Related papers: Sequenceable Event Recorders
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Recently, feature selection has become an increasingly important area of research due to the surge in high-dimensional datasets in all areas of modern life. A plethora of feature selection algorithms have been proposed, but it is difficult…
Formal methods apply algorithms based on mathematical principles to enhance the reliability of systems. It would only be natural to try to progress from verification, model checking or testing a system against its formal specification into…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
We investigate the problem of transforming an input sequence into a high-dimensional output sequence in order to transcribe polyphonic audio music into symbolic notation. We introduce a probabilistic model based on a recurrent neural…
We present the results of an R&D study of a specialized processor capable of precisely reconstructing events with hundreds of charged-particle tracks in pixel detectors at 40 MHz, thus suitable for processing LHC events at the full crossing…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
With the progressive scale-down of semiconductor's feature size, people are looking forward to More Moore and More than Moore. In order to offer a possible alternative implementation process, people are trying to figure out a feasible…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
The increasing popularity of server usage has brought a plenty of anomaly log events, which have threatened a vast collection of machines. Recognizing and categorizing the anomalous events thereby is a much salient work for our systems,…
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…