Job Description:
Based in Leuven, Belgium, the incumbent will contribute to a project exploring the biodiversity of banana towards drought tolerance and will bring expertise in the area of genome curation and proteogenomics.
The selected candidate will work as part of a multidisciplinary team, including experienced scientists in genetics, proteomics, mass spectrometry, bioinformatics and computer science.
The successful candidate will analyze RNA-seq data and mass spectrometry data in order to study polymorphisms and variants in banana for which a reference genome is available.
With the current annotation tools, an accuracy of more than 80% is rarely achieved on model organisms and many gene annotations contain errors, meaning that most gene predictions need to be improved based on evidence-driven gene prediction. Misannotations have a major impact on genetic variation experiments, transcriptomics and proteomics experiments in the same organism, but also on other projects who use these data to structurally annotate their own genomes. EST, RNA-seq and protein data should be aligned to a reference genome and tools need to be developed to use the external evidence to improve the gene predictions and find gene isoforms across genotypes.
Website unit: http://www.biw.kuleuven.be/DTP/TRO/_data/home.htm
Responsibilities
In particular, the incumbent will:
Contribute to the analyse of the proteome of different banana genotypes by LC-MSMS (thermo orbitrap QExactive).
Perform, manipulate, filter SNP datasets and study SNP effects and the predicted exon/intron structure on the protein level.
Perform mapping of RNAseq reads and use the information to reannotate the reference A and Musa B genome and create variety specific protein databases. (SNP calling and structural annotation (exon/intron structure) for polyploid accessions).
Contribute to the identification of A and B genome specific alleles in the Musa genus.
Profile
•At least 1 year of professional experience; experience working on NGS data analyses and proteomics data.
•Competence in the use of relevant software tools and formats (Samtools, Fastq, BAM, VCFtools, Hapmap, IGV, mascot, R, etc…).
•Good programming skills in Perl and/or Python, Java.
•Experience in data management with relational databases (MySQL, PostgreSQL) and or NoSQL.
•Good command of the English language, both written and spoken.
•Good communication and interpersonal skills.
•Ability to work both independently and as part of a team in a multicultural environment (Collaboration with Bioversity office in Montpellier).
Offer
We offer a fulltime position for one year. The grade of salary of this position is 6 or 7, exceptional 8 depending on your qualifications and your relevant experience.
Interested?
You can apply for this job no later than November 12, 2014 via the online application tool…
Additional Info:
[Click Here to Access the Original Job Post]
Based in Leuven, Belgium, the incumbent will contribute to a project exploring the biodiversity of banana towards drought tolerance and will bring expertise in the area of genome curation and proteogenomics.
The selected candidate will work as part of a multidisciplinary team, including experienced scientists in genetics, proteomics, mass spectrometry, bioinformatics and computer science.
The successful candidate will analyze RNA-seq data and mass spectrometry data in order to study polymorphisms and variants in banana for which a reference genome is available.
With the current annotation tools, an accuracy of more than 80% is rarely achieved on model organisms and many gene annotations contain errors, meaning that most gene predictions need to be improved based on evidence-driven gene prediction. Misannotations have a major impact on genetic variation experiments, transcriptomics and proteomics experiments in the same organism, but also on other projects who use these data to structurally annotate their own genomes. EST, RNA-seq and protein data should be aligned to a reference genome and tools need to be developed to use the external evidence to improve the gene predictions and find gene isoforms across genotypes.
Website unit: http://www.biw.kuleuven.be/DTP/TRO/_data/home.htm
Responsibilities
In particular, the incumbent will:
Contribute to the analyse of the proteome of different banana genotypes by LC-MSMS (thermo orbitrap QExactive).
Perform, manipulate, filter SNP datasets and study SNP effects and the predicted exon/intron structure on the protein level.
Perform mapping of RNAseq reads and use the information to reannotate the reference A and Musa B genome and create variety specific protein databases. (SNP calling and structural annotation (exon/intron structure) for polyploid accessions).
Contribute to the identification of A and B genome specific alleles in the Musa genus.
Profile
•At least 1 year of professional experience; experience working on NGS data analyses and proteomics data.
•Competence in the use of relevant software tools and formats (Samtools, Fastq, BAM, VCFtools, Hapmap, IGV, mascot, R, etc…).
•Good programming skills in Perl and/or Python, Java.
•Experience in data management with relational databases (MySQL, PostgreSQL) and or NoSQL.
•Good command of the English language, both written and spoken.
•Good communication and interpersonal skills.
•Ability to work both independently and as part of a team in a multicultural environment (Collaboration with Bioversity office in Montpellier).
Offer
We offer a fulltime position for one year. The grade of salary of this position is 6 or 7, exceptional 8 depending on your qualifications and your relevant experience.
Interested?
You can apply for this job no later than November 12, 2014 via the online application tool…
Requeriments :
Skills :
- Bioinformatics
- Database design
- Next Generation Sequencing
- Programing in Python
- Programing Skills
- Programming in Java
- Programming in R
- RNA-seq
Areas :
Additional Info:
[Click Here to Access the Original Job Post]