A5057893272- Web and Library Services
- Computational and Text Analysis Methods
- American Sports and Literature
- Pluripotent Stem Cells Research
- Biomedical Text Mining and Ontologies
- Ideological and Political Education
- Legal Education and Practice Innovations
- Gene expression and cancer classification
- Congenital heart defects research
- Single-cell and spatial transcriptomics
- Tissue Engineering and Regenerative Medicine
- Cell Image Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Digital Humanities and Scholarship
- Animal Genetics and Reproduction
- Genomics and Phylogenetic Studies
- Semantic Web and Ontologies
- Developmental Biology and Gene Regulation
- Genetic and phenotypic traits in livestock
- Medical Image Segmentation Techniques
- Renal and related cancers
- Mathematics, Computing, and Information Processing
- Nuclear physics research studies
University of Edinburgh
2012-2025
Institute of Genetics and Cancer
2011-2023
Edinburgh Cancer Research
2022-2023
Universities UK
2023
Edinburgh College
2016-2022
Western General Hospital
2005-2015
Medical Research Council
1991-2015
MRC Human Genetics Unit
1998-2011
Wellcome Sanger Institute
2011
Molecular Oncology (United States)
2011
Current techniques for three-dimensional (3D) optical microscopy (deconvolution, confocal microscopy, and coherence tomography) generate 3D data by “optically sectioning” the specimen. This places severe constraints on maximum thickness of a specimen that can be imaged. We have developed technique uses projection tomography (OPT) to produce high-resolution images both fluorescent nonfluorescent biological specimens with up 15 millimeters. OPT allows rapid mapping tissue distribution RNA...
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide unified interface biomedical databases that are distributed worldwide. portal provides access numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the independently administered funded their host data federation...
The manuscript describes the "digital transcriptome atlas" of developing mouse embryo, a powerful resource to determine co-expression genes, identify cell populations and lineages functional associations between genes relevant development disease.
The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is an international consortium working to generate gene expression data and transgenic mice. GUDMAP includes from large-scale in situ hybridisation screens (wholemount section) microarray of microdissected, laser-captured FACS-sorted components the developing mouse genitourinary (GU) system. These are annotated using a high-resolution anatomy ontology specific murine GU freely accessible at www.gudmap.org via easy-to-use...
The position of genes within the nucleus has been correlated with their transcriptional activity. interchromosome domain model nuclear organization suggests that preferentially locate at surface chromosome territories. Conversely, high resolution analysis chromatin fibers territories do not present accessibility barriers to transcription machinery. To clarify relationship between and gene expression, we have used fluorescence in situ hybridization analyze spatial a contiguous ∼1 Mb stretch...
ABSTRACT The mouse Hox-7.1 gene has previously been shown to be related the Drosophila Msh homeobox-containing gene. Here we report isolation of a new member this family which resides at an unlinked chromosomal location and designated Hox-8.1. Both Hox-8.1 are expressed in embryo during early stages eye development distinct spatial temporal relationship. is surface ectoderm optic vesicle before invagination occurs regions corresponding prospective corneal epithelium neural retina,...
The European Mouse Mutagenesis Consortium is the initiative contributing to international effort on functional annotation of mouse genome. Its objectives are establish and integrate mutagenesis platforms, gene expression resources, phenotyping units, storage distribution centers bioinformatics resources. combined efforts will accelerate our understanding function human health disease.
BioMart Central Portal is a first of its kind, community-driven effort to provide unified access dozens biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource the Portal, allowing it be exposed shared with research community, linking other resources in portal. Users take advantage common interface quickly utilize different sources without learning new system for each. The...
EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries mouse developmental expression. unique providing both text-based descriptions plus spatial maps patterns. This mapping be accomplished alongside more traditional queries. Here, we describe our recent progress and data integration. has developed method spatially 3D embryo images captured using optical projection tomography, through the use an...
Malformation of the urogenital tract represents a considerable paediatric burden, with many defects affecting lower urinary (LUT), genital tubercle and associated structures. Understanding molecular basis such frequently draws on murine models. However, human anatomical terms do not always superimpose mouse, lack accurate standardised nomenclature is hampering utility animal We previously developed an ontology for system. Here, we present comprehensive update this pertaining to mouse LUT,...
Abstract Motivation: Sources of neuroscience data in Drosophila are diverse and disparate making integrated search retrieval difficult. A major obstacle to this is the lack a comprehensive logically structured anatomical framework an intuitive interface. Results: We present online resource that provides convenient way study query fly brain anatomy, expression genetic data. extended newly developed BrainName nomenclature for adult into ontology relates set published neuron classes regions...
Digital brain atlases are used in neuroscience to characterize the spatial organization of neuronal structures [1]–[3], for planning and guidance during neurosurgery [4], [5], as a reference interpreting other modalities such gene expression or proteomic data [6]–[9]. The field digital atlasing is extensive, includes high quality mouse [10], rat [11], rhesus macaque [12], human [13], [14], several model organisms. In addition based on histology, [15], [16], magnetic resonance imaging [17],...
EMAGE (http://www.emouseatlas.org/emage) is a freely available online database of in situ gene expression patterns the developing mouse embryo. Gene domains from raw images are extracted and integrated spatially into set standard 3D virtual embryos at different stages development, which allows data interrogation by spatial methods. An anatomy ontology also used to describe sites expression, be queried using text-based Here, we recent enhancements including: release completely re-designed...
The International Knockout Mouse Consortium (IKMC) aims to mutate all protein-coding genes in the mouse using a combination of gene targeting and trapping embryonic stem (ES) cells make generated resources readily available research community. IKMC database web portal ( www.knockoutmouse.org ) serves as central public site for data facilitates coordination prioritization work within consortium. Researchers can access up-to-date information on knockout vectors, ES mice specific genes, follow...
Identifying genes that are important for embryo development is a crucial first step towards understanding their many functions in driving the ordered growth, differentiation and organogenesis of embryos. It can also shed light on origins developmental disease congenital abnormalities. Current international efforts to examine gene function mouse provide unique opportunity pinpoint involved embryogenesis, owing emergence embryonic lethal knockout mutants. Through internationally coordinated...
Mouse anatomy ontologies provide standard nomenclature for describing normal and mutant mouse anatomy, are essential the description integration of data directly related to such as gene expression patterns. Building on our previous work anatomical embryonic adult mouse, we have recently developed a new substantially revised ontology covering all life stages mouse. Anatomical terms organized in complex hierarchies enabling multiple relationships between terms. Tissue classification well...
Abstract Background The developing mouse limb is widely used as a model system for studying tissue patterning. Despite this, few references are available that can be the correct identification of structures, such muscles and tendons. Existing textual consist two-dimensional (2D) illustrations adult rat or difficult to apply when attempting describe complex three-dimensional (3D) relationship between tissues. Results To improve resources in model, we have generated free, web-based,...