeyedKasra Tabatabaei

Yongbo Yuan

Jian Ma

Xiuling Li

Jean-Pierre Leburton

Apratim Khandelwal

Bo Li

Nagendra B Athreya

João Ribeiro

Mahdi Cheraghchi Bashi Astaneh

Seyed Kasra Tabatabaei

Chao Pan

The present disclosure provides systems and methods that relate to storing encoded information in, and reading the encoded information from, nucleotide sequences. An example method includes receiving, at a DNA readout system, a nucleotide sequence. The method also includes reading the nucleotide sequence based on an alphabet consisting of {adenine (A), cytosine (C), guanine (G), and thymine (T)}. The method further includes determining positions of unique markers between a plurality of encoded blocks in the nucleotide sequence. The method yet further includes decoding each encoded block of the plurality of encoded blocks according to an inner code, so as to form a plurality of decoded blocks. The method also includes appending the decoded blocks to one another to provide a decoded message with message length n bits.

Coded trace reconstruction

The disclosure relates to a re-writable DNA-based digital storage system with a random access feature. An example embodiment includes reading a physical nucleotide sequence of 2n+L bases to form a digital representation of the physical nucleotide sequence; dividing the digital representation of the physical nucleotide sequence into an address representation of n bases, followed by a data representation of L bases, followed by a further address representation of n bases; decoding the data representation into an integer value less than 3L that is a sum of a first addend and a second addend, wherein the data representation includes a first subsequence of bases encoding the first addend followed by a second subsequence of bases encoding the second addend; and storing, in a computer memory, the integer value.

Re-writable DNA-based digital storage with random access

An embodiment may involve obtaining an image composed of color channels, wherein each of the color channels represents colors therein with n bits per pixel; quantizing each of the color channels to be represented by m bits per pixel; using a space-filling curve to convert each of the color channels as quantized into respective vectors; generating, for each of the respective vectors, a respective set of m arrays, wherein the m arrays for a particular vector of the respective vectors contain indices of where a fixed value selected from a range of 0 to m&#x2212;1 is found in the particular vector; applying, to each of the m arrays for each of the respective vectors, differential encoding and compression of the indices therein; mapping each of the m arrays for each of the respective vectors to blocks of nucleotides; synthesizing the blocks; and storing, in a DNA-based storage medium, the blocks.

DNA-based image storage and retrieval

The present disclosure provides systems and methods that can provide portable, real-time accessible DNA memories. An example DNA-based data storage system includes a loading region configured to receive a plurality of DNA-based data storage elements in a suspension fluid and a plurality of microtubes disposed in a capture/release region. The microtubes are configured to capture and release the DNA-based data storage elements. The DNA-based data storage system also includes a linearization region configured to linearize the DNA-based data storage elements and a readout region with a readout device configured to provide information indicative of the respective DNA-based data storage elements.

On-chip nanoscale storage system using chimeric DNA

Nick-based methods, devices, and systems for nick-based data storage in a deoxyribonucleic acid (DNA) sequence are disclosed. Digital information is encoded in a register of at least one copy of a double-stranded DNA sequence having a plurality of nickable positions. The data is translated into a sequence of values from a nick alphabet that is subsequently mapped to the plurality of nickable positions, and the DNA sequence is nicked according to the mapped values. Because the digital information is encoded as a series of nicked and non-nicked positions of a double-stranded DNA sequence, the nucleotide sequence of the DNA can be non-synthetic, or 'native' DNA.

Nick-based data storage in native nucleic acids

The disclosure relates to a re-writable DNA-based digital storage system with a random access feature. An example embodiment includes selecting address representations of m nucleotide sequences of n bases each. Each of the address representations of m nucleotide sequences (i) consists of approximately 50% guanine and cytosine content and (ii) is self-uncorrelated. The address representations are mutually uncorrelated with one another. All of the address representations end with a particular base. The embodiment also includes selecting, for a particular address representation from the address representations of the m nucleotide sequences, a corresponding data representation of a nucleotide sequence of L bases. The embodiment further includes concatenating the particular address representation with the data representation to form a representation of a target nucleotide sequence of n+L bases. In addition, the embodiment includes synthesizing the target nucleotide sequence.

The present disclosure provides DNA-based storage system demonstrated through experimental and theoretical verification that such a platform can easily be implemented in practice using portable, nanopore-based sequencers. The gist of the approach is to design an integrated pipeline that encodes data to avoid synthesis and sequencing errors, enables random access through addressing, and leverages efficient portable nanopore sequencing via new anchored iterative alignment and insertion/deletion error-correcting codes. The embodiments herein represent the only known random access DNA-based data storage system that uses error-prone portable, nanopore-based sequencers and produces low-error readouts with the highest reported information rate and density.

Growing community of inventors

Urbana, IL, United States of America

Olgica Milenkovic