The European community requires early stage researchers (ESRs) who can work across the boundaries of traditional disciplines, integrating experimental and in silico approaches to understand and manage highly prevalent multifactorial disorders, such as musculoskeletal disorders. The Disc4All training network utilises intervertebral disc degeneration (LDD) leading to low back pain (LBP) as a relevant application for the integration of data and computational simulations in translational medicine, to enable rational interpretations of the complexity of the interactions that eventually lead to symptoms.
Open Positions for Early Stage Researchers (ESR)
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
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