Related papers: Trace Reconstruction Problems in Computational Bio…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
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…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We introduce a new algorithm called {\sc Rec-Gen} for reconstructing the genealogy or \textit{pedigree} of an extant population purely from its genetic data. We justify our approach by giving a mathematical proof of the effectiveness of…
The magnetic inverse source problem of reconstructing the positions and currents of very long parallel conductors is considered in a two-dimensional situation, with applications to power line measurements. The input data is the magnetic…
Due to its longevity and enormous information density, DNA is an attractive medium for archival data storage. Thanks to rapid technological advances, DNA storage is becoming practically feasible, as demonstrated by a number of experimental…
In the trace reconstruction problem, one attempts to reconstruct a fixed but unknown string $x$ of length $n$ from a given number of traces $\tilde{x}$ drawn iid from the application of a noisy process (such as the deletion channel) to $x$.…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Motivated by the sequence reconstruction problem initiated by Levenshtein, reconstruction codes were introduced by Cai \emph{et al}. to combat errors when a fixed number of noisy channels are available. The central problem on this topic is…
To address a looming crisis of unreproducible evaluation for named entity recognition, we propose guidelines and introduce SeqScore, a software package to improve reproducibility. The guidelines we propose are extremely simple and center…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
Particle tracking in biological imaging is concerned with reconstructing the trajectories, locations, or velocities of the targeting particles. The standard approach of particle tracking consists of two steps: first reconstructing…
The {\em insertion-deletion channel} takes as input a binary string $x \in\{0, 1\}^n$, and outputs a string $\widetilde{x}$ where some of the bits have been deleted and others inserted independently at random. In the {\em trace…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
The idea of computing with DNA was given by Tom Head in 1987, however in 1994 in a seminal paper, the actual successful experiment for DNA computing was performed by Adleman. The heart of the DNA computing is the DNA hybridization, however,…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
Reconstruction of gene regulatory networks or 'reverse-engineering' is a process of identifying gene interaction networks from experimental microarray gene expression profile through computation techniques. In this paper, we tried to…
DNA replication stands as one of the fundamental biological processes crucial for cellular functioning. Recent experimental developments enable the study of replication dynamics at the single-molecule level for complete genomes,…