Related papers: Coding for Composite DNA to Correct Substitutions,…
This paper focuses on error-correcting codes that can handle a predefined set of specific error patterns. The need for such codes arises in many settings of practical interest, including wireless communication and flash memory systems. In…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Motivated by applications in DNA storage, we study a setting in which strings are affected by tandem-duplication errors. In particular, we look at two settings: disjoint tandem-duplication errors, and equal-length tandem-duplication errors.…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
We describe a novel extension of subspace codes for noncoherent networks, suitable for use when the network is viewed as a communication system that introduces both dimension and symbol errors. We show that when symbol erasures occur in a…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
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…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
This paper addresses the problem of learning binary hash codes for large scale image search by proposing a novel hashing method based on deep neural network. The advantage of our deep model over previous deep model used in hashing is that…
In this paper, we study how often unique decoding from $t$ insertions or $t$ deletions occurs for error correcting codes. Insertions and deletions frequently occur in synchronization problems and DNA, a medium which is beginning to be used…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…