Vacancy 1
Postdoctoral appointment on single-cell and spatial ‘omics of rare cancers
Keywords: medical genomics, cancer, single-cell sequencing, data science
Location: International Agency for Research on Cancer / World Health Organization, Lyon (Gerland bio-district), France
Start date: early 2024 (flexible)
Duration: 2 years with expectation of renewal
Salary: 2,950€ net per month
Contact: Candidates should send a CV with publication list, cover letter, and 2 letters of reference to Matthieu Foll, Lynnette Fernandez-Cuesta, and Nicolas Alcala.
Background: Although individually infrequent, rare cancers, defined as <5 cases/10,000 individuals, collectively account for ~25–30% of all cancer diagnoses and 25% of cancer deaths, representing a substantial burden of disease. Despite this, basic science research, clinical trials, and approval of new therapies for rare cancers are lacking. The Rare Cancers Genomics team therefore aims to investigate the genomics of these neglected cancers. We have recently provided multi-omic characterizations of rare thoracic cancers1—4. Our results unveiled specialized genomic, transcriptomic, and epigenomic profiles that shape the clinical behavior of the tumors. Nevertheless, the biological processes responsible for these profiles and the extent of intra-tumor heterogeneity are still poorly understood. The Rare Cancers Genomics team is seeking a postdoctoral scientist to further explore the biological processes of rare cancers through single-cell and spatial transcriptomics.
Environment: IARC-WHO is located in the city of Lyon, France — a stunning UNESCO world-heritage city offering exceptional quality of life perfectly embodying the French “art de vivre.” The Rare Cancers Genomics team at IARC-WHO is a multicultural and multidisciplinary team including bioinformaticians, data scientists, and molecular biologists from four different nationalities, piloting large international consortia, and well-supported by multiple competitive grants. It is a vibrant environment ideal for someone willing to pursue an international career in medical bioinformatics or data science to make high-impact contributions and gain experience in state-of-the-art bioinformatics and big data analysis. Team alumni pursued their careers in world-leading medical research institutions (Barcelona Institute for Research in Biomedicine, Lausanne University Hospital, University of Calgary, Stanford University), at IARC-WHO, and in private companies (bioMerieux). IARC welcomes approximately 60 postdoctoral scientists distributed across its research branches. The cost of travel for the postdoctoral scientist will be covered. Dependence and health insurance allowances will be paid, if applicable. For additional information about postdoctoral stays at IARC-WHO, you can consult the postdoctoral charter.
Duties:
The selected candidate will work under the supervision of Matthieu Foll and Nicolas Alcala and closely collaborate with other members of the team to enhance their competencies in the following activities:
- – Analyze unique single-cell and spatial transcriptomic datasets (10X genomics) of rare tumors from our rare cancers genomics initiative
- – Perform statistical analyses
- – Write manuscripts
- – Present results internally and at international conferences
Required skills and background:
- – PhD in relevant area (bioinformatics/computational biology, biostatistics, genetics/genomics)
- – Experience in single-cell and/or spatial transcriptomic analysis
- – Expert knowledge of R or python
- – Expert knowledge in statistics
- – English proficiency
- – Good communication skills
- – Team player
References:
Vacancy 2
Postdoctoral appointment on deep-learning image and ‘omics data analysis of rare cancers
Keywords: medical genomics, cancer, data science, deep-learning
Location: International Agency for Research on Cancer / World Health Organization, Lyon (Gerland bio-district), France
Start date: early 2024 (flexible)
Duration: 2 years with expectation of renewal
Salary: 2,950€ net per month
Contact: Candidates should send a CV with publication list, cover letter, and 2 letters of reference to Matthieu Foll, Lynnette Fernandez-Cuesta, and Nicolas Alcala.
Background: Although individually infrequent, rare cancers, defined as <5 cases/10,000 individuals, collectively account for ~25–30% of all cancer diagnoses and 25% of cancer deaths, representing a substantial burden of disease. Despite this, basic science research, clinical trials, and approval of new therapies for rare cancers are lacking. The Rare Cancers Genomics team therefore aims to investigate the genomics of these neglected cancers. We have recently provided multi-omic characterizations of rare thoracic cancers1—4. Our results unveiled specialized genomic, transcriptomic, and epigenomic profiles that shape the clinical behavior of the tumors. Therefore, while the gold standard for cancer diagnosis remains histopathological images, there is a need to identify diagnostic and prognostic morphological features, as well as features associated with these clinically-relevant molecular profiles. The Rare Cancers Genomics team is seeking a postdoctoral scientist to develop deep learning and computer vision techniques to integrate `omics and whole-slide images with the aim of understanding the nuanced morphological and molecular changes that signal a shift toward more aggressive cancer phenotypes. Building on the foundation of our richly characterized in-house multi-omics datasets (whole genome, transcriptome, and methylome) from rare thoracic tumors, as well as newly generated single-cell and spatial transcriptomic datasets (10X genomics), this project also aims to extend its analytical reach by incorporating publicly available datasets to explore the broader landscape of rare cancers.
Environment: IARC-WHO is located in the city of Lyon, France — a stunning UNESCO world-heritage city offering exceptional quality of life perfectly embodying the French “art de vivre.” The Rare Cancers Genomics team at IARC-WHO is a multicultural and multidisciplinary team including bioinformaticians, data scientists, and molecular biologists from four different nationalities, piloting large international consortia, and well-supported by multiple competitive grants. It is a vibrant environment ideal for someone willing to pursue an international career in medical bioinformatics or data science to make high-impact contributions and gain experience in state-of-the-art bioinformatics and big data analysis. Team alumni pursued their careers in world-leading medical research institutions (Barcelona Institute for Research in Biomedicine, Lausanne University Hospital, University of Calgary, Stanford University), at IARC-WHO, and in private companies (bioMerieux). IARC welcomes approximately 60 postdoctoral scientists distributed across its research branches. The cost of travel for the postdoctoral scientist will be covered. Dependence and health insurance allowances will be paid, if applicable. For additional information about postdoctoral stays at IARC-WHO, you can consult the postdoctoral charter.
Duties:
The selected candidate will be under the supervision of Matthieu Foll and closely collaborate with other members of the team, as well as the Department of Mathematics and Computer Science from the Ecole Centrale Lyon to enhance their competencies in the following activities: Design and implement deep learning algorithms to analyze and integrate complex datasets including whole-slide images and high-dimensional omics data from rare cancer types, with the aim of unveiling morphologic and molecular markers indicative of cancer aggressiveness.
- – Engage in the rigorous statistical analysis of research data to ensure robust and reproducible results, which extends to the development of novel methodologies as needed to address the unique challenges presented by rare cancer data.
- – Write scientific manuscripts for submission to peer-reviewed journals.
- – Present research findings at internal meetings as well as international conferences, seminars, and symposia.
- – Provide mentorship to junior members of the research team, such as graduate students and research assistants.
Required skills and background:
- – PhD in relevant area (bioinformatics/computational biology, biostatistics, genetics/genomics, computer science)
- – Experience in deep-learning or AI, ideally within a biomedical imaging or omics data analysis context
- – Proficient in programming with Python or R
- – Experience working with Linux HPC and GPU environments
- – Expert knowledge in statistics
- – English proficiency
- – Good communication skills
- – Team player
References: