A5046292307- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Cell Image Analysis Techniques
- RNA and protein synthesis mechanisms
- Algorithms and Data Compression
- Software Testing and Debugging Techniques
- Real-time simulation and control systems
- Software System Performance and Reliability
- CRISPR and Genetic Engineering
- Genetic factors in colorectal cancer
- Single-cell and spatial transcriptomics
- Genetic Mapping and Diversity in Plants and Animals
- Bacteriophages and microbial interactions
- Species Distribution and Climate Change
- Legume Nitrogen Fixing Symbiosis
- Plant Disease Resistance and Genetics
- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Plant Parasitism and Resistance
Wellcome Trust
2024
European Bioinformatics Institute
2023-2024
Earlham Institute
2013-2020
Norwich Research Park
2013-2020
Plant innate immunity relies on nucleotide binding leucine-rich repeat receptors (NLRs) that recognize pathogen-derived molecules and activate downstream signaling pathways. We analyzed the variation in NLR gene copy number identified plants with a low of genes relative to sister species. specifically focused four from two distinct lineages, one monocot lineage (Alismatales) eudicot (Lentibulariaceae). In these loss coincides well-known immune complex ENHANCED DISEASE SUSCEPTIBILITY 1...
Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene protein expression localisation in bulk at single cell level. These resources aim to allow users investigate their normal tissue (baseline) or response perturbations such as disease changes genotype (differential) across multiple species. Users invited search genes metadata terms species biological conditions a standardised consistent interface....
BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors influenced growth user and developer community, outline our strategy building this growth. The lessons have learned may also be relevant to other projects.
BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development has been prompted by growing need for bioinformatics visualisation tools be easily shared, reused discovered. Its modular architecture makes it easy users find specific functionality without needing know how built, while can extended or created implementing new functionality. community developers currently provides range that open access freely...
Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts time. Additionally, techniques such as multiplex allow one run to contain hundreds different samples. With comes a significant challenge understand its quality and how the yield are changing across instruments over As well desire historical data, centres often have duty provide clear summaries individual performance collaborators or customers. We present StatsDB, an open-source software package for...
Abstract Background Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological, environmental adaptations. The study homologous genes helps us understand evolution families. It plays vital role in finding ancestral events as well identifying that have diverged from common ancestor under positive selection. There are various tools available, such MSOAR, OrthoMCL,...
Abstract Motivation The increasing rate of submission genetic sequences into public databases is providing a growing resource for classifying the organisms that these represent. To aid viral classification, we have developed ViCTree, which automatically integrates relevant sets in NCBI GenBank and transforms them an interactive maximum likelihood phylogenetic tree can be updated automatically. ViCTree incorporates ViCTreeView, JavaScript-based visualization tool enables to explored...
<ns4:p>Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts time. Additionally, techniques such as multiplex allow one run to contain hundreds different samples. With comes a significant challenge understand its quality and how the yield are changing across instruments over As well desire historical data, centres often have duty provide clear summaries individual performance collaborators or customers. We present StatsDB, an open-source software package...
<ns4:p>Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts time. Additionally, techniques such as multiplex allow one run to contain hundreds different samples. With comes a significant challenge understand its quality and how the yield are changing across instruments over As well desire historical data, centres often have duty provide clear summaries individual performance collaborators or customers. We present StatsDB, an open-source software package...
We present a new web-based genomics browser with novel rendering and annotation capabilities designed to overcome some of the shortcomings in available approaches. Most popular current browsers use on-the-fly server-side tracks features which is not efficient terms performance or scalability. In addition, these often rely on very specific library dependencies, where writing plugins modifying existing code can be troublesome resource expensive. focus functionality many cases tools but an...
Abstract Background Phylogenetic information inferred from the study of homologous genes helps us to understand evolution and gene families, including identification ancestral duplication events as well regions under positive or purifying selection within lineages. Gene family orthogroup characterisation enables syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview a whole, limited level, none provide further...
<ns4:p><ns4:bold>Summary:</ns4:bold><ns4:italic> wigExplorer</ns4:italic> is a BioJS component whose main purpose to provide platform for visualisation of wig-formatted data. Wig files are extensively used by genome browsers such as the UCSC Genome Browser. <ns4:italic>wigExplorer </ns4:italic>follows standard specification, requiring simple configuration and installation. <ns4:italic>wigExplorer</ns4:italic> provides an easy way navigate visible region canvas allows interaction with other...
wigExplorer is a BioJS component whose main purpose to provide platform for visualisation of wig-formatted data. Wig files are extensively used by genome browsers such as the UCSC Genome Browser. follows standard specification, requiring simple configuration and installation. provides an easy way navigate visible region canvas allows interaction with other components via predefined events. Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7721.
Phylogenetic information inferred from the study of homologous genes helps us to understand evolution and gene families, including identification ancestral duplication events as well regions under positive or purifying selection within lineages. Gene family orthogroup characterization enables syntenic blocks, which can then be visualized with various tools. Unfortunately, currently available tools display only an overview a whole, limited level, none provide further details about structural...
<ns4:p><ns4:bold>Summary: </ns4:bold>Compositional GC/AT content of DNA sequences is a useful feature in genome analysis. provides information about evolution, structure and function genomes, giving clues their biological organisation. We have developed <ns4:italic>DNAContentViewer</ns4:italic>, BioJS component for visualisation compositional raw sequences. <ns4:italic>DNAContentViewer </ns4:italic>has been integrated the project as part registry components....
Sequencing centres differ not only in terms of their scale and output, but also requirements for information management. platforms are becoming more accessible, the efficient storage genomic metadata is vital large small sequencing alike. Off-the-shelf solutions often very expensive cost-effective smaller centre. Furthermore, support contracts required, extensibility these systems hands generators. In implementation, as well desire to tailor an system in-house, data formats can change evolve...
Abstract Background Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological environmental adaptations. The study homologous genes helps us understand evolution families. It plays vital role in finding ancestral events as well identifying that have diverged from common ancestor under positive selection. There are various tools available, such MSOAR, OrthoMCL...