Related papers: Mapping the File Systems Genome: rationales, techn…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
Block devices in computer operating systems typically correspond to disks or disk partitions, and are used to store files in a filesystem. Disks are not the only real or virtual device which adhere to the block accessible stream of bytes…
As scientific frameworks become sophisticated, so do their data structures. Current data structures are no longer simple in design and they have been progressively complicated. The typical trend in designing data structures in scientific…
In many areas of science multiple sets of data are collected pertaining to the same system. Examples are food products which are characterized by different sets of variables, bio-processes which are on-line sampled with different…
We propose a disk encryption method, called secure disk mixed system (SDMS) in this paper, for data protection of disk storages such as USB flash memory, USB hard disk and CD/DVD. It is aimed to solve temporal and spatial limitation…
Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the…
Volatile memory dump and its analysis is an essential part of digital forensics. Among a number of various software and hardware approaches for memory dumping there are authors who point out that some of these approaches are not resilient…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
Hardware aliasing occurs when the same logical address sporadically accesses different physical memory locations and is a problem encountered by systems programmers (the opposite, software aliasing, when different addresses access the same…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Genomic phenotypes, such as DNA methylation and chromatin accessibility, can be used to characterize the transcriptional and regulatory activity of DNA within a cell. Recent technological advances have made it possible to measure such…
Code clones are duplicate code fragments that share (nearly) similar syntax or semantics. Code clone detection plays an important role in software maintenance, code refactoring, and reuse. A substantial amount of research has been conducted…
This paper analyzes various distributed storage systems that use data fragmentation and dispersal as a way of protection.Existing solutions have been organized into two categories: bitwise and structurewise. Systems from the bitwise…
In this work, we present an approach towards constructing executable specifications of existing filesystems and verifying their functional properties in a theorem proving environment. We detail an application of this approach to the FAT32…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility still remain imprecise. Here, we argue…
Fossil DNA preservation varies with depositional environments and diagenesis, producing fragments of heterogeneous origins and degradation states. We use first-principles biomolecular analysis to classify fossil molecular environments into…
Discovering genes with similar functions across diverse biomedical contexts poses a significant challenge in gene representation learning due to data heterogeneity. In this study, we resolve this problem by introducing a novel model called…