PhD thesis in multiscale bacterial and viral epigenomics

 CDD · Thèse  · 36 mois    Bac+5 / Master   CEA - GENOSCOPE · Évry-Courcouronnes (France)

 Date de prise de poste : 2 septembre 2024


epigenomics methylation chromosome conformation


Multiscale characterization of bacterial and viral methylomes

Offer description

Applications are invited from suitably qualified candidates for a full-time fixed term 3-4 year position as a Ph.D. Researcher with the Atomic Energy and Alternative Energies Commission (CEA), Genoscope, France. The Genoscope (French National Sequencing Centre) has a long-standing tradition in the broad field of genomics. After having been one of the players in the human genome project, and supporting more than 650 projects serving the national and international scientific community, it currently focuses on the genomics of environmental organisms (e.g. TARA, BGE, ATLASEA projects), bacterial flora of the human digestive tract, among others. The candidate will benefit from a highly dynamic and interdisciplinary environment, including biologists, microbiologists, computer scientists, and bioinformaticians. This Ph.D. position will be funded pending the successful outcome of a joint candidate / lab application to CEA (CFR fellowships) or to one of the Doctoral Schools of University of Paris-Saclay (ranked in the world’s top 15 universities). The contract is expected to start in September 2024.


Job description

Our team is engaged in better understanding the role of microbial methylation not only as key moderator of the flow of genetic information, but also as essential component for cellular viability and survival in a particular environment [1-6]. Your work will focus on the diversity of bacterial and viral methylomes in complex environmental communities and on the links between methylome and global chromosome structure across multiple bacterial species of interest. This Ph.D. project proposes to use short- and long-read sequencing technologies combined with microbial genetics, and comparative genomics to answer these questions. You will build on a diverse cohort of metagenome sequences as well as key human pathogens, map their MTases, methylomes, and multiple other families of genes encoding mechanisms of transfer and protection against transfer.

1. Oliveira PH et al (2014). Nucleic Acids Res 42(16), 10618-31

2. Oliveira PH et al (2016). Proc Natl Acad Sci USA 113(20), 5658-63

3. Oliveira PH et al (2020). Nat Microbiol 5(1), 166-80

4. Oliveira PH and Fang G (2020). Trends Microbiol 29: 28-40

5. Oliveira PH (2021). mSystems, 6

6. Beavogui et al (2023). Biorxiv DOI: 10.1101/2023.08.12.553040



The successful candidate is expected to:

• Actively participate as a member of the research team and carry out research in microbial epigenomics with a particular emphasis on large-scale computational analysis of methylomes.

• Provide leadership in conducting innovative and independent research, including planning, organizing, execution, and communicating research studies within the overall scope of the research project.

• Assume responsibility for writing critical technical reports, manuscripts for publication and periodic reports as required by the funding agency, present the results of the research in project meetings, seminars and conference presentations as required.

• Assume responsibility for methods development and training of team members as required.

• Maintain research records and documentation in compliance with Good Laboratory Practices.

• Participate in project and lab meetings as required.


Essential Requirements:

• Ph.D. in Biological Sciences, Bioinformatics, or similar.

• Strong, proven track record in working in the integration, interpretation and visualization of large biological datasets.

• Proficiency in UNIX-Linux shell as well as proficiency in at least one of the following programming languages (R/Bioconductor, Python, Perl, C++).

• Experience in working on high performance computing/cluster platforms.

• Demonstrable evidence of published work in the essential areas.

• Excellent verbal and written communication skills.


Procédure : Please send your CV, letter of motivation, and contacts of 3 references to

Date limite : 11 décembre 2023


Pedro H. Oliveira

Offre publiée le 9 novembre 2023, affichage jusqu'au 31 décembre 2023