Offer Description
The principal objective of DANIO-ReCODE is to provide world-class doctoral training to a new generation of early-career researchers interested in understanding the complex and multilayered process of tissue regeneration. DANIO-ReCODE will combine the multidisciplinary expertise of 15 research laboratories at renowned EU and UK scientific institutions to unravel the regulatory mechanisms of heart, brain, and eye regeneration by employing the unique and highly tractable zebrafish model system. Unlike humans, teleosts can repair damaged tissues or even regrow entire appendages. In mammals, regeneration is rare, limited to skin, liver, and toes. Regenerative medicine, however, promises to restore tissue function via the use of stem cells, tissue engineering, and the production of artificial organs, with its importance being recognised as one of the EU strategic missions. A fundamental gap of knowledge is the understanding of the shared and distinct regulatory mechanisms defining regeneration in highly regenerative species and those with lower regeneration potential such as mammals. Since the vertebrate gene complement is highly conserved, applying the knowledge of regeneration mechanisms from non-mammalian models such as zebrafish could identify genetic underpinnings, which when manipulated in mammals, could strongly boost the mammalian regenerative potential. DANIO-ReCODE will thus nurture a cohort of exceptional doctoral candidates and turn them into interdisciplinary experts in computational and developmental biology, providing comprehensive training that spans experimental work, bioinformatics, visualisation, and industry applications. Through the integration of state-of-the-art genomics, computational, and data visualisation techniques, DANIO-ReCODE will result in an enhanced understanding of molecular determinants implicated in vertebrate regenerative processes while providing new avenues for the repair or replacement of damaged or diseased tissues and organs.
The list of individual positions and lead contacts is provided below:
DC1: Cis-regulation during in vivo and in vitro organ development
Partner: Spanish National Research Council (Andalusian Centre for Developmental Biology, Seville, Spain)
Lead PI: Ozren Bogdanovic (obog@upo.es)
Regenerative medicine relies heavily on organoid research to be able to accurately recapitulate organ development in vitro and to ultimately use such organs to replace diseased or ageing ones. Reproducible morphology is currently the main landmark used to rank organoid formation; however, the epigenetic landscape of the organ representing underlying genomic activity states, should also be reproduced in order to obtain representative and functional organoid differentiation. Mammalian organoids have the limitation of long developmental times and the lack of an in vivo model for direct reference. The doctoral candidate will tackle this question by comparing the profiles of regulatory elements in vivo (embryo) versus in vitro, in zebrafish eye organoids, by performing single cell multiome, histone modification, and base-resolution DNA methylome profiling. Overall, the candidate will integrate these data to identify a core set of gene-regulatory regions that drive optimal eye development in vitro.
DC2: Identification of cis-regulatory elements that support optimal eye organoid morphogenesis
Partner: Spanish National Research Council (Andalusian Centre for Developmental Biology, Seville, Spain)
Lead PI: Maria Almuedo Castillo (malmcas@upo.es)
Differentiation, regeneration and other morphogenetic processes crucially depend on the mechanical forces acting on differentiating cells. The doctoral candidate will investigate how the mechanical state of zebrafish eye organoids translates into changes in epigenetic patterning and find which matrix compositions better support the in vivo epigenetic state. The candidate will first modify the tensional forces of eye organoids by: 1) modification of YAP signalling, and 2) the use of ferrofluidic droplets to alter the mechanical integrity of the tissue. The changes in epigenetic signatures in response to these perturbations will be analysed by RNA-seq, ATAC-seq and WGBS to identify specific gene regulatory regions of the chromatin that adapt to changes in those cell-extrinsic mechanical inputs. The candidate will use these mechanically sensitive gene regulatory regions to explore which matrices or alternative synthetic hydrogels mimic better the in vivo gene-regulatory state. This approach will permit for the efficient selection of settings that support optimal organoid morphogenesis.
DC3: Deciphering molecular mechanisms underlying successful brain regeneration in zebrafish
Partner: Karlsruhe Institute of Technology, Karlsruhe, Germany
Lead PI: Sepand Rastegar (sepand.rastegar@kit.edu)
Our lab is offering a PhD position for a project aimed at identifying key genes involved in the regeneration of the nervous system in zebrafish, with a specific focus on the adult telencephalon. This project will employ advanced techniques such as ATAC-seq and CAGE-seq to identify regulatory sequences responsible for transcriptional regulation during both constitutive and regenerative neurogenesis. The ultimate goal is to decipher the signaling pathways that control these regenerative events.
DC4: Characterisation of cis-regulatory networks in cardiac muscle de- and re-differentiation in heart regeneration
Partner: University Hospital Schleswig-Holstein/ Christian Albrecht University Kiel, Kiel, Germany
Lead PI: Daniela Panakova (Daniela.Panakova@uksh.de)
During heart regeneration, dedifferentiated and newly proliferated cardiomyocytes re-differentiate and integrate with existing heart muscle cells. A key question is whether the same genetic programs, including cis-regulatory elements (CREs) that control cardiac muscle differentiation during development, are reactivated in the heart regeneration process. In this project, the doctoral candidate will generate new datasets and analyze existing ones from bulk and single-cell RNA sequencing (scRNA-seq) and ATAC-seq of isolated cardiomyocytes from developing zebrafish embryos and regenerating adult zebrafish hearts. The candidate will also explore and compare the CREs and downstream transcriptional targets activated in developing versus regenerating cardiomyocytes using integrative genomics and imaging techniques.
DC5: Promoter architecture and usage during zebrafish, axolotl, and mouse regenerative neurogenesis
Partner: Ruder Boskovic Institute, Zagreb, Croatia
Lead PI: Damir Baranasic (damir.baranasic@lms.mrc.ac.uk)
This position focuses on conducting cutting-edge research in comparative genomics and computational biology to investigate promoter architecture during adult and regenerative neurogenesis in zebrafish, mice, and axolotl. The candidate will use advanced ML techniques and AI to interpret CAGE-seq data on the regulatory mechanisms involved in gene expression during neurogenesis. The goal is to uncover the commonalities and differences in these processes across species, contributing to a deeper understanding of vertebrate regenerative capabilities.
DC6: Novel approaches to integrate genomic information from model organisms into human regulatory landscapes
Partner: Ruđer Bošković Institute, Zagreb, Croatia
Lead PI: Anja Baresic (abaresic@irb.hr)
This position focuses on integrating multiomics data from model organisms into human disease and phenotype contexts. The researcher will develop innovative visualization methods to map single-cell, DNA methylation, and other genomic datasets against known human disease and phenotype information. They will enhance existing web resources by adding regulatory features related to development and regeneration, providing a human-centric perspective. Additionally, the researcher will generate and prioritize novel hypotheses regarding regulatory elements involved in human diseases, subsequently validated in collaboration with experimental partners. The work will bridge insights from model organisms to human health, driving forward our understanding of disease mechanisms.
DC7: Identifying the gene regulatory code for regeneration
Partner: Institute of Molecular Biotechnology, Vienna, Austria
Lead PI: Elly Tanaka (elly.tanaka@imp.ac.at)
Axolotls have the remarkable ability to regenerate multiple body parts. Interestingly, we have observed some genes that are commonly up regulated across different regenerating organs. We will use advanced chromatin profiling and bioinformatics methods, including comparison across species to identify the conserved and non-conserved gene regulatory elements that initiate regeneration.
DC8: Deciphering molecular programs regulating the reversible quiescence of mammalian neural stem cells
Partner: Universidad de Valencia, Valencia, Spain
Lead PI: Isabel Fariñas (Isabel.Farinas@uv.es)
Our lab is offering a PhD position for a project aimed at identifying gene expression programs involved in the transitions of neural stem cells from quiescence to activation and back in the mouse brain. This project will employ advanced techniques such as Single-cell Nucleosome, Methylome and Transcriptome (scNMT-seq) to characterize chromatin accessibility, methylome and transcriptome at the single cell level in neural stem cells at different states of activation. The ultimate goal is to identify molecular mechanisms and gene expression programs involved in the regulation of reversible quiescence.
DC9: Conversational AI for exploring complex data in tissue regeneration research
Partner: University of Ljubljana, Ljubljana, Slovenia
Lead PI: Blaz Zupan (bzupan@gmail.com)
In this PhD project, you will develop an AI-powered chatbot to transform how researchers interact with complex, heterogeneous data in regenerative biology. You will work on creating a literature-focused chatbot that integrates scientific references, build tools to chat about project-specific data, such as gene expression patterns, and design solutions for integrating diverse data sources, including literature, datasets, and biological knowledge bases, into a cohesive, interactive platform. Your work will empower biologists studying tissue regeneration, such as heart, brain, and eye regeneration, by providing them with faster access to data, more efficient generation of insights, and advanced visualization tools, ultimately enhancing their ability to unravel the complex mechanisms underlying regenerative processes.
DC10: An innovative genome browser to integrate time-resolved single-cell and bulk-cell data
Partner: University of Tübingen, Tübingen, Germany
Lead PI: Kay Nieselt (kay.nieselt@uni-tuebingen.de)
A fundamental visualisation strategy for genomics and abundance multi-omics data is a genome browser. The basic feature of genome browser is that a reference sequence provides a coordinate system, and that any annotation as well as any experimental data mappable to genomic coordinates can be visualised. Typical genome browsers lack the ability to visualise single cell datasets. Furthermore, time-series data are difficult to represent in genome browsers. In this PhD project novel genome browser approaches for the combined visualisation of time-resolved single-cell and bulk data shall be developed and implemented. This will be applied to bulk and single-cell CAGE, RNA-seq and ATAC-seq data generated in the DANIO-ReCODE training network to enhance the understanding of vertebrate regenerative processes.
DC11: Novel solutions for combining multi-omics embeddings and regulatory network visualisations
Partner: Johannes Kepler University Linz, Linz, Austria
Lead PIs: Marc Streit (marc.streit@jku.at), Andreas Hinterreiter (andreas.hinterreiter@jku.at)
This project aims at developing novel, hybrid embedding algorithms to visualize regulatory network data as low-dimensional representations. These algorithms should combine the information from high-dimensional data attributes and from topological network relationships. Additionally, the project aims at designing visual enrichment techniques and interactions that help users interpret these low-dimensional representations effectively.
DC12: Annotation, characterisation, and conservation of 3D chromatin topology in telencephalon injury
Partner: University of Birmingham, Birmingham, UK
Lead PI: Csilla Varnai (c.varnai@bham.ac.uk)
The aim of this position is to understand the role of chromatin topology in the regeneration of injured telencephalon in adult zebrafish. The doctoral candidate will analyse Hi-C and PCHi-C data in injured telencephalon in adult zebrafish to identify regeneration specific chromatin topology. She/he will use data integration methods for Hi-C, single-cell epigenomics and CAGE-seq data to characterise the chromatin topology around genes implicated in regeneration focusing on cis-regulatory interactions. The candidate will also use comparative analysis of chromatin topology between zebrafish and mouse, to study the conservation of chromatin topology around genes implicated in tissue regeneration.
DC13: Multi-omic characterisation of transcription initiation regulation in development and injury response
Partner: University of Birmingham, Birmingham, UK
Lead PI: Ferenc Mueller (f.mueller@bham.ac.uk)
In this project the student will work in a team formed by an international, interdisciplinary consortium to explore the transcription regulatory landscape and codes of transcription initiation variation in developmental and neural injury models. The student will learn developmental gene manipulation in zebrafish, single cell genomics technologies, computational analyses of multi-omic datasets to study promoter level regulation of normal development and injury response.
DC14: Comparative epigenomics of vertebrate regeneration
Partner: Imperial College London, London, UK
Lead PI: Boris Lenhard (b.lenhard@imperial.ac.uk)
This project explores the regulatory genomics underlying vertebrate regeneration, aiming to uncover shared and distinct mechanisms with embryonic development. Through a comparative approach, the project will investigate highly conserved regulatory features, integrating experimental data across species to generate and test hypotheses on the fundamental properties of gene regulation in embryonic development and its evolution. The student will engage in cutting-edge research combining computational genomics, statistics, and machine learning, with opportunities for cross-disciplinary training within a collaborative international network. This work will contribute to creating an atlas of key regulatory genes and pathways involved in regeneration and development, with the potential to revolutionise our understanding of these biological processes.
DC15: Cross-species cell atlases for regeneration
Partner: Earlham Institute, Norwich, UK
Lead PI: Irene Papatheodorou (Irene.Papatheodorou@earlham.ac.uk)
This project will aim to develop comprehensive cell atlases of regeneration in three different species, zebrafish, mouse and axolotl. The doctoral candidate will integrate single cell transcriptomic as well as epigenetic data to assemble the atlases within each species and to compare cell types and regulatory processes across species. The project will use data generated by our partners within the DANIO-ReCODE doctoral network, as well as publicly available datasets. It will be fully computational and will aim to further advance our methods in cross-species comparisons of transcriptomics data sets, as well as develop new methods for identifying conserved or divergent key cell types and
Website
https://danio-recode.eu/available-positions/
Additional Information
Benefits
The DANIO-ReCODE MSCA Doctoral Network will provide a prestigious platform for Doctoral Candidates (DCs), offering a wealth of benefits that will help them excel academically, professionally, and personally. Those include:
1. International and Interdisciplinary Exposure
Global Research Network: DANIO-ReCODE brings together universities, research institutions, and companies across Europe and UK, thus enabling the PhD candidates to work within a collaborative environment that spans national and disciplinary boundaries.
Multidisciplinary Projects: The program encourages interdisciplinary approaches, allowing candidates to tackle research problems from various perspectives and gain expertise across fields.
Cultural Exchange and Networking: Working internationally, DCs will build a strong network with peers, mentors, and industry professionals from diverse cultural and academic backgrounds.
2. Industry-Driven and Hands-On Experience
Non-Academic Partners: DANIO-ReCODE DCs will collaborate with private sector companies, thus fostering practical industry engagement. This collaboration prepares students to apply their research in real-world scenarios.
Professional Development: DCs will work on projects that will allow them to gain practical insights, enhancing employability, and learning skills highly valued outside academia.
3. Comprehensive Research Training
Structured Training Program: DANIO-ReCODE DN will provide formal training in both research-specific skills (e.g., laboratory techniques, advanced analysis tools) and transferable skills (e.g., project management, entrepreneurship, communication).
Secondments and Mobility: DCs will spend time at other partner institutions or companies, gaining exposure to different research environments and methodologies.
4. Attractive Financial Package
Generous Funding: MSCA PhDs come with competitive salaries, which include living, mobility, and family allowances.
Funding for Research Costs: The program includes funding for materials, travel, and conference participation, which enables DCs to attend international events and share their work.
5. Enhanced Career Prospects
Global Recognition: MSCA fellowships are widely recognized and respected, making graduates more attractive to potential employers, both in academia and industry.
Skill Development: MSCA's focus on transferable skills and real-world applications prepares PhD holders for diverse career paths, increasing their versatility and adaptability in the job market.
6. Personal Growth and Development
Cultural and Linguistic Immersion: The international setting fostered by the DANIO-ReCODE DN encourages personal growth, adaptability, and language skills, fostering resilience and global understanding.
Supportive Research Community: DANIO-ReCODE DN will provide strong mentorship and a supportive environment, with clear structures in place for guidance, feedback, and career advice.
7. Commitment to Equality and Inclusivity
Diversity and Inclusion: MSCA Doctoral Networks emphasize inclusivity and gender equality, creating an environment that supports underrepresented groups and encourages participation across demographics.
Work-Life Balance: The program promotes a healthy work-life balance, ensuring students have the flexibility needed for both professional and personal pursuits.
8. Increased Visibility and Dissemination Opportunities
Publication and Presentation Support: DANIO-ReCODE DCs will have the opportunity to present research at high-profile conferences, increasing candidates' visibility within their field.
Public Engagement: DANIO-ReCODE DN will teach and encourage DCs to communicate their research to the public, improving their outreach skills and fostering greater societal impact.
Overall, the DANIO-ReCODE DN will offer an exceptionally well-rounded PhD experience, equipping students with the knowledge, skills, and networks necessary to excel in both academic and non-academic careers.
Eligibility criteria
Please note that the following rules apply:
At the time of first recruitment by the host organisation, researchers must not have resided or carried out their main activity (work, studies, etc. ) in the country of their host organisation for more than twelve months in the three years immediately before the reference date.
All researchers recruited in a DN must be doctoral candidates (i.e. not already in possession of a doctoral degree at the date of the recruitment).
Selection process
Unless specified otherwise on the https://danio-recode.eu/available-positions/ webpage, applicants should apply directly to the lead Principal Investigator (PI) of the project they are interested in, using the email contact provided above. Applications should include:
1) A CV
2) A motivation letter with a brief description of a recent project that the applicant has worked on
3) Academic transcriptsAdditional comments
For general inquiries, please contact daniorecode@csic.es
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