Related papers: Partial DNA Assembly: A Rate-Distortion Perspectiv…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Recent experiments have demonstrated the feasibility of storing digital information in macromolecules such as DNA and protein. However, the DNA storage channel is prone to errors such as deletions, insertions, and substitutions. During the…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is…
The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the…
We consider the problem of reconstructing graphs or labeled graphs from neighborhoods of a given radius r. Special instances of this problem include the well known: DNA shotgun assembly; the lesser-known: neural network reconstruction; and…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been…
Uniform sampling of simple graphs having a given degree sequence is a known problem with exponential complexity in the square of the mean degree. For undirected graphs, randomised approximation algorithms have nonetheless been shown to…
Current literature on posterior approximation for Bayesian inference offers many alternative methods. Does our chosen approximation scheme work well on the observed data? The best existing generic diagnostic tools treating this kind of…
Computing the rate-distortion function for continuous sources is commonly regarded as a standard continuous optimization problem. When numerically addressing this problem, a typical approach involves discretizing the source space and…
Reassembly tasks play a fundamental role in many fields and multiple approaches exist to solve specific reassembly problems. In this context, we posit that a general unified model can effectively address them all, irrespective of the input…
In this paper we propose new solution methods for designing tag sets for use in universal DNA arrays. First, we give integer linear programming formulations for two previous formalizations of the tag set design problem, and show that these…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Learning properties of large graphs from samples has been an important problem in statistical network analysis since the early work of Goodman \cite{Goodman1949} and Frank \cite{Frank1978}. We revisit a problem formulated by Frank…