Job Information
- Organisation/Company: Champalimaud Foundation
- Department: Botton-Champalimaud Pancreatic Cancer Center (BCPCC)
- Research Field: Computer science » Other
- Researcher Profile: First Stage Researcher (R1)
- Positions: Master Positions
- Application Deadline: 1 Oct 2026 - 16:37 (Europe/Lisbon)
- Country: Portugal
- Type of Contract: Other
- Type of Contract Extra Information: Fellowship Contract
- Job Status: Full-time
- Hours Per Week: 40
- Offer Starting Date: 1 Oct 2026
- Is the job funded through the EU Research Framework Programme? Not funded by a EU programme
Offer Description
We are seeking 2 highly motivated and skilled Bioinformaticians to join our dynamic research team at Botton-Champalimaud Pancreatic Cancer Centre. The successful candidates will play a critical role in developing and implementing robust bioinformatics pipelines in cloud environments, analysing complex genomic datasets, and contributing to the advancement of our research programs. This position is ideal for individuals with a strong background in bioinformatics and hands-on experience with cloud computing and complex biological data.
Key Responsibilities:
- Cloud Pipeline Development & Management: Design, implement, and maintain scalable bioinformatics pipelines in cloud environments (e.g., AWS, Azure, GCP) for processing and analysing large-scale omics data. This includes optimising workflows for efficiency, robustness and cost-effectiveness.
- Multi-omic data analysis: Handle diverse multi-omic data types, including cancer WGS, RNA-seq, single-cell, spatial transcriptomics, and long-read sequencing, and contribute to the development and evaluation of novel computational pipelines for analysing omics data.
- Data Integration & Visualisation: Integrate genomic data with other relevant biological datasets (e.g., bulk RNA-seq, single-cell and spatial transcriptomics) and develop compelling visualisations to communicate complex findings.
- Collaboration: Provide timely and expert bioinformatics support through our research department, including experimental biologists, clinicians, and other bioinformaticians, to achieve core research goals.
- Documentation & Reproducibility: Ensure rigorous documentation of all analyses, code, and pipelines to promote reproducibility and facilitate knowledge transfer.
Where to apply
E-mail: recruitment.botton@research.fchampalimaud.org
Requirements
- Research Field: Biological sciences » Other
- Education Level: Master Degree or equivalent
Skills/Qualifications
Required Qualifications:
- MSc in Bioinformatics, Computational Biology, Computer Science, or a closely related field with a strong computational focus.
- Proven experience in developing and running bioinformatics pipelines in high-performance computing (HPC) or cloud computing environments (e.g. AWS Batch, GCP, etc.).
- Demonstrable hands-on experience with bioinformatic software for cancer or human genomics.
- Strong programming skills, preferably in Python and/or R.
- Experience with workflow management systems (e.g., Nextflow).
- Proficiency with version control systems (e.g., Git).
- Excellent written and verbal communication skills in English.
- A collaborative mindset and motivation to work in an international and interdisciplinary team and environment
Desirable Qualifications:
- PhD in Bioinformatics, Computational Biology, Genomics, Computer Science, or a closely related field with a strong computational focus or 3 years of professional experience in a similar role.
- Experience with containerization technologies (e.g., Docker, Singularity).
- Familiarity with Nanopore sequencing data analysis pipelines and tools.
- Familiarity with single-cell and spatial transcriptomics data analysis.
- Proven track record in conducting research, including designing, executing, and interpreting experiments.
We encourage applications from candidates who meet most, even if not all, of the listed criteria.
Languages: ENGLISH
Level: Good
Research Field: Biological sciences » Other; Computer science » Other
Years of Research Experience: 1 - 4
Additional Information
Benefits
Medical Insurance
Social Security
Eligibility criteria
How to apply: Candidates must provide a single PDF file named “NameSurname_BI2_BCPCC” to "recruitment.botton@research.fchampalimaud.org", containing:
- (i) A letter of motivation (max. 2 pages), highlighting your suitability for the role, salary expectations and notice period;
- (ii) CV (max. 2 pages);
- (iii) Names and contact information for at least 2 references. If you do not wish that we contact current or past employers, please state so and why in your letter of motivation.
Selection process
All CVs and motivation letters will be reviewed by the selection committee. Reference letters will be requested from shortlisted candidates, and those candidates deemed particularly well suited for the position will be invited for an interview.
Additional comments
More about us. The Botton-Champalimaud Pancreatic Cancer Centre is a state-of-the-art facility comprising research laboratories, a day hospital, a surgical centre, as well as inpatient and intensive care facilities. The mission of the Botton-Champalimaud Pancreatic Cancer Centre is to develop new and effective treatments for pancreatic cancer. To accomplish this goal a multidisciplinary team of surgeons, clinicians, clinical trials specialists, cancer scientists, genomics experts and computational biologists work together to deliver world-leading outcomes for patients with pancreatic cancer.
The Botton-Champalimaud Pancreatic Cancer Centre is also closely integrated with the Champalimaud Centre for the Unknown. Members of the Champalimaud Research Programme (CR) and the Champalimaud Clinical Centre (CCC), work together to investigate fundamental biological processes and search for effective solutions to alleviate the burden of oncological, neurological and mental diseases, while providing state-of-the-art care to the patients of the CCC. With 479 members, including group leaders, postdocs, PhD and MSc students, research technicians and highly specialised research staff, the CR community encompasses 39 nationalities. Within the Lisbon Ocean Campus, CF will expand its research, technological development, innovation, and clinical practice in the digital therapeutics field.
Additional Institutional Information. In line with our community guidelines and Equality, Diversity and Inclusion policy and Gender Equality Plan, no candidate may be privileged, favoured, prejudiced or deprived of any right or excluded from any duty on the basis of age, sex, gender identity, sexual orientation, race/ethnicity, disability, chronic illness, language, nationality, territory of origin, family status (marital, pregnancy and maternity, having or not having dependents), socioeconomic situation, education, religion, political or ideological beliefs, trade union membership, or on any other grounds which are irrelevant to decision-making.
Legal Notices. The present call has the sole purpose of filling the indicated research position. This call may be cancelled at any time on or before the jury’s evaluation of all eligible candidates and the recruitment process shall be concluded on the day of the full execution of the contract between the Champalimaud Foundation and the selected candidate.
Work Location(s)
Number of offers available: 1
- Company/Institute: Champalimaud Foundation
- Country: Portugal
- State/Province: Lisbon
- City: Lisboa
- Postal Code: 1400-038
- Street: Fundação Champalimaud
Contact
- State/Province: Lisbon
- City: Lisboa
- Website: https://fchampalimaud.org/champalimaud-research
- Street: Champalimaud Centre for the Unknown
- Postal Code: 1400-038
- E-Mail: recruitment.botton@research.fchampalimaud.org
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