Postdoctoral Researcher in AI-Based Red Fluorescent Proteins

• A fully funded, two-year postdoctoral employment contract with a competitive salary commensurate with experience and in line with Spanish national research funding scales.
• The opportunity to work on a cutting-edge project at the intersection of AI-driven protein engineering, advanced bioimaging and neuroscience, with direct relevance to translational research.
• Access to leading research infrastructure, including advanced microscopy platforms, structural biology facilities and high-performance computing resources at IBF and collaborating institutions.
• An international, collaborative and multidisciplinary research environment, with strong links to academic institutions and industry, including Onava (San Francisco).
• Opportunities to publish in high-impact scientific journals and present research at major international conferences.
• Direct collaboration with AI industry partners and exposure to advanced protein design technologies.
• Dedicated mentoring and support to develop an independent research profile, including guidance on applications for individual fellowships (e.g. Marie Skłodowska-Curie Actions, Juan de la Cierva and Ramón y Cajal programmes) and competitive research funding.

We are seeking a highly motivated and outstanding Postdoctoral Researcher to join the Padilla-Parra Laboratory at Instituto Biofisika (IBF), working at the intersection of artificial intelligence, protein engineering and advanced neuroimaging. (Financial support received from the IKUR Strategy under the collaboration agreement between Ikerbasque Foundation and Fundación Biofísica Bizkaia on behalf of the Department of Science, Universities and Innovation of the Basque Government).

The successful candidate will join an international and multidisciplinary team to design and develop next-generation red and far-red fluorescent proteins (FPs) using state-of-the-art AI-driven protein language models, with direct applications in deep-tissue imaging of the mammalian brain.

The project combines cutting-edge AI-based protein engineering with advanced two- and three-photon microscopy to address a major challenge in neurobiology: developing genetically encoded fluorescent probes with the optical and photophysical properties required for non-invasive imaging deep within brain tissue.

• Apply AI-driven protein language models (ESM3, ProteinMPNN, RFdiffusion, AlphaFold3 and EvoProtGrad) to design novel red and far-red fluorescent protein sequences with improved photophysical properties for deep-tissue imaging.
• Clone, express and purify candidate fluorescent proteins using bacterial and mammalian expression systems, including primary neuronal cultures.
• Perform comprehensive biophysical characterisation, including absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime measurements, photobleaching kinetics and two-photon absorption cross-section measurements.
• Contribute to the structural characterisation of lead fluorescent protein variants in collaboration with structural biology partners.
• Acquire and analyse imaging data from brain tissue sections and intact tissue preparations using two-photon and three-photon microscopy, and develop and apply quantitative image analysis pipelines.
• Co-supervise PhD and Master's students within the Padilla-Parra Laboratory.
• Contribute actively to scientific publications and the preparation of grant applications and funding proposals.
• Present research findings at national and international scientific conferences.

This fully funded, two-year postdoctoral position is supported by a multi-institutional collaboration and is expected to start in January 2027.

The successful candidate will be appointed through a two-year postdoctoral employment contract and will join Instituto Biofisika (IBF).

Red and far-red fluorescent proteins are essential tools for deep-tissue imaging. However, their current photophysical properties remain a limiting factor for two- and three-photon neuroimaging at depth.

This project will apply state-of-the-art protein language models, including ESM3 (Meta), ProteinMPNN, RFdiffusion, AlphaFold3 and EvoProtGrad, to computationally design novel red and far-red fluorescent protein variants with optimised brightness, photostability and two-photon absorption cross-sections for in vivo brain imaging.

The designed candidates will be synthesised, expressed in bacterial and mammalian systems, including primary neuronal cultures, purified and subjected to comprehensive biophysical and structural characterisation. Selected variants will subsequently be evaluated in intact brain tissue using advanced two- and three-photon microscopy.

The project will be conducted in close collaboration with Dr. Pamina Winkler (CIC biomaGUNE, San Sebastián), Dr. Nora Bengoa-Vergniory (Achucarro Basque Center for Neuroscience, Bilbao) and Dr. Sharroll Bachas (CSO, Onava, San Francisco), a company specialising in AI-driven protein engineering. This collaboration provides an exceptional network of scientific and industrial expertise.

1. Eligibility Check

Compliance with formal degree requirements and application completeness.

Pass / Fail

2. Academic Record & CV

Academic excellence, technical background, research experience, scientific publications and overall suitability for the project.

50%

3. Interview

Motivation, scientific reasoning, technical knowledge, communication skills, English proficiency and project fit.

40%

4. Reference Check

Confidential assessment of academic potential, research experience, commitment and teamwork from two or three academic referees.

10%