Mammalian genome editing

1. Mammalian gene writing and gene therapy technologies

We are working on new principles to write long messages into genomes.


  • Gene writing
  • Novel CRISPR systems
  • Directed evolution

2. Bioinformatics for genome editing assessment

We develop analysis pipelines for the analysis and prediction of gene and genome editing experiments.


We are focused, on the one hand, in the screen of integrations on the genome for precise and secure genome engineering. On the other hand, we are interested in the characterization of on-target edition profiles and efficiency. Since reproducibility in bioinformatics can be an issue to overcome, we take care of this in our analysis. We develop pipelines with Nextflow and Docker containers to achieve reproducibility and allow the easy usage of our tools.

Related publications

Find and cut-and-transfer (FiCAT) mammalian genome engineering

Maria Pallarès-Masmitjà+, Dimitrije Ivančić+, Júlia Mir-Pedrol, Jessica Jaraba-Wallace, Tommaso Tagliani, Baldomero Oliva, Amal Rahmeh, Avencia Sánchez-Mejías* & Marc Güell*

Nature Communications 2021
(Horizon 2020, Fundació Ramón Areces)


Microbiome engineering

1. Human microbiome engineering

Our lab is focused on the development of new skin microbiome technologies.

The skin is the largest organ of the human body and is home to millions of microbes. Using diverse tools from genomics and synthetic biology, we seek to engineer the natural adaptability of these microbes. Our approach is to develop biological devices (”biodevices”) able to act as smart drug-delivery systems upon the sensing of relevant skin molecules like pro-inflammatory markers, among others. Our interests span from common acne to chronic inflammatory disorders like Atopic Dermatitis (AD). Specifically, we use Cutibacterium acnes as a stable and robust chassis for synthetic biology in the skin using a wide range of techniques from classic genomics and transcriptomics to cell-free systems and phage engineering.

Related publications

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Nastassia Knoldlseder, Guillermo Nevot, Mariajosé Fábrega, Júlia Mir-Pedrol, Nil Campanà-Sanz, Roolf Lood, Marta Sanvicente and Marc Güell

PLOS Pathogens 2022 in press

DNA Damage Protection for Enhanced Bacterial Survival Under Simulated Low Earth Orbit Environmental Conditions in Escherichia coli

Jaume Puig, Nastassia Knoldlseder, Jaume Quera, Manuel Algara and Marc Güell

frontiers in Microbiology –
Extreme biology section 2021

Establishing a cell-free transcription-translation platform for Cutibacterium acnes to prototype engineered metabolic and synthetic biology

Fabrega, Maria-Jose; Knödlseder, Nastassia; Nevot, Guillermo; Sanvicente, Marta; Toloza, Lorena; Santos-Moreno, Javier; Güell, Marc

ACS Biomaterials Science and Engineering 2021