Related papers: DNA-MGC+: A versatile codec for reliable and resou…
We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded…
Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
Neural image codecs achieve higher compression ratios than traditional hand-crafted methods such as PNG or JPEG-XL, but often incur substantial computational overhead, limiting their deployment on energy-constrained devices such as…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
This paper addresses the persistent challenge of accurately digitizing paper-based electrocardiogram (ECG) recordings, with a particular focus on robustly handling single leads compromised by signal overlaps-a common yet under-addressed…
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…
DNA storage has matured from concept to practical stage, yet its integration with neural compression pipelines remains inefficient. Early DNA encoders applied redundancy-heavy constraint layers atop raw binary data - workable but primitive.…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
With recent advancements in next-generation data storage, especially in biological molecule-based storage, insertion, deletion, and substitution (IDS) error-correcting codes have garnered increased attention. However, a universal method for…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…