Related papers: Constructing a genome assembly that has the maximu…
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.…
Combinatorial optimization can be described as the problem of finding a feasible subset that maximizes a objective function. The paper discusses combinatorial optimization problems, where for each dimension the set of feasible subsets is…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Genetic algorithms are modeled after the biological evolutionary processes that use natural selection to select the best species to survive. They are heuristics based and low cost to compute. Genetic algorithms use selection, crossover, and…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
We present a unified framework for modelling genomes and their rearrangements in a genome algebra, as elements that simultaneously incorporate all physical symmetries. Building on previous work utilising the group algebra of the symmetric…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
We consider the problem of sequencing a set of positive numbers. We try to find the optimal sequence to maximize the variance of its partial sums. The optimal sequence is shown to have a beautiful structure. It is interesting to note that…
How do we estimate the probability of an abundant objects' formation, with minimal context or assumption about is origin? To explore this we have previously introduced the concept of pathway assembly (as pathway complexity), in a graph…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
Any process in which competing solutions replicate with errors and numbers of their copies depend on their respective fitnesses is the evolutionary optimization process. As during carcinogenesis mutated genomes replicate according to their…
A composite likelihood is an inference function derived by multiplying a set of likelihood components. This approach provides a flexible framework for drawing inference when the likelihood function of a statistical model is computationally…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
Given a model in algebraic statistics and some data, the likelihood function is a rational function on a projective variety. Algebraic algorithms are presented for computing all critical points of this function, with the aim of identifying…
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
A theoretical construction of the genetic material establishes the unique and ideal character of DNA. A similar conclusion is reached for amino acids and proteins.