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ChromDesign-ITN: Integration of experimental data into a single framework to 3D genomics models (subproject ESR3); Hosting institution: National Center for Genomic Analysis (CNAG-CRG) / National Genome Sequencing Centre, Barcelona, Spain

Project Description

"ChromDesign” is a European innovative and interdisciplinary Research and Training network, which aims to characterize the impact of the 3D chromatin organization on gene regulation during cellular differentiation and in several human disorders, and to train junior researchers in the biomedical field, either in academia or in the private sector. The "ChromDesign" training programme will foster mobility across countries, disciplines and sectors. Through secondments and network-events, we will ensure that all ESRs have opportunities for exposure to different disciplines and environments: academia, industry, design and communication, hospitals, publishing, and non-for-profit funding entities. Most network training will be based around five summer and winter schools that combine hands-on research workshops, academic lectures as well as transferable skills, and innovation and entrepreneurship training sessions.

Description subproject ESR3:

Develop a single framework to model 3D genomes based on diverse datasets obtained by ESRs. The global aim will be accomplished with 3 objectives:
1. Proper genome description/representation.
2. Implementation of new restraints types to represent the input data.
3. Development of new sampling strategies to identify the minima that satisfies the input restraints.

Computational development of a Python modules to TADbit for the use of diverse and additional input restraints.

Expected Results
An updated TADbit module to deal with diverse datasets interrogating the genome structure. The resulting methods and software will be used within the ETN for modelling genomes and genomic domains.

Planned Secondments:
FMI, Switzerland (3 months): Imaging
EMBL, Germany (3 months): Hi-C experiments
ELISAVA, Spain (1 month): Design of new ways of representing genomes
MPIMG, Germany (4 months): Analysis of genetic alterations

Eligibility criteria:

• Applicants may be a national of a Member State, of an Associated Country or of any other third country.

• The candidate should hold an academic degree that enables her/him to undertake doctoral studies. Preference is given to applicants with MSc or equivalent degree.

• At the time of recruitment* by the host organisation, candidates must be in the first four years (full-time equivalent research experience**) of their research careers and not yet have been awarded a doctoral degree.

• At the time of recruitment* by the host organisation, candidates must not have resided or carried out their main activity (work, studies, etc.) in the country of their host organisation for more than 12 months in the 3 years immediately prior to the reference date.


Funding Notes

• Depending on the hosting institute, individual projects start between November 2018 and August 2019.

• The positions are fully funded for 36 months by the European Comission under the H2020 Marie Curie Innovative Training Network Programme.

• Marie Curie ITNs provide a highly competitive salary to the ESR, including a competitive monthly living and mobility allowance and (if eligible) a monthly family allowance.


Goodstadt, M. & Marti-Renom, M. A. Challenges for visualizing three-dimensional data in genomic browsers. FEBS Lett 591, 2505-2519, doi:10.1002/1873-3468.12778 (2017).

Serra, F. et al. Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors. PLoS Comput Biol 13, e1005665, doi:10.1371/journal.pcbi.1005665 (2017).

Trussart, M. et al. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Res 43, 3465-3477, doi:10.1093/nar/gkv221 (2015).

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