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Protein engineering from AI design to preclinical validation.

Biomedical engineer combining computational protein design, wet-lab validation, and translational models across antimicrobial discovery and gene therapy.

Amino acid residues coalescing into a folded protein.
  • Research Officer, CMRI Sydney
  • 20+ publications
  • 300+ citations
  • 2 patents

Publications

20+

Citations

300+

Patents

2

Countries

3

Current position

Research Officer

Children's Medical Research Institute, Sydney

We built a computational platform for antimicrobial peptide discovery — from protein language model predictions to preclinical validation in mouse models — and extended the same approach to AAV capsid engineering for gene therapy.

Protein Language Models

AAV Capsid Engineering

Python & Data Science

Antimicrobial Discovery

Selected research

Selected research

Protein engineering from computational design to preclinical validation, spanning antimicrobial discovery and gene therapy.

01

2024

Molecular Therapy

AAV-mediated CAR-T generation

Evolved AAV capsids that improved targeted CAR-T generation and reduced the vector dose needed for primary T cell editing.

Capsid EvolutionAAVGene Therapy

02

2024

Nature Communications

Normothermic Liver Perfusion

Used whole human liver perfusion to compare AAV vectors in a clinically relevant preclinical model.

PreclinicalAAVTranslational

03

2023

Molecular Therapy Methods & Clinical Development

FRG Mouse Model & AAV-LK03

Characterized the humanized FRG mouse model and developed an AAV-LK03 variant with improved liver lobular biodistribution.

BiodistributionModelsVectorology

Research focus

Finding the therapeutic signal in a sea of biological noise.

Protein Language Models

ESM-2, ProtTrans, pLM-based sequence analysis

AAV Capsid Engineering

Directed evolution, capsid libraries, tropism engineering

Python & Data Science

PyTorch, scikit-learn, pandas, data pipelines

Antimicrobial Discovery

Peptide design, MIC assays, in vivo efficacy

Preclinical Validation

Mouse models, pharmacokinetics, toxicology

Molecular Biology

Cloning, protein expression, functional assays

Experience

Experience and evidence

Three countries, three labs, and a consistent focus on turning sequence-level ideas into experimental proof.

I trained in Biotechnology at UAB Barcelona, took a Master's in Biomedical Engineering at UC Irvine, then returned to UAB for a PhD where we designed antimicrobial proteins end-to-end — from sequence design through recombinant production and functional assays. That stage produced two patents and four first-author papers.

At CMRI Sydney we built a platform to analyse millions of sequences and surface hundreds — sometimes thousands — of new antimicrobial peptides. With protein language models and recent advances in AI, we tested those predictions in the lab and in preclinical models. In parallel we applied generative AI to protein engineering, designing AAV capsids for gene therapy.

  1. 2021 - 2026

    Research Officer

    Children's Medical Research Institute, Sydney

    We built a computational platform for antimicrobial peptide discovery — from protein language model predictions to preclinical validation in mouse models — and extended the same approach to AAV capsid engineering for gene therapy.

  2. 2016 - 2020

    Pre-doctoral Researcher

    UAB & IRTA, Barcelona

    We designed antimicrobial proteins from scratch — cloning, recombinant production, functional assays. Two patents and four first-author papers, eight total.

  3. 2015 - 2016

    Graduate Researcher

    University of California, Irvine

    We tracked estrogen receptor dynamics in living cells with single-molecule fluorescence microscopy and quantitative image analysis.

Discuss a role

Proteins built for the part after prediction.

Open to roles and collaborations where computational design, molecular biology, and translational validation need to work together.

© 2026 Ramon Roca Pinilla. All rights reserved.