IRB Barcelona is seeking a Bioinformatics Postdoctoral Fellow in Cancer Drug Resistance to work on the project entitled “Improved Clinical Decisions Via Integrating Multiple Data Levels to Overcome Chemotherapy Resistance In High-Grade Serous Ovarian Cancer (DECIDER)”, funded by the European Union’s Horizon 2020 research and innovation programme (propsal No 965193).
DECIDER is an international consortium consisting of 14 academic labs and 4 companies spread across 7 EU countries and coordinated by University of Helsinki. The project has a strong translational component, aiming to bringing actionable insight to the clinic to improve treatment of recurrent, drug-resistant ovarian cancer and improve patient outcomes.
The role of the Genome Data Lab of the IRB in the DECIDER project is to chart tumor genetic and epigenetic changes through time and therapy, with the aim of being able to anticipate the next step of cancer evolution.
The work of the bioinformatics postdoctoral fellow will have these objectives:
1- identifying mutations, structural variations incl. copy number alterations and indels at high sensitivity in genomes of chemotherapy-treated ovarian tumors using custom bioinformatics pipelines that (s)he will create and/or maintain.
2- prioritizing the cancer driver and/or drug resistance alterations (from multi-omics analysis) with highest impact on the course of tumor evolution, and organizing them into a catalog for downstream use by DECIDER partners for e.g training of machine learning algorithms, and integration in knowledge bases.
3- devising a statistical methodology for multi-modal mutational signature analysis that unites CNA, other structural variation, indels, and point mutations. She/he will implement this as a software tool and apply it to ovarian cancers, deriving subtypes relevant to drug resistance prediction.
Additionally, the bioinformatics postdoctoral fellow may collaborate with project partners in Finland, Italy, France, Germany or Sweden to boost the quality of the work above e.g. by incorporating network analysis (to better characterize driver potential), RNA-Seq analysis (to better characterize rearrangements, or detect splicing changes), and histology image analysis (to use as validation for subtyping).
The research will be performed in the Genome Data Science lab (https://agendas.irbbarcelona.org/), under supervision of ICREA Professor and EMBO YIP Fran Supek, and in collaboration with the diverse, international team in the lab, which consists of genomics biologists, wet-lab biologists and mathematicians at the PhD and postdoc level.
Start date is flexible; earlier dates are preferable.
Informal inquiries can be directed to the PI at email@example.com.
Early applications are encouraged.
Lindeboom, Vermeulen, Lehner and Supek (2019) Nature Genetics “The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy”
Mas-Ponte and Supek (2020) Nature Genetics, “DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers”
Salvadores, Fuster and Supek (2020) Science Advances, “Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns”
Supek and Lehner. (2017) Cell. “Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes”
Supek et al. (2014) Cell. “Synonymous mutations frequently act as driver mutations in human cancers”
- Perform excellent research according to the high standards of the Supek lab and the IRB Barcelona
- Publish results in top-tier computational biology and/or genetics journals
- Present at weekly lab meetings and journal clubs, at department seminars, and conferences
- Engage in teamwork with other members of the host lab to facilitate progress on the project
- Participate in the DECIDER project activities: meetings, presentations, visits to other labs, collaboration, exchange of data sets, preparing project reports/deliverables.
EXPERIENCE, KNOWLEDGE, SKILLS:
Must Have – Required:
- Experience: PhD in the natural sciences, engineering or mathematics. Some experience with genomic or transcriptomic data analysis is required.
- Knowledge: good level of spoken English. Intermediate-to-advanced knowledge of one programming language (e.g. R or Python).
- Skills: a highly motivated experienced researcher with enthusiasm to work on challenging, important topics in cancer genomics.
- Experience: Experience with various genomics and/or epigenomics and/or transcriptomics software tools (esp. genetic variant calling, gene expression analysis from RNA-Seq). Experience with machine learning methods might be helpful.
- Knowledge: Previous research work that involved evolutionary genomics or population genomics or cancer genomics-related topics.
- Skills: independent, self-learning, goal-oriented.
WORKING CONDITIONS & ENTITLEMENTS:
- Working conditions: Employed in compliance with Spanish legislation and regulations under a full-time contract. Employees receive the benefits of the Spanish Social Security system covering sickness, maternity/paternity leaves and injuries at work.
- Training and Career: Postdoctoral researchers joining IRB Barcelona gain access to the Institute’s advanced research training and career development opportunities, all within in a competitive international environment. Courses and workshops on themes of particular interest to postdocs are offered regularly by the Institute.
- International environment: Nearly 90 Postdoctoral researchers (more than a half non-Spanish nationals) are currently working at IRB Barcelona.
HOW TO APPLY & SELECTION PROCESS:
- Deadline for applications: 12/03/2021 (If no suitable candidate is found, the deadline will be extended)
- Number of positions available: 1
- Pre-selection: Will be based on CV, motivation letter, experience, management of research and innovation.
- Interviews: Short-listed candidates will be interviewed.
- Job offer: Will be sent to the successful candidate after the interview.
Note: The strengths and weaknesses of the applications will be provided upon request.
'If you, as an applicant, have any suggestion or wish to make a complaint regarding the selection process, please contact us at the following email address: firstname.lastname@example.org You will receive a response within a month.'