Related papers: A new DNA alignment method based on inverted index
This work addresses the problem of billion-scale nearest neighbor search. The state-of-the-art retrieval systems for billion-scale databases are currently based on the inverted multi-index, the recently proposed generalization of the…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
Social network alignment, aligning different social networks on their common users, is receiving dramatic attention from both academic and industry. All existing studies consider the social network to be static and neglect its inherent…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
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…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
We study two systems of tangle equations that arise when modeling the action of the Integrase family of proteins on DNA. These two systems--direct and inverted repeats--correspond to two different possibilities for the initial DNA sequence.…
The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment…
DNA replication stands as one of the fundamental biological processes crucial for cellular functioning. Recent experimental developments enable the study of replication dynamics at the single-molecule level for complete genomes,…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
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…
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…
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…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
DNA-based storage is an emerging storage technology that provides high information density and long duration. Due to the physical constraints in the reading and writing processes, error correction in DNA storage poses several interesting…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…