Related papers: Fast genomic optical map assembly algorithm using …

Binary code clone analysis is an important technique which has a wide range of applications in software engineering (e.g., plagiarism detection, bug detection). The main challenge of the topic lies in the semantics-equivalent code…

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.…

The evolution of encryption algorithms have led to the development of very complicated and highly versatile algorithms that sacrifice efficiency for better and harder to decrypt results. But by the application of a genetic schema to the…

Optical Coherence Tomography (OCT) is a widely used non-invasive biomedical imaging modality that can rapidly provide volumetric images of samples. Here, we present a deep learning-based image reconstruction framework that can generate…

Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…

The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…

There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…

De novo genome assembly is the process of stitching short DNA sequences to generate longer DNA sequences, without using any reference sequence for alignment. It enables high-throughput genome sequencing and thus accelerates the discovery of…

Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…

Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…

Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…

Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases…

A frame is a generalization of a basis of a vector space to a redundant overspanning set whose vectors are linearly dependent. Frames find applications in signal processing and quantum information theory. We present a genetic algorithm that…

Persistence diagrams have been widely used to quantify the underlying features of filtered topological spaces in data visualization. In many applications, computing distances between diagrams is essential; however, computing these distances…

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…

As synthetic genomics scales toward the construction of increasingly larger genomes, computational strategies are needed to address technical feasibility. We introduce an algorithmic framework for the Minimum-Cost Synthetic Genome Planning…

Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…

Ensuring the security of software supply chains requires reliable identification of upstream dependencies. We present the Automatic Bill of Materials, or ABOM, a technique for embedding dependency metadata in binaries at compile time.…

We consider a multi-stage distributed detection scenario, where $n$ sensors and a fusion center (FC) are deployed to accomplish a binary hypothesis test. At each time stage, local sensors generate binary messages, assumed to be spatially…

We study the problem of selecting control clones in DNA array hybridization experiments. The problem arises in the OFRG method for analyzing microbial communities. The OFRG method performs classification of rRNA gene clones using binary…