Related papers: Optimal Assembly for High Throughput Shotgun Seque…
Diffractive lenses have recently been applied to the domain of multispectral imaging in the X-ray and UV regimes where they can achieve very high resolution as compared to reflective and refractive optics. Conventionally, spectral…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
With the development of deep learning, the single super-resolution image reconstruction network models are becoming more and more complex. Small changes in hyperparameters of the models have a greater impact on model performance. In the…
We study coverage processes in which each draw reveals a subset of $[n]$, and the goal is to determine the expected number of draws until all items are seen at least once. A classical example is the Coupon Collector's Problem, where each…
Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
Computerized Tomography assembly and system configuration are optimized for enhanced invertibility in sparse data reconstruction. Assembly generating maximum principal components/condition number of weight matrix is designated as best…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…
This paper presents a novel construction of $(n,k,d=n-1)$ access-optimal regenerating codes for an arbitrary sub-packetization level $\alpha$ for exact repair of any systematic node. We refer to these codes as general sub-packetized because…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
This paper studies the sequence reconstruction problem for a channel inspired by protein identification. We introduce a coloring channel, where a sequence is transmitted through a channel that deletes all symbols not belonging to a fixed…
In this paper, we perform an experimental study of optimal recombination operator for makespan minimization problem on single machine with sequence-dependent setup times ($1|s_{vu}|C_{\max}$). The computational experiment on benchmark…