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Bioinformatics PhD scholarship UK
An exciting Bioinformatics PhD scholarship on characterisation of virus populations of food security crops using Next Generation Sequencing (NGS) is available at the Natural Resources Institute, University of Greenwich UK.
Description: Next Generation Sequencing (NGS) has revolutionized research on viral pathogens and has been emerging as a rapid and reliable tool for plant virus diagnostics but the characteristic rapid evolution rates and compact genomes of viruses presents bioinformatic challenges in the determination of viral genetic diversity. Specialized bioinformatic approaches are thus required.
The Natural Resources Institute (NRI) seeks an enthusiastic bioinformatician to study plant viral diversity and host interactions using NGS data from West African yam lines, thereby improving food security and yam yields for West African farmers. The aim of the PhD will be to drive the design and implementation of diagnostic tools to mitigate the spread and transmission of viruses in yam and other vegetatively propagated root and tuber crops using NGS datasets.
The Bioinformatician will apply existing and novel algorithms focused on studying viruses and virus-host interactions through comparative genomics, transcriptomics and metagenomics. Existing viral databases will be used for a priori and de novo assembly, identification and annotation of existing and novel virus populations in yams. Resulting viral genomes will be curated in custom databases running PostgreSQL or MySQL. Phylogenetics and evolution of identified viruses will inform selection of potential markers for diagnostic tests by comparative analysis of viral repeats and highly conserved regions.
Proficiency in Perl or Python and R is essential, as is experience working on Linux/Unix batch systems. Previous experience working with databases systems (MySQL/PostgreSQL) on Linux systems is desirable.
For more information please contact: Prof Sue Seal ([email protected])
Application closed
Description: Next Generation Sequencing (NGS) has revolutionized research on viral pathogens and has been emerging as a rapid and reliable tool for plant virus diagnostics but the characteristic rapid evolution rates and compact genomes of viruses presents bioinformatic challenges in the determination of viral genetic diversity. Specialized bioinformatic approaches are thus required.
The Natural Resources Institute (NRI) seeks an enthusiastic bioinformatician to study plant viral diversity and host interactions using NGS data from West African yam lines, thereby improving food security and yam yields for West African farmers. The aim of the PhD will be to drive the design and implementation of diagnostic tools to mitigate the spread and transmission of viruses in yam and other vegetatively propagated root and tuber crops using NGS datasets.
The Bioinformatician will apply existing and novel algorithms focused on studying viruses and virus-host interactions through comparative genomics, transcriptomics and metagenomics. Existing viral databases will be used for a priori and de novo assembly, identification and annotation of existing and novel virus populations in yams. Resulting viral genomes will be curated in custom databases running PostgreSQL or MySQL. Phylogenetics and evolution of identified viruses will inform selection of potential markers for diagnostic tests by comparative analysis of viral repeats and highly conserved regions.
Proficiency in Perl or Python and R is essential, as is experience working on Linux/Unix batch systems. Previous experience working with databases systems (MySQL/PostgreSQL) on Linux systems is desirable.
For more information please contact: Prof Sue Seal ([email protected])
Application closed