DNA and Biological Computing

Multidimensional Data Organization and Random Access in Large-Scale DNA Storage Systems

This paper introduces a multidimensional data organization strategy for DNA storage systems to improve capacity and reduce primer requirements for random access.

Molecular Learning of a Soft-Disks Fluid

This paper demonstrates that a Lennard-Jones fluid can be trained using logic-gate patterns, showing its ability to learn and predict outputs through intrinsic minimizing properties.

DNA-based data storage via combinatorial assembly

This paper demonstrates a combinatorial DNA data encoding scheme achieving megabits per second write speeds using inkjet printing and nanopore sequencing for reading.

An Empirical Comparison of Preservation Methodsfor Synthetic DNA Data Storage

The paper evaluates nine preservation methods for synthetic DNA data storage by aging 29,000 sequences and finds no significant difference in error rates between methods.

A single layer artificial neural network type architecture with molecular engineered bacteria for complex conventional and reversible computing

The paper demonstrates a single-layer artificial neural network architecture using molecular engineered bacteria to perform complex irreversible and reversible computing tasks.

Robust retrieval of data stored in DNA by de Bruijn graph-based de novo strand assembly

A de Bruijn graph-based algorithm enables robust retrieval of DNA-stored data even from severely corrupted samples.

Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage

This paper introduces a method to store digital data in DNA using enzymatic synthesis guided by light patterns, demonstrating storage of 110 bits of data.

Photochemical NOT Gate for DNA Computing

The paper introduces a photochemical NOT gate for DNA computing that uses photocaging groups to enable temporal control, allowing for the design of NAND and NOR gates and demonstrating their use in multi-layer circuits.

Quantifying Molecular Bias in DNA Data Storage

This paper quantifies molecular bias in DNA data storage by analyzing synthesis and PCR processes, identifying their contributions to copy number unevenness and proposing a statistical model to optimize storage efficiency.

Image Processing in DNA

This paper proposes a method to store quantized images in DNA using signal processing and machine learning to reduce errors and costs without redundant oligos or rewriting.

Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands

Porcupine enables rapid, reliable, and lab-free molecular tagging of physical objects using nanopore-orthogonal DNA strands for custom labels.

Mixed Culture of Bacterial Cell for Large Scale DNA Storage

The paper presents a method for large-scale DNA data storage using mixed bacterial cultures carrying high-copy plasmids with massive oligo pools, achieving 445 KB of stored data.

Genomic encryption of digital data stored in synthetic DNA

The paper demonstrates storing encrypted digital data in synthetic DNA using keys derived from human DNA's short tandem repeats, with successful decryption via sequencing.

In vivo multi-dimensional information-keeping in Halobacterium salinarum

This paper demonstrates efficient in vivo DNA-encoded digital archives for 3D and 4D information storage using Halobacterium salinarum, with improved durability through mineral salt preservation.

Low-Bias Amplification for Robust DNA Data Readout

This study demonstrates that PCR introduces significant amplification bias in DNA data readout and introduces iDR, an isothermal method that enables robust and efficient data retrieval from complex DNA sequences.

DNA Punch Cards: Storing Data on Native DNA Sequences via Nicking

This paper introduces a DNA-based data storage method using nicks in native DNA to encode information, demonstrating proof of concept with restriction enzyme-mediated nicking and sequencing-based data reconstruction.

Chamaeleo: a robust library for DNA storage coding schemes

Chamaeleo provides a library for DNA storage coding schemes, offering flexibility and expandability over existing single-scheme implementations.

Minimally Complex Nucleic Acid Feedback Control Systems for First Experimental Implementations

This paper presents minimally complex DNA-based control circuits for experimental implementation of feedback control systems in synthetic biology.

Dynamic DNA-based information storage

This paper introduces a dynamic DNA-based information storage system using a hybrid toehold structure, improving storage density and enabling non-destructive file access.

eMED-DNA: An in silico operating system for clinical medical data storage within the human genome

The paper introduces eMED-DNA, an in silico operating system for storing electronic health records within a sequenced genome to integrate genomic and clinical data in real-world practice.

Simulating the Monty Hall problem in a DNA sequencing machine

The paper simulates the Monty Hall problem using DNA sequencing to demonstrate a counter-intuitive decision problem and highlights DNA sequencing as a tool for DNA computing.

Incorporating Randomness into DNA Steganography to Realize Secondary Secret key, Self-destruction, and Quantum Key Distribution-like Function

This paper introduces a DNA steganography method that uses randomness, secondary secret keys, and self-destruction to enhance data security.

Encoding information in synthetic metabolomes

The paper demonstrates storing and retrieving digital image data in synthetic metabolomes with high accuracy.

Enzymatic DNA synthesis for digital information storage

This paper develops an enzymatic DNA synthesis method for digital information storage, demonstrating error-tolerant retrieval of 144 bits and validating kilobyte-scale storage with 1 bit per nucleotide.

Addition of Degenerate Bases to DNA-based Data Storage for Increased Information Capacity

The paper proposes using eleven degenerate bases to increase DNA-based data storage capacity and reduce costs, achieving 3.37 bits/character and projecting a 50% cost reduction.

Network cloning using DNA barcodes

The paper introduces a method to clone neural networks using DNA barcodes by solving a synthesis problem with efficient computational approaches.

Demonstration of End-to-End Automation of DNA Data Storage

The paper demonstrates an end-to-end DNA data storage system capable of automated writing, storage, and reading of data.

Experimental Assessment of PCR Specificity and Copy Number for Reliable Data Retrieval in DNA Storage

The paper demonstrates reliable PCR-based data retrieval from a complex DNA storage pool with high density and varying file sizes.

Dynamical Task Switching in Cellular Computers

This paper describes a method for task switching in engineered bacteria using plasmid copy number manipulation and presents computational simulations of the model.

A highly parallel strategy for storage of digital information in living cells

This paper introduces an error-correcting DNA data storage strategy that enables reliable, scalable, and secure long-term storage of digital information in living cells.