Related papers: Thermodynamically Stable DNA Code Design using a S…
Unsupervised hashing methods typically aim to preserve the similarity between data points in a feature space by mapping them to binary hash codes. However, these methods often overlook the fact that the similarity between data points in the…
Deep hashing has shown to be a complexity-efficient solution for the Approximate Nearest Neighbor search problem in high dimensional space. Many methods usually build the loss function from pairwise or triplet data points to capture the…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
Because of their excellent asymptotic and finite-length performance, spatially-coupled (SC) codes are a class of low-density parity-check codes that is gaining increasing attention. Multi-dimensional (MD) SC codes are constructed by…
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
SAXS studies of four 60 base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…