Related papers: Hypothesis: Homologous recombination depends on pa…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
In this paper we present Ethane, a parallel search algorithm specifically designed for its execution on heterogeneous hardware environments. With Ethane we propose an algorithm inspired in the structure of the chemical compound of the same…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…
We wish to suggest an algorithm for biological search including DNA search. Our argument supposes that biological search be performed by quantum search.If we assume this, we can naturally answer the following long lasting puzzles such that…
The method of action of many antibiotics is to interfere with DNA replication - quinolones trap DNA gyrase and topoisomerase proteins onto DNA while metronidazole causes single and double stranded breaks in DNA. To understand how bacteria…
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…
Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These…
We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four…
Suppressing charge recombination is key for organic solar cells to become commercial reality. However, there is still no conclusive picture of how recombination losses are influenced by the complex nanoscale morphology. Here, new insight is…
Mutations can arise from the chance misincorporation of nucleotides during DNA replication or from DNA lesions that are not repaired correctly. We introduce a model that relates the source of mutations to their accumulation with cell…
A tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1,…
Combinatorial branch and bound searches are a common technique for solving global optimisation and decision problems. Their performance often depends on good search order heuristics, refined over decades of algorithms research. Parallel…
Upcoming many core processors are expected to employ a distributed memory architecture similar to currently available supercomputers, but parallel pattern mining algorithms amenable to the architecture are not comprehensively studied. We…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
The seriation problem seeks to reorder a set of elements given pairwise similarity information, so that elements with higher similarity are closer in the resulting sequence. When a global ordering consistent with the similarity information…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
A probabilistic clustering algorithm is proposed for the analysis of forensic DNA mixtures in which individual cells are isolated and short tandem repeats are amplified using the polymerase chain reaction to generate single cell…
In this paper, we consider an approach to the parallelizing of the algorithms realizing the modified probability changigng method with adaptation and partial rollback procedure for constrained pseudo-Boolean optimization problems. Existing…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…