Related papers: GC+ Code: A Systematic Short Blocklength Code for …
The genetic code has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimisation problem as a Quadratic…
In order to achieve fault tolerance, highly reliable system often require the ability to detect errors as soon as they occur and prevent the speared of erroneous information throughout the system. Thus, the need for codes capable of…
Erasure coding techniques are getting integrated in networked distributed storage systems as a way to provide fault-tolerance at the cost of less storage overhead than traditional replication. Redundancy is maintained over time through…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
Maximum run-length limited codes are constraint codes used in communication and data storage systems. Insertion/deletion correcting codes correct insertion or deletion errors caused in transmitted sequences and are used for combating…
The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to…
The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Despite its benefits, storing…
Due to the lack of parallel data in current Grammatical Error Correction (GEC) task, models based on Sequence to Sequence framework cannot be adequately trained to obtain higher performance. We propose two data synthesis methods which can…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Distributed data storage systems are essential to deal with the need to store massive volumes of data. In order to make such a system fault-tolerant, some form of redundancy becomes crucial, incurring various overheads - most prominently in…
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…
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…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
We offer a theoretical design of new systems that show promise for digital biochemical computing, including realizations of error correction by utilizing redundancy, as well as signal rectification. The approach includes information…
In this paper, we propose a novel conservative chaotic standard map-driven dynamic DNA coding (encoding, addition, subtraction and decoding) for the image encryption. The proposed image encryption algorithm is a dynamic DNA coding algorithm…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
The problem of designing codes for deletion-correction and synchronization has received renewed interest due to applications in DNA-based data storage systems that use nanopore sequencers as readout platforms. In almost all instances,…
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 unique string…
Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…
Erasure codes provide a storage efficient alternative to replication based redundancy in (networked) storage systems. They however entail high communication overhead for maintenance, when some of the encoded fragments are lost and need to…