Related papers: Champuru 2: Improved scoring of alignments and a u…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and…
Medical report generation is crucial for clinical diagnosis and patient management, summarizing diagnoses and recommendations based on medical imaging. However, existing work often overlook the clinical pipeline involved in report writing,…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for…
PolyChord is a novel nested sampling algorithm tailored for high-dimensional parameter spaces. This paper coincides with the release of PolyChord v1.3, and provides an extensive account of the algorithm. PolyChord utilises slice sampling at…
Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster…
The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
Fast access to large catalogs is required for some astronomical applications. Here we introduce the catsHTM tool, consisting of several large catalogs reformatted into HDF5-based file format, which can be downloaded and used locally. To…
Heterogeneous systems, consisting of CPUs and GPUs, offer the capability to address the demands of compute- and data-intensive applications. However, programming such systems is challenging, requiring knowledge of various parallel…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
We develop a cross-platform open-source Java application (BACOM2) with graphic user interface (GUI), and users also can use a XML file to set the parameters of algorithm model, file paths and the dataset of paired samples. BACOM2 implements…
DeepXube is a free and open-source Python package and command-line tool that seeks to automate the solution of pathfinding problems by using machine learning to learn heuristic functions that guide heuristic search algorithms tailored to…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
PolyChord is a novel nested sampling algorithm tailored for high dimensional parameter spaces. In addition, it can fully exploit a hierarchy of parameter speeds such as is found in CosmoMC and CAMB. It utilises slice sampling at each…