CV INFORMATICO
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Divisione : San Raffaele Area Ricerca

Località : MILANO MILANO IT 20132 VIA OLGETTINA 58

Tipo contratto : Co.Co.Pro

Livello di carriera : Livello iniziale

Istruzione : Laurea Spec./Vecchio Ord. in Informatica, Bioinformatica, Ingegneria Informatica/Biomedica/TLC

Categoria : Ricercatore

Descrizione lavoro :

Our group is in charge of handling data from viral integration studies [1, 2, 3] at TIGET for both clinical and preclinical studies. Vector integration sites (VIS) are genomic positions annotated with respect to reference genome (human or mouse): we built a bioinformatics pipeline to identify VIS from sequencing reads (454 and Illumina) and we collected data (BED-like file format) in a database storing metadata such as cell type, harvest time point and tissue.

We need to update our pipeline by (1) optimizing and improving VIS identification and storage (analytical workflow, interfaces, database, Galaxy plug-in), (2) and we need to build an internal reference VIS database.

Candidates could apply to PhD programs in Bioinformatics or Computer Science working on our project.

 

[1] Naldini, L. (2011). Ex vivo gene transfer and correction for cell-based therapies. Nature reviews. Genetics, 12(5), 301–15. doi:10.1038/nrg2985

[2] Biffi, A., Bartolomae, C. C., Cesana, D., Cartier, N., Aubourg, P., Ranzani, M., Cesani, M., et al. (2011). Lentiviral vector common integration sites in preclinical models and a clinical trial reflect a benign integration bias and not oncogenic selection. Blood, 117(20), 5332–9. doi:10.1182/blood-2010-09-306761

[3] Biasco, L., Baricordi, C., & Aiuti, A. (2012). Retroviral Integrations in Gene Therapy Trials. Molecular therapy : the journal of the American Society of Gene Therapy, 1–8. doi:10.1038/mt.2011.289

 

Requirements

The ideal candidate is seeking a long-term commitment. He/she is a young motivated and enthusiastic researcher, strongly committed to undertake a PhD program in Bioinformatics or Computer Science/Engineering.

Preferred experiences/skills: programming languages (i.e. Java, Python, Perl, Bash, PHP, Ajax, etc), databases and query languages (MySQL, PostgreSQL, X-Query).

 

Contact:

Please send your application including a synopsis of research interest, Curriculum vitae, and, if available, contact for reference by email to: Eng. Andrea Calabria (calabria.andrea@hsr.it)

 

Starting date January 2013

 

================================== Divisione : San Raffaele Area Ricerca

Località : MILANO MILANO IT 20132 VIA OLGETTINA 58

Tipo contratto : Co.Co.Pro

Livello di carriera : Livello iniziale

Istruzione : Laurea Spec./Vecchio Ord. in Statistica, Matematica, Bioinformatica, Ingegneria Informatica/Biomedica/TLC

Categoria : Ricercatore

Descrizione lavoro :

Our group is in charge of handling data from viral integration studies [1, 2, 3] at TIGET for both clinical and preclinical studies. Vector integration sites (VIS) are genomic positions annotated with respect to reference genome (human or mouse): we built a bioinformatics pipeline to identify VIS from sequencing reads (454 and Illumina) and we collected data (BED-like file format) in a database storing metadata such as cell type, harvest time point and tissue.

We are studying VIS within systems biology perspectives, trying to understand cell dynamics during time and modeling stem cells growth and differentiation to analyze safety of gene therapy and biological data mining. Our candidate will be involved in statistical methods for VIS data analysis and systems modeling and simulation.

Candidates could apply to PhD programs in Statistics, Bioinformatics or Computer Science working on our project.

 

[1] Naldini, L. (2011). Ex vivo gene transfer and correction for cell-based therapies. Nature reviews. Genetics, 12(5), 301–15. doi:10.1038/nrg2985

[2] Biffi, A., Bartolomae, C. C., Cesana, D., Cartier, N., Aubourg, P., Ranzani, M., Cesani, M., et al. (2011). Lentiviral vector common integration sites in preclinical models and a clinical trial reflect a benign integration bias and not oncogenic selection. Blood, 117(20), 5332–9. doi:10.1182/blood-2010-09-306761

[3] Biasco, L., Baricordi, C., & Aiuti, A. (2012). Retroviral Integrations in Gene Therapy Trials. Molecular therapy : the journal of the American Society of Gene Therapy, 1–8. doi:10.1038/mt.2011.289

 

Requirements

The ideal candidate is seeking a long-term commitment. He/she is a young motivated and enthusiastic researcher, strongly committed to undertake a PhD program in Statistics, Bioinformatics or Computer Science/Engineering.

Preferred experiences/skills: data mining and/or modeling, stochastic and Bayesian approaches, algorithm development; basic programming languages and statistical frameworks (i.e. Python/Perl, R/Matlab).

 

Contact:

Please send your application including a synopsis of research interest, Curriculum vitae, and, if available, contact for reference by email to: Eng. Andrea Calabria (calabria.andrea@hsr.it)

 

Starting date January 2013

 

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