A5042849331- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Plant Disease Resistance and Genetics
- Plant-Microbe Interactions and Immunity
- Bacteriophages and microbial interactions
- Plant Virus Research Studies
- Plant Pathogens and Resistance
- Cancer Genomics and Diagnostics
- Plant Pathogens and Fungal Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Microbial Community Ecology and Physiology
- Biomedical Text Mining and Ontologies
- Probiotics and Fermented Foods
- Gut microbiota and health
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- HIV Research and Treatment
- Identification and Quantification in Food
- Environmental DNA in Biodiversity Studies
- Gene expression and cancer classification
- Genetic factors in colorectal cancer
Wellcome Sanger Institute
2022-2024
University of California, Berkeley
2010-2023
European Bioinformatics Institute
2013-2021
Wellcome Trust
2011-2017
Cold Spring Harbor Laboratory
2013
Cornell University
2013
Walter and Eliza Hall Institute of Medical Research
2010
Lawrence Berkeley National Laboratory
2010
University of California, San Francisco
2010
Instituto Gulbenkian de Ciência
2010
A rich microbial environment in infancy protects against asthma [1], [2] and infections precipitate exacerbations [3]. We compared the airway microbiota at three levels adult patients with asthma, related condition of COPD, controls. also studied bronchial lavage from asthmatic children controls.We identified 5,054 16S rRNA bacterial sequences 43 subjects, detecting >70% species present. The tree was not sterile, contained a mean 2,000 genomes per cm(2) surface sampled. Pathogenic...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in context of project (http://www.ensembl.org). Together, two provide a consistent set programmatic and interactive interfaces to rich range including reference sequence, gene models, transcriptional data, genetic variation comparative analysis. This paper provides update previous publications about resource,...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in project (http://www.ensembl.org). Together, two provide a consistent set of programmatic and interactive interfaces to rich range including genome sequence, gene models, transcript genetic variation, comparative analysis. This paper provides update previous publications about resource, with focus on recent...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources vertebrate genomics developed in context of project (http://www.ensembl.org). Together, two provide a consistent set interfaces to genomic across tree life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform...
The pathogen-host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of reported in peer reviewed research articles. also curates literature describing specific gene alterations that did not disease interaction phenotype, order provide complete datasets for comparative purposes. Viruses are included, due their extensive coverage other databases. In this article, we...
Abstract Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the project (https://www.ensembl.org). The two collectively present genome annotation through a consistent set of interfaces spanning tree life presenting sequence, annotation, variation, transcriptomic data comparative analysis. Here, we our largest increase in plant, metazoan fungal since project's inception creating one world's...
The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations did not disease interaction phenotype are provide complete datasets for comparative purposes. Viruses included. Here we describe a revised Version 4 data platform with improved search,...
Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well human, animal ecosystem health.To combat infection greater comparative knowledge is required on the pathogenic process in multiple species.The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence effector genes from bacterial, fungal protist pathogens.Mutant phenotypes are associated with gene information.The included...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies genome annotation, analysis dissemination, developed in the context of vertebrate-focused project, provides a complementary set resources species through consistent programmatic interactive interfaces. These provide access to including reference sequence, gene models, transcriptional data, polymorphisms comparative...
Abstract The Catalogue Of Somatic Mutations In Cancer (COSMIC), https://cancer.sanger.ac.uk/cosmic, is an expert-curated knowledgebase providing data on somatic variants in cancer, supported by a comprehensive suite of tools for interpreting genomic data, discerning the impact alterations disease, and facilitating translational research. catalogue accessed used thousands cancer researchers clinicians daily, allowing them to quickly access information from immense pool curated over 29...
Abstract Since 2005, the Pathogen–Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to identification presentation of phenotype information on pathogenicity their host interactions. Specific gene alterations that did not alter in interaction are also presented. invaluable for...
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis dissemination) developed in the context of (vertebrate-focused) provides a complementary set resources species through consistent programmatic interactive interfaces. These provide access to including reference sequence, gene models, transcriptional data, polymorphisms comparative analysis....
Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects cancer genesis and progression. These observations motivated a genome-wide assessment AS breast cancer. We accomplished this measuring exon level expression 31 nonmalignant immortalized cell lines representing luminal, basal, claudin-low subtypes using Affymetrix Human Junction Arrays. analyzed these data computational pipeline specifically designed to detect with low false-positive...
Background With an estimated 38 million people worldwide currently infected with human immunodeficiency virus (HIV), and additional 4.1 becoming each year, it is important to understand how this mutates develops resistance in order design successful therapies. Methodology/Principal Findings We report a novel experimental method for amplifying full-length HIV genomes without the use of sequence-specific primers high throughput DNA sequencing, followed by assembly full length viral genome...
PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates genes PHI-base, an expertly curated catalog of with experimentally verified pathogenicity, the Ensembl tools visualization analysis. The focused on fungi, protists (oomycetes) bacterial pathogens have genomes been sequenced annotated. Genes associated PHI-base can be easily identified across all species using BioMart-based query tool visualized in their context genome...
Abstract The Catalogue of Somatic Mutations in Cancer (COSMIC) is a vital resource for cancer genomics, offering extensive data on somatic mutations, cell lines, and mutation signatures. While the existing COSMIC dataset provides wealth diverse, high-quality information, accessing fully utilising it requires significant processing expertise analysis. To address this, we are developing new suite tools to enhance integration, usability exploration.The Cell Line Explorer serves as starting...
Fusarium culmorum is a soilborne fungal plant pathogen that causes foot and root rot head blight on small-grain cereals, in particular wheat barley. We report herein the draft genome sequence of 1998 field strain called FcUK99 adapted to temperate climate found England.
Accurate and comprehensive annotation of genomic sequences underpins advances in managing plant disease. However, important pathogens still have incomplete inconsistent gene sets; lack dedicated funding or teams to improve this annotation. This paper describes a collaborative approach curation address shortcoming. In the first instance, over forty members Botrytis cinerea community from eight countries, with training infrastructural support Ensembl Fungi, used editing tool Apollo...
Abstract In 2004, COSMIC was one of the first initiatives to integrate global data on somatic mutations in cancer. At time it explicit that fragmentation genetic datasets a major obstacle understand processes driving A team expert curators and bioinformaticians tasked with identifying cataloguing related variants, as well relevant demographic, clinical, patient information from published studies making these easily accessible research community. Over last two decades we have witnessed...
Abstract Somatic mutations accumulate in cells throughout their life. Most of them do not bring any negative effect. However, certain change protein behaviour, structure, or level expression. More importantly, some are known to initiate and drive oncogenic transformation. These often make good therapeutic targets but recognising this small subset a cancer sample is major challenge. The average cell carries life-long baggage somatic mutations, the mutational process sped up these through...
<p>Supplementary Figures S1-S2 and Supplementary Tables S2-S4.</p>
<p>Supplementary Figures S1-S2 and Supplementary Tables S2-S4.</p>
<div>Abstract<p>Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects cancer genesis and progression. These observations motivated a genome-wide assessment AS breast cancer. We accomplished this measuring exon level expression 31 nonmalignant immortalized cell lines representing luminal, basal, claudin-low subtypes using Affymetrix Human Junction Arrays. analyzed these data computational pipeline specifically designed to...