Related papers: Pairwise alignment of the DNA sequence using hyper…
Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have…
In both criminal cases and civil cases there is an increasing demand for the analysis of DNA mixtures involving relationships. The goal might be, for example, to identify the contributors to a DNA mixture where the donors may be related, or…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
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…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
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…
The paper proposes to employ deep convolutional neural networks (CNNs) to classify noncoding RNA (ncRNA) sequences. To this end, we first propose an efficient approach to convert the RNA sequences into images characterizing their…
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
The application of Shapley values to high-dimensional, time-series-like data is computationally challenging - and sometimes impossible. For $N$ inputs the problem is $2^N$ hard. In image processing, clusters of pixels, referred to as…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…
We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…