Project: “Next generation sequencing for studying viruses and RNA silencing-based antiviral defense in model and crop plants”
We shall apply the Illumina deep-sequencing technology and develop bioinfomatic tools to study the viral genome, transcriptome and small RNA populations in experimentally infected Arabidopsis plants and naturally-infected crop plants with the ultimate goal to obtain knowledge for designing an effective RNA-based antiviral vaccine.
Virus-infected crop plants including rice, cassava, blackgram, cotton, banana and tomato, collected in fields worldwide, will be investigated by deep-sequencing of fractionated nucleic acids in order to (i) identify and de novo assemble complete genomes of newly emerging and resistance-breaking viruses, viral strains and viral satellites; (ii) determine the nucleotide polymorphism in virus populations; (ii) de novo assemble the viral transcriptome and (ii) create genome-wide maps of virus-derived siRNAs.
The project is part of a large COST action network with more than 20 member-countries (http://costfa0806.aua.gr/).
A successful candidate should have a master/diploma degree in molecular biology and a background and/or a strong interest in boinformatics.
The position is available from the 1st of January 2011; earlier or later starting dates will also be considered.
The working places will be:
1) Institute of Botany, University of Basel, Basel, Switzerland
2) Fasteris AG, Geneva, Switzerland (www.fasteris.com)
The PhD project will be co-supervised by PD Dr. Mikhail Pooggin (University of Basel) and Dr. Laurent Farinelli (Fasteris AG).
Contact info:
Mikhail.Pooggin@unibas.ch; Tel. 41 61 267 27 29
or
Laurent.Farinelli@fasteris.com; Tel. 41 22 794 22 23
We shall apply the Illumina deep-sequencing technology and develop bioinfomatic tools to study the viral genome, transcriptome and small RNA populations in experimentally infected Arabidopsis plants and naturally-infected crop plants with the ultimate goal to obtain knowledge for designing an effective RNA-based antiviral vaccine.
Virus-infected crop plants including rice, cassava, blackgram, cotton, banana and tomato, collected in fields worldwide, will be investigated by deep-sequencing of fractionated nucleic acids in order to (i) identify and de novo assemble complete genomes of newly emerging and resistance-breaking viruses, viral strains and viral satellites; (ii) determine the nucleotide polymorphism in virus populations; (ii) de novo assemble the viral transcriptome and (ii) create genome-wide maps of virus-derived siRNAs.
The project is part of a large COST action network with more than 20 member-countries (http://costfa0806.aua.gr/).
A successful candidate should have a master/diploma degree in molecular biology and a background and/or a strong interest in boinformatics.
The position is available from the 1st of January 2011; earlier or later starting dates will also be considered.
The working places will be:
1) Institute of Botany, University of Basel, Basel, Switzerland
2) Fasteris AG, Geneva, Switzerland (www.fasteris.com)
The PhD project will be co-supervised by PD Dr. Mikhail Pooggin (University of Basel) and Dr. Laurent Farinelli (Fasteris AG).
Contact info:
Mikhail.Pooggin@unibas.ch; Tel. 41 61 267 27 29
or
Laurent.Farinelli@fasteris.com; Tel. 41 22 794 22 23