Related papers: Agptools: a utility suite for editing genome assem…
This paper presents an underlying framework for both automating and accelerating malware classification, more specifically, mapping malicious executables to known Advanced Persistent Threat (APT) groups. The main feature of this analysis is…
Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware…
Recently, AI-generated content (AIGC) has gained significant traction due to its powerful creation capability. However, the storage and transmission of large amounts of high-quality AIGC images inevitably pose new challenges for recent file…
With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…
SpectraPlot is a web-based application for simulating spectra of atomic and molecular gases. At the time this manuscript was written, SpectraPlot consisted of four primary tools for calculating: 1) atomic and molecular absorption spectra,…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These algorithms take as input epigenomic datasets, such as chromatin immunoprecipitation-sequencing (ChIP-seq)…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Template-based program repair research is in need for a common ground to express fix patterns in a standard and reusable manner. We propose to build on the concept of generic patch (also known as semantic patch), which is widely used in the…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
Topology diagrams are widely seen in power system applications, but their automatic generation is often easier said than done. When facing power transmission systems with strongly-meshed structures, existing approaches can hardly produce…
In Search Based Software Engineering, Genetic Programming has been used for bug fixing, performance improvement and parallelisation of programs through the modification of source code. Where an evolutionary computation algorithm, such as…
Datatype-generic programming increases program abstraction and reuse by making functions operate uniformly across different types. Many approaches to generic programming have been proposed over the years, most of them for Haskell, but…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Generic programming is an effective methodology for developing reusable software libraries. Many programming languages provide generics and have features for describing interfaces, but none completely support the idioms used in generic…
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 pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Understanding which genes control which traits in an organism remains one of the central challenges in biology. Despite significant advances in data collection technology, our ability to map genes to traits is still limited. This…
Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…