Description
We are seeking a highly motivated and experienced Computational Scientist for the Prostate Cancer Clinical Research Unit to work in a Department of Defense-(CDMRP) and a Prostate Cancer Foundation funded projects involving the molecular characterisation of DNA deficient prostate cancer as well as clinical trials in this disease.
The task involves computational analysis of “omics” data, developing analysis pipelines for research and diagnostic purposes, presenting data, writing grants, reports, abstracts and manuscripts for meetings and peer-reviewed journals.
This position would be transversal between our group and the Bioinformatics Unit where the candidate would also be integrated. As part of this position the candidate have to interact with different members at the lab team at CNIO, including physicians, our associated researchers in the joint CNIO-IBIMA clinical unit, as well as collaborators from other centres in Spain and abroad.
Prostate Cancer Clinical research Unit
The Prostate Cancer Unit is a multidisciplinary team led by Dr David Olmos, in which researchers from two institutions are integrated: The Spanish National Cancer Research Centre (CNIO) and our associated clinical site at the Institute of Biomedical Research in Málaga (IBIMA). Currently the team counts with 2 senior clinicians scientists, Dr Olmos (team leader) and Dr Castro, 2 post-doctoral researchers, 1 clinical fellow, 1 senior lab officer, 3 predoctoral students, 2 lab technicians, 2 clinical data managers and clinical projects coordinator. We also count with a visiting pathologist and a medical statistician. Our team is leading several national and international projects including a national prospective studies platform seeking for novel biomarkers through a better molecular and clinical characterisation of advanced and high-risk prostate cancer. We also conduct clinical trials as well as translational projects in therapeutics and mechanistic research, in which we use multiple preclinical in vivo and in vitro tools.
Our associated CNIO-IBIMA unit at the Málaga University Hospital, which is also led by Dr Olmos and Dr Castro, is considered one of the leading European units in Prostate Cancer Clinical Research, with over 20 actives trials and over 150 patients enrolled in research projects every year. This unit integrates 5 Medical Oncologist, 2 Radiation Oncologist, 3 Urology surgeons, 2 research nurses, 1 study coordinator and 2 data managers.
Justification of the position
This position is essential due to the growing amount of work related to computational analyses of genomic, transciptomics and epigenetic data and future plans of wide-screening using shRNA and/or CRISP based tools.
Responsabilities
- Bioinformatics analysis of genomes for research or diagnostic use in the clinic
- Bioinformatics analysis of expression and epigenetic data for research
- Developing analysis pipelines for “omics” data and results report
- Integrative analysis of “omics” data
- Writing abstracts, manuscripts and grants in collaboration with the team
- Present data in lab meeting and conferences
- Supervise junior personnel in the team and support to other researchers in the team
Essential Requirements
- Bachelor in Medical, biosciences, statistics, informatics or related discipline
- Master in bioinformatics or computational sciences
- PhD in biomedicine or computational sciences
Experience
- Probed experience in bioinformatics, Post-doctoral experience in “omics” analyses.
- Cancer biology knowledge, specially genomics and/or prostate cancer would be valued.
- Data analyses using NGS technologies, including WGS, WES, RNAseq. Variant calling and variant classification.
- Experience in expression and CNV analyses using arrays
- Development and implementation of analyses pipelines
- Expertise in software tools for implementing analyses and reporting pipelines: FastQC, BWA, Bowtie, SAMtools, GATK, Cytoscape, IGV…
- Experience with GNU/Linux cluster environments and experience using scripting and programming languages
Technical abilities
- Unix
- Perl, Python or similar languages
- R and (SPSS/stata/sas or other similar statistical packages)
- Database managing and developing. Relational and non-relational databases
- Basic statistical knowledge. Advanced knowledge would be valued
Languages
- Spoken and written English: high-level
- Spoken and written Spanish: optional
Others
- Capacity to establish good interpersonal relationship, team-work and communicating complex concepts
- Initiative, autonomy, work planning and organization capacity
- Creativity and ability to resolve unexpected problems
- learning interest, willingness to improve, team-work abilities, flexibility and adaptation
Contact
David Olmos: dolmos@cnio.es