49 publication(s) trouvée(s)
Article scientifique
Uncovering the effects of heterogeneity and parameter sensitivity on within-host dynamics of disease: malaria as a case study
BACKGROUND: The fidelity and reliability of disease model predictions depend on accurate and precise descriptions of processes and determination of …
Article scientifique
In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines: evidence of a possible putative protective effect
BACKGROUND: Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, …
Article scientifique
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models
BACKGROUND: Manual microscopic examination of Leishman/Giemsa stained thin and thick blood smear is still the "gold standard" for malaria diagnosis. …
Article scientifique
PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data
BACKGROUND: Recent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases …
Article scientifique
The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research
BACKGROUND: Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available …
Article scientifique
BayesMetab: treatment of missing values in metabolomic studies using a Bayesian modeling approach
BACKGROUND: With the rise of metabolomics, the development of methods to address analytical challenges in the analysis of metabolomics data …
Article scientifique
A comparative study of topology-based pathway enrichment analysis methods
BACKGROUND: Pathway enrichment extensively used in the analysis of Omics data for gaining biological insights into the functional roles of …
Article scientifique
GenGraph: a python module for the simple generation and manipulation of genome graphs
BACKGROUND: As sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of …
Article scientifique
Correction to: The Kendrick modelling platform: language abstractions and tools for epidemiology
Following publication of the original article [1], the author noticed that the following lines were missing from the published article. …
Article scientifique
Optimising orbit counting of arbitrary order by equation selection
BACKGROUND: Graphlets are useful for bioinformatics network analysis. Based on the structure of Hočevar and Demšar's ORCA algorithm, we have …
Article scientifique
VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
BACKGROUND: With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of …
Article scientifique
Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis
BACKGROUND: The use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. However, storing …
Article scientifique
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
BACKGROUND: The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human …
Article scientifique
Cluster oligonucleotide signatures for rapid identification by sequencing
BACKGROUND: Oligonucleotide signatures (signatures) have been widely used for studying microbial diversity and function in wet-lab settings, but using them …
Article scientifique
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
BACKGROUND: Aligning short reads to a reference genome is an important task in many genome analysis pipelines. This task is …
Article scientifique
Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools
BACKGROUND: Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant …
Article scientifique
bioSyntax: syntax highlighting for computational biology
BACKGROUND: Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB …
Article scientifique
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes
BACKGROUND: Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions …
Article scientifique
Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity
BACKGROUND: Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of …
Article scientifique
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming
BACKGROUND: During the last years, several approaches were applied on biomedical data to detect disease specific proteins and genes in …