Related papers: Optimal Assembly for High Throughput Shotgun Seque…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
Motivated by applications in DNA-based data storage, constrained codes have attracted a considerable amount of attention from both academia and industry. We study the maximum cardinality of constrained codes for which the constraints can be…
Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…
Depth acquisition, based on active illumination, is essential for autonomous and robotic navigation. LiDARs (Light Detection And Ranging) with mechanical, fixed, sampling templates are commonly used in today's autonomous vehicles. An…
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
A novel simulation strategy is proposed to search for semiconductor quantum devices which are optimized with respect to required performances. Based on evolutionary programming, a tecnique implementing the paradigm of genetic algorithms to…
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…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
In real life, it is always an urge to reach our goal in minimum effort i.e., it should have a minimum constrained path. The path may be shortest route in practical life, either physical or electronic medium. The scenario is to represents…
In this study, we propose a novel deep learning-based method to predict an optimized structure for a given boundary condition and optimization setting without using any iterative scheme. For this purpose, first, using open-source topology…
Given access to the vertex set $V$ of a connected graph $G=(V,E)$ and an oracle that given two vertices $u,v\in V$, returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? Firstly, we show…
Generalized sampling is a recently developed linear framework for sampling and reconstruction in separable Hilbert spaces. It allows one to recover any element in any finite-dimensional subspace given finitely many of its samples with…
High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult…
Graph reconstruction can efficiently detect the underlying topology of massive networks such as the Internet. Given a query oracle and a set of nodes, the goal is to obtain the edge set by performing as few queries as possible. An algorithm…
In a recent work, Huang and Tikhomirov considered the shotgun assembly for Erd\H os-R\'enyi graphs $\mathcal G(n,p_n)$ with $p_n=n^{-\alpha}$, and showed that the graph is reconstructable if $0<\alpha < \frac{1}{2}$ and not reconstructable…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…
Optical molecular tomographic imaging is to reconstruct the concentration distribution of photon-molecular probes in a small animal from measured photon fluence rates. The localization and quantification of molecular probes is related to…