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A doctoral student is admitted to third-cycle/doctoral education. A doctoral education consists of supervised research, combined with courses and other educational activities. An individual study plan is established for each doctoral student. For a doctoral degree, the equivalent of four years of full-time doctoral education is required.
A doctoral position funded through the Marie Sklodowska-Curie Integrative Training Network ‘aDDRess’ is available in the Crosetto group in the Bienko-Crosetto Laboratory for Quantitative Biology of the Nucleus (https://bienkocrosettolabs.org).
The main research project associated with this position consists in building an atlas of genome fragility in normal and cancer cells, and studying the relationship between genome fragility and DNA copy number alterations in cancer cells.
The primary task of the doctoral student will be developing and applying advanced bioinformatic tools to analyze large datasets obtained through various next-generation sequencing based methods, including the BLISS method which we recently developed to map DNA double-strand breaks genome-wide (Yan et al, Nat Commun 2017). Therefore, this is to be considered as a computational (dry-lab) position.
In addition to carrying on the aforementioned project in the Crosetto lab, the doctoral student will take part to various activities organized by the aDDRess network, and perform one or more short secondments in other network labs
Research group
The Bienko-Crosetto Laboratory is located at SciLifeLab Stockholm (www.scilifelab.se), an interdisciplinary center for life sciences featuring state-of-the-art facilities and a broad range of groups working at the interface between biology, medicine, and computational sciences.
The main scientific interest in the Crosetto group is in understanding why certain parts of the human genome break more often than others, and how DNA transcription and 3D genome architecture influence genome fragility. In particular, we are interested in deciphering how transcription-associated DNA breaks contribute to the formation of DNA copy number alterations and other mutations associated with cancer and neurodevelopmental disorders.
The Bienko-Crosetto lab offers a highly dynamic and interdisciplinary environment where senior scientists, postdocs and students from multiple disciplines—ranging from biology, engineering, physics, and computer science—work closely together on a daily basis. The team currently features seven postdocs (molecular biology, bioinformatics, microscopy, image analysis), seven PhD students, and one lab administrator.
The successful candidate will be immersed in a thriving scientific atmosphere and have the opportunity to join the active SciLifeLab PhD community and interact with peers from three different universities (KI, KTH, SU).
The doctoral education project and the duties of the student
In this project, the doctoral student will pursue three major tasks:
Eligibility requirements for doctoral education
In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.
It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.
You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:
Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.
*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.
You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:
Follow the instructions on the web page English language requirements for doctoral education.
Verification of your documents Karolinska Institutet checks the authenticity of your documents. Karolinska Institutet reserves the right to revoke admission if supporting documents are discovered to be fraudulent. Submission of false documents is a violation of Swedish law and is considered grounds for legal action.
Skills and personal qualities
Proven expertise in standard bioinformatic tools for the analysis of NGS data is mandatory (i.e., the candidate must be able to prove her/his knowledge of Bash scripting, SAMtools, BEDtools, Python including packages such as Biopython, and R including packages for DNA copy number and SNV analysis and visualization). We will prioritize candidates who have previously worked on the analysis of cancer sequencing data, and can demonstrate experience in mining large cancer genome datasets such as those from TCGA and COSMIC. In addition to proven competence with various bioinformatic tools, we require the candidate to have a solid basic knowledge in the fields of cancer genomics and genome integrity, and to be driven by fundamental biological questions rather than solely by affinity towards bioinformatic tools.
A Master Degree in Biomedicine, Biotechnology or equivalent is required. Proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school. Proficiency in the English language can be documented by an internationally recognized test such as TOEFL or IELTS, see web-link below for more information. Applicants who meet the general entry requirements (1 or 2 above) from a university in one of the Nordic countries fulfill the requirements in English. For more information regarding general and specific entry requirements: http://ki.se/en/education/entry-requirements-eligibility-for-doctoral-education
The doctoral student will be employed on a doctoral studentship maximum 4 years full-time.
We are seeking for enthusiastic candidates who are truly passionate and curious about Nature, and have a keen fascination for how the genome is arranged and functions in the cell nucleus. We require candidates to have a strong motivation to work in a highly interdisciplinary and collaborative environment, and willingness to interact with scientists with computational background is mandatory.
Application process
Submit your application and supporting documents through the Varbi recruitment system. Use the button in the top right corner and follow the instructions.
Your application should contain the following documents:
Selection
A selection will be made among eligible applicants on the basis of the ability to benefit from doctoral education. The qualifications of the applicants will be evaluated on an overall basis.
KI uses the following bases of assessment:
All applicants will be informed when the recruitment is completed.
Type of employment | PhD placement |
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Contract type | Full time |
First day of employment | Upon agreement |
Full-time equivalent | 100% |
City | Solna |
County | Stockholms län |
Country | Sweden |
Reference number | 2-3024/2019 |
Contact |
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Union representative |
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Published | 20.May.2019 |
Last application date | 02.Jun.2019 11:59 PM CEST |