Ph.D. in Microbial Epigenomics

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. Your work will focus on the functional roles of DNA methyltransferases and on the links between methylome, DNA topology, and the clinical success of certain human pathogens. This doctoral 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 the genome sequence of a large cohort of clinical isolates of 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(1):28-40
5. Oliveira (2021). mSystems 6 
6. Beavogui et al (2024). Nature Comms 15:2146
 
Duties 
The successful candidate will carry out the following:
 
·       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.
 
 

Applications are invited from suitably qualified candidates for a full-time fixed term 3-year position (+1 year extension possible) as a Ph.D. Researcher with the Atomic Energy and Alternative Energies Commission, 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 scientific community, it currently focuses on the genomics of environmental organisms (e.g. TARA, ERGA 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.
 

Essential Requirements
·       MSc 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. 
·       Excellent verbal and written communication skills.