Publications by authors named "Helder Pedro"

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.

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Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.

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Accurate and comprehensive annotation of genomic sequences underpins advances in managing plant disease. However, important plant pathogens still have incomplete and inconsistent gene sets and lack dedicated funding or teams to improve this annotation. This paper describes a collaborative approach to gene curation to address this shortcoming.

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Article Synopsis
  • * The latest version (4.8) includes data on 6,780 genes from 268 pathogens and 210 host species, focusing on plant pathogens and their effects on major crops.
  • * The article also highlights future developments for PHI-base, new features, increased data content, and some challenges in the data curation process.
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Article Synopsis
  • Ensembl Genomes is an online resource that offers genome-scale data specifically for non-vertebrate species, complementing the vertebrate data available through the Ensembl project.
  • The resource provides a consistent interface for accessing various genomic data, including genome sequences, gene models, and genetic variations, which is updated four times a year.
  • Recent developments have focused on better organizing orthologues and paralogues, enhancing gene expression data, particularly in plants, and strengthening integration with the Ensembl project to manage the growing amount of genomic data.
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Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.

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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 pathogen-host interactions reported in peer reviewed research articles.

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Fusarium culmorum is a soilborne fungal plant pathogen that causes foot and root rot and Fusarium head blight on small-grain cereals, in particular on wheat and barley. We report herein the draft genome sequence of a 1998 field strain called FcUK99 adapted to the temperate climate found in England.

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Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.

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PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis.

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Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and 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 and effector genes from bacterial, fungal and protist pathogens.

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Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species.

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Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species.

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Background: With an estimated 38 million people worldwide currently infected with human immunodeficiency virus (HIV), and an additional 4.1 million people becoming infected each year, it is important to understand how this virus mutates and develops resistance in order to 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 for high throughput DNA sequencing, followed by assembly of full length viral genome sequences from the resulting large dataset.

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Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects of cancer genesis and progression. These observations motivated a genome-wide assessment of AS in breast cancer. We accomplished this by measuring exon level expression in 31 breast cancer and nonmalignant immortalized cell lines representing luminal, basal, and claudin-low breast cancer subtypes using Affymetrix Human Junction Arrays.

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Background: A rich microbial environment in infancy protects against asthma [1], [2] and infections precipitate asthma exacerbations [3]. We compared the airway microbiota at three levels in adult patients with asthma, the related condition of COPD, and controls. We also studied bronchial lavage from asthmatic children and controls.

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