Related papers: Closing the complexity gap of the double distance …
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…
Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
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…
While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns of gene mutations. These gene mutational data, which can be…
Deep learning has redefined the field of artificial intelligence (AI) thanks to the rise of artificial neural networks, which are architectures inspired by their neurological counterpart in the brain. Through the years, this dualism between…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…