CNRS PhD in Computational Systems Biology: A Multiscale Retinal Digital Twin for AMD

CNRS PhD in Computational Systems Biology: A Multiscale Retinal Digital Twin for AMD

Quick Decision

How can a model connect molecular changes in age-related macular degeneration (AMD) to cell interactions and retinal tissue behaviour, while keeping computational predictions distinct from experimental validation? PANDORA DC8 tackles this multiscale problem by linking molecular-interaction maps, Boolean models, consortium omics data and agent-based modelling. It suits an applicant with substantial systems-biology or bioinformatics modelling experience. The MSCA network provides the scientific and funding setting; personal mobility eligibility, French immigration, doctoral registration and net pay still require individual confirmation. PANDORA CORDIS fact sheet MSCA Doctoral Networks guidance The CNRS recruitment record cited here lists a 36-month full-time doctoral contract (35 hours per week) in Toulouse, a 1 February 2027 start and EUR 3,630.25 gross per month. The deadline is 10 November 2026 00:00. The role record specifies UTC, while the cited CNRS recruitment text gives 00:00 without identifying a time zone. Since 00:00 is the start of that date, confirm the governing time zone and submit before 10 November at 00:00 in that zone; do not treat the date as a full application day. CNRS job offer Excellent English is a stated requirement. A separate qualification record lists basic French, while the CNRS recruitment text cited here emphasizes English. Confirm whether basic French applies to onboarding, lab work or doctoral registration; it should not be treated as an independently confirmed mandatory threshold. CNRS job offer

Research Problem and Doctoral Work

What is unsolved and why it matters

The advertised project addresses AMD, complement-system biology and therapy optimisation through computational modelling. The CNRS project description characterises AMD as a complex disease whose pathological mechanisms are not fully understood, making it suitable for systems-level modelling. The doctoral work is not simply “AI for ophthalmology”: it is mechanistic and multi-scale. The candidate is expected to construct large retinal molecular-interaction maps linked to AMD and the complement system, convert them into executable Boolean models using a map-to-model framework, contextualise them with consortium omics data, and integrate them into an agent-based model that simulates intercellular communication and tissue homeostasis. CNRS job offer The translational aim is to compare in silico predictions with in vitro data from PANDORA partners and then use the model to prioritise new therapeutic targets for experimental validation. That makes the project valuable for applicants who want a thesis where modelling generates testable biomedical hypotheses rather than only descriptive data analysis. Data delivery, partner timelines and validation protocols are material points to clarify. Before accepting, ask which omics datasets, in vitro models and AMD perturbation experiments are expected to be available during the 36-month contract. CNRS job offer

Work, methods and potential outputs

The likely doctoral outputs are a curated AMD/complement molecular-interaction map, executable Boolean models, contextualised omics-driven model variants, an ABM layer for cell/tissue interactions, and ranked hypotheses for therapeutic reorientation. The official offer says the host laboratory has recently developed technology scaling Boolean models up to 1,000 biomolecules and ABM models to thousands of agents. This is a strong technical platform signal, but it should be read as lab capability, not as a guarantee that the doctoral model will include every relevant retinal cell type or all AMD mechanisms. CNRS job offer PANDORA’s CORDIS profile supports the scientific setting: the network focuses on complement-mediated AMD pathomechanisms, therapy development, omics, imaging, model systems, biomarkers and drug discovery. This aligns well with a DC8 project focused on computational integration and target prioritisation. PANDORA CORDIS fact sheet

Supervisor and Lab Assessment

Supervisor research directions

The named supervisor is Professor Anna Niarakis. CBI’s official profile identifies her as a professor of computational systems biology with expertise in complex human diseases, disease maps, tool development for model inference, network integration, dynamical modelling and immune digital twins. The CoSysBio page she leads describes digital twins and computational models for complex human pathologies, including omics, data integration and predictive modelling. This is a close match to the advertised AMD digital-twin work. Anna Niarakis CBI profile Computational Systems Biology Hub The wider environment is credible for interdisciplinary biology. CBI describes itself as a CNRS and University of Toulouse centre for integrative biology with more than 400 people, research teams, platforms and support services. Its Computational and Systems Biology axis explicitly promotes quantitative and modelling approaches at the interface of biology, physics, computer science, statistics and mathematics. CBI Toulouse CBI Computational and Systems Biology axis

Recent important publications

Three papers offer methodological context, not direct validation of an AMD retinal model. The saved materials do not give the complete author order, so this report does not infer Niarakis’s individual contribution from those papers. Rheumatoid-arthritis and immune-system models remain distinct from AMD.

A 2023 npj Systems Biology and Applications paper co-authored by Niarakis built a large-scale Boolean model of rheumatoid arthritis fibroblast-like synoviocytes and used it for drug-synergy and drug-repurposing predictions. This is directly relevant to the project’s use of executable disease maps and target prioritisation. Boolean model drug-synergy paper A 2024 npj Systems Biology and Applications paper on immune digital twins discusses applications, limitations and implementation challenges for immune-system digital twins. It matters here because AMD/complement modelling will face similar problems: multiscale biological representation, model credibility, data integration, and the gap between a computational twin and experimentally validated intervention. Immune digital twins paper A 2024 npj Digital Medicine paper on a modular and multi-cellular virtual twin of the synovial joint shows the group’s recent movement from single-network models toward multi-cellular virtual-twin architectures. That is useful prior art for this project’s plan to integrate Boolean models into agent-based multi-scale models. Virtual twin paper

School, Programme and Field Context

CNRS is a strong research-employer signal. Its official profile presents it as a major worldwide basic-research organisation active across all scientific fields, with a large budget, staff base and laboratory network. For a doctoral applicant, the relevant strength is less a university ranking and more the CNRS/University of Toulouse/CBI research setting and the MSCA network connection. CNRS profile CBI Toulouse The likely doctoral registration path needs verification. The CNRS vacancy identifies CBI as a joint CNRS–University of Toulouse unit, while University of Toulouse doctoral pages explain that first enrolment requires doctoral-school approval, a complete file, fee payment and administrative validation. The 2026-27 doctorate registration fee shown on Toulouse doctoral guidance is 398 EUR, but the exact enrolling institution and doctoral school for this offer should be confirmed with the supervisor or HR. University of Toulouse doctoral registration Science PhD enrolment The field context is positive. France has an active digital-health innovation strategy, and OECD discussion of AI in healthcare highlights life-science innovation, computational biology and drug-development use cases. The project’s mix of disease modelling, bioinformatics, digital twins, omics and drug repurposing fits that direction, although the immediate academic niche remains specialised. France 2030 digital health strategy OECD AI in healthcare

Funding, Application and Living Cost

The project is materially better funded than a standard French doctoral minimum. The CNRS recruitment page cited for this role states 3,630.25 EUR gross per month for 36 months, plus 44 days annual leave/RTT, remote-work practice/compensation, 75% public-transport reimbursement and a sustainable mobility allowance up to 300 EUR. CNRS’s general doctoral contract salary context is lower, which reinforces that the project-specific CNRS page is the source to rely on for this position. CNRS job offer CNRS compensation page For a Chinese applicant, the eligibility boundary is favourable but not automatic. MSCA Doctoral Networks generally recruit doctoral candidates of any nationality, but candidates must satisfy the mobility rule: they must not have lived or carried out their main activity in France for more than 12 months during the 36 months before recruitment, and they must not already hold a doctoral degree at the date of recruitment. A Chinese citizen living in China or another non-French country will usually pass the nationality side, but prior study/work in France must be counted carefully. MSCA Doctoral Networks guidance MSCA Doctoral Networks 2026 guide The salary and an appropriate hosting agreement provide grounds to assess a French researcher-residence route, but neither guarantees approval. French national doctoral guidance and Campus France describe the researcher-talent route for foreign doctoral candidates/researchers with funding or a work contract and a hosting agreement. Service-Public also states that the research talent residence card requires a hosting agreement with an approved body. Research hosting agreement Campus France researcher-talent visa Service-Public talent card Use the stated salary as a starting point for a personal budget. Campus France gives a general French student reference of EUR 600–800 per month for food, transport and housing; Toulouse housing guides and Crous tariffs describe lower-cost options subject to availability. That student reference is not an employee budget or a guarantee of affordable housing. Confirm net pay, social charges, any family allowance, relocation costs and first-month deposits from the CNRS contract and an actual housing offer. Campus France cost of life Campus France Toulouse housing guide Crous Toulouse rent tariffs

Applicant Fit and Preparation

Required background and skills

The strongest applicant profile is a master’s-level candidate in bioinformatics, computational biology, systems biology, quantitative biology, computer science, applied mathematics or a close field, with demonstrated programming in Python, R or similar. The application should show network biology, mathematical modelling and/or omics data analysis, plus enough cellular and molecular biology to work with AMD/complement biology rather than treating biology as a black box. CNRS job offer The CNRS recruitment text cited here requires excellent spoken and written English and presentation skills. Logical/Boolean modelling, agent-based modelling, molecular-interaction maps, complement biology, ocular biology and therapeutic reorientation are advantages. A separate qualification record lists basic French; candidates should ask whether this applies to HR/onboarding, lab work or doctoral registration. CNRS job offer

Preferred preparation

The highest-value preparation is a short, concrete modelling portfolio: one Boolean/logical model, one omics or network-analysis example, one reproducible Python/R workflow, and a concise explanation of how model predictions were validated or could be validated experimentally. A candidate with strong wet-lab biology but weak coding should treat the role as high risk; a candidate with strong computer science but no molecular/cell biology should show evidence of learning complement biology, retinal disease or disease-map curation before applying. Computational Systems Biology Hub Boolean model drug-synergy paper

Next Actions and Questions to Verify

Before applying, confirm the deadline time zone: “10 November 2026 00:00” is the start of the stated date, while the role record specifies UTC. Submit before 10 November at 00:00 in the confirmed governing time zone. Also ask whether the separately listed basic French requirement applies. CNRS job offer At interview, ask which PANDORA datasets will be available in year one, what in vitro validation data will arrive from partners, how much secondment travel is expected, and whether the thesis is registered with University of Toulouse under a specific doctoral school. Also ask how the ABM and Boolean layers are divided across the student, supervisor, INRIA/CNRS collaborators and consortium partners. Before accepting an offer, verify the full CNRS contract: gross-to-net salary, MSCA allowances, family allowance if applicable, social-security deductions, visa/hosting-agreement timeline, doctoral-registration fee responsibility, relocation timing, publication-review rules and data-sharing constraints. These are execution risks rather than reasons to reject the opportunity.

Evidence and Sources

Current application status has not been checked; confirm the vacancy and submission route with CNRS. The cited papers provide methodological context only and do not establish that the planned AMD model has been validated. The saved materials do not give the complete author order, so individual author contributions are not assessed.

Key Official Project Source

• CNRS job offer
• CNRS profile
• CBI Toulouse
• Computational Systems Biology Hub
• Anna Niarakis CBI profile
• PANDORA CORDIS fact sheet
• MSCA Doctoral Networks guidance
• MSCA Doctoral Networks 2026 guide
• Research hosting agreement
• Boolean model drug-synergy paper
• Immune digital twins paper
• Virtual twin paper
• Campus France cost of life
• Campus France Toulouse housing guide
• Crous Toulouse rent tariffs

Additional project and methods sources

• CNRS job offer French version
• Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology