[09/04/2014]Bioinformatician/informatician in proteogenomics

Based  in  University of 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  to study  polymorphisms and variants in banana for which a  reference genome is available.  Gene  annotation  is  challenging  in  non-model  organisms  and  many  gene annotations  contain errors,  meaning  that  most  gene  predictions  need  to be  improved.
Moreover,  misannotations  have  a  major  impact  on  genetic  variation  experiments, transcriptomics and proteomics experiments.  Transcriptomics  and proteomics  data  should be  aligned to the  reference  genome and tools need to be developed to  use the external evidence to improve the gene  predictions  of the reference  and find gene isoforms  and
allelic variants across genotypes.

In particular, the incumbent will:
- Contribute to  the  analysis  of  the proteome of different  banana genotypes by LCMSMS (thermo orbitrap QExactive).
- Study SNP effects and the predicted exon/intron structure on the protein level.
- Reannotate the reference A and  Musa B genome  and create variety specific protein
databases.
- Contribute  to  the  identification  of  A  and  B  genome  specific  alleles  in  the  Musa
genus.

Essential qualifications & competencies:
- A Master degree in bioinformatics.
- At  least  1  years  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 in Montpellier).