Call for PhD Candidate Vacancies - Disc4All

Centre / Institution:
Pompeu Fabra University
Bioinformatics expertise:
Bioinformatics of Disease and Treatment, Biomedical Informatics, Medical Imaging

Job description

  • Application open for ESR 1: Management of clinical, biological & simulated data for uniform simulation workflows​
    ESR 1 will exploit large research data infrastructure and will be responsible for the systematic treatment and machine interpretability of heterogeneous datasets (organ phenotype, patient condition, molecular signatures, sex & gender, psychological status, known comorbidities, ...), to enable integration of data into holistic disease models and decision support systems.
    HOST: InSilicoTrials, Italy - Secondments: OULU; AQUAS; BSC-CNS - PhD delivered by: UPF - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 31/10/2020

  • Application open for ESR 2: Integrated solvers for bidirectional coupling of physical & biological events over multiple scales
    The ESR will work on creating models and algorithms for simulation of Intervertebral disc degeneration pathologies. The main task will be to develop a multiscale mechanistic modelling software by coupling an Agent Based (AB) simulation solver with a Finite Element(FE) solver for High Performance Computing. The Finite Element solver will be adapted to couple mechanical deformations and solute transport to perform osmoporoviscoelastic simulations, by using the processed MRI data of patient-specific disc geometries. The candidate will be expected to cover the following tasks: 1) Adapt the FE solver Alya to tackle solute transport simulations coupled with porous media finite deformations & with Donnan osmotic swelling; 2) Adapt AB solver Pandora to integrate regulation network and work with 3D meshes; 3) Couple Alya & Pandora over 3D meshes and generate a new multiscale AB-FE solver; 4) Verify and validate the multiscale solver & simulations; 5) Optimize for massive multiscale simulations on HPC; 6) Generate software package & provide initial support for integration into final platform - Host: BSC-CNS, Spain - Secondments: ULG; UBern - PhD delivered by: UPF - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 30/09/2020

  • Application open for ESR 4: Classification of IVD radiological signs and relation with SNP & multi-omics profiles
    The ESR 4 will focus on developing machine learning based prediction and severity assessment models for intervertebral disc (IVD) degeneration. The primary aim will be to combine radiomic features from magnetic resonance (MR) and X-ray images, omics data, and other background data of the patients - in order to discover multiple phenotypes of the IVD degenerative disease. In this project, we will leverage patient material from TwinsUK and Northern Finland Birth Cohort datasets.
    HOST: OULU, Finland - Secondments: Cluster UPF, BSC-CNS, GALGO; PLEXALIS - PhD delivered by: OULU - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 31/10/2020​

  • Application open for ESR 5: 3D modelling of the lumbar spine & automatic extraction of 3D morphological features in LDD
    ERS 5 will address 3D modelling of the lumbar spine from medical images. Methods using deep learning and statistical modelling will be developed to segment the lumbar vertebrae and intervertebral disks in 3D MRI sequences and CT image, and provide 3D subject-specific lumbar spine models from 2D medical images (X-rays or mid-sagital MR images) used in clinical practices. Those methods will be used in combination with finite-element-based simulation methods developed within other ESR14 and 15 to develop a diagnosis and predictive tool for intervertebral disk degeneration.
    HOST: GALGO, Spain - Secondments: OULU; InSilicoTrials - PhD delivered by: UPF - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 15/10/2020​​

  • Pre-application open for ESR 6: GWAS & Microbiome associated with main IVD phenotypes.
    The ESR will provide initial seeds for gene prioritization as well as evidences about the validity of microbiome biomarkers in LDD, by exploiting the data from the TwinsUK and NFBC population cohorts. Candidate gene and GWAS-based approaches will be used to identify novel associations between gene variants and a variety of spine phenotypes. Bioinformatic methods will be further used for general confirmation. In particular, DisGeNET and genetic correlation with known risk factors for LDD will be interrogated. Additionally, the ESR will seek to address the question of whether the gut microbiome differs in people with Modic change. To do this, we will leverage existing MR scans available and collect stools (by post) in a process that has become routine in TwinsUK. HOST: KCL, United Kingdom - Secondments: IMIM, UPF - PhD delivered by: KCL - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 01/11/2020​

  • Pre-application open for ESR 7: Experimental exploration of the microbiome in degenerated IVD
    This doctoral research program will investigate the potential role of infective agents and the microbiome in low back pain. Utilising human intervertebral disc samples from surgery the IVD microbiome will be characterised together with associated microbiome sites using high throughput microbiome sequencing. In vitro co-culture systems will then be deployed to investigate the potential roles of infective agents and the microbiome on disc cell behaviour and implications in the pathogenesis of disc degeneration. Culture systems will be utilised which mimic the cellular niche of human intervertebral disc during disc degeneration.
    HOST: SHU, United Kingdom - Secondments: UBern; ULG - PhD delivered by: SHU - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 01/11/2020​

  • Application open for ESR 9: Standardized in vitro static modelling & mechanism- based analyses of gene /protein /SNP at the cell /tissue & organ levels
    The contribution will consist of standardized in vitro static modelling & mechanism- based analyses of gene /protein / SNP at the cell /tissue & organ levels. The research will be to test physiological conditions using different pre-clinical 3D culture models. Laboratory methods involve qPCR, Western blotting, ELISA, immune-histology and microscopy but also biomechanical testing.
    HOST: UBern, Switzerland - Secondments: SHU; IMIM; RIT - PhD delivered by: UBern - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 20/09/2020

  • Application open for ESR 12: In vitro & In silico modelling of CEP degeneration mechanisms
    ESR12 will be using the mesofluidics setup available at the host institute to test bovine IVD endplates under different fluid regimes defined through FE simulations with endplate micromodels by other partners in the consortium. Experiments consist of testing various biological conditions in the set-up and monitoring the tissue response through multiplex (elisa) and multi-omics (transcriptomics & metabolomics) assays. These experiments will serve to gain a system-level understanding of the interactions taking place in the IVD endplates and validate the computational models developed by other partners in the project.
    HOST: ULG, Belgium - Secondments: UBern; PAO; UPF - PhD delivered by: ULG - Deadline for recruitment: January 2021
    SEE JOB OFFER & APPLY - Deadline: 31/10/2020


Desired skills and expertise

a) To apply for these MSCA Training positions, applicants must fulfil the following criteria:

· Mobility: to be eligible for a position, you should not have resided in the country of the host institution for more than 12 months over the three years before the starting date of the position, excluding holidays and (refugee status) asylum application.

· Early Stage Researcher (ESR): At the time of recruitment by the host organisation, an ESR shall be in the first four years (full-time equivalent research experience) of his/her research career and not have been awarded a doctoral degree.

Candidates must prove that they fulfil the aforementioned criteria through relevant documentation (certificates, official statements, residency card, ...).

b) Applicants will also be required to successfully complete the relevant local application process at the host institution, if applicable (see individual job offers)

c) Specific requirements (see individual job offers for detail):

· Educational Level: MSc degree or equivalent by the time of enrolment

· Required languages: English mandatory

· Skills/Qualifications: See individual job offers

Contract duration and other benefits

The MSCA programme offers a competitive salary and attractive working conditions, in accordance with the MSCA regulations for early stage researchers (See individual job offers). You will be enrolled in the PhD programme of your hiring institution or of its academic partner, if the hiring institution is a company, and you will have the opportunity to learn from a consortium of 19 institutions (11 Beneficiaries, 8 Partner organizations -

In addition to the individual scientific projects, all ESRs will benefit from further continuing education, which includes secondment to other institutions of the Consortium (see individual job offers), a variety of training courses for specific and transferable skills and active participation in international conferences.

In addition to the 36 months full-time employment contract and monthly salary (see individual job offers), successful candidates will be offered an additional mobility and family (if applicable) allowances (see individual job offers) 

Required information and contact

All the documents that prove the eligibility of the candidate and should be provided. As for the selection process candidates are expected to provide at least the following documents:

· A brief introduction letter (no more than one A4 page) that summarizes the documents and the nature of the information provided for the selection

· A full CV

· The three requested reference letters

· The letter of purpose (no more than two A4 pages)

All documents must be sent by email to the Principal Investigator of the proposed project (see individual job offers) and to the Management of the Disc4All project ( before the application deadline (see individual job offers)