Filippo Caschera

Latest #CDlab paper on nanopore protein sequencing on @biorxivpreprint.bsky.social: www.biorxiv.org/cgi/content/...

Here, Justas Ritmejeris, @xiuqichen.bsky.social, collaborator @albadalab.bsky.social and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!

That looks big 📊 🙌🏼 🧬 ✂️

Genome synthesis, assembly, and rebooting of therapeutically useful high G+C% mycobacteriophages | PNAS Bacteriophages show therapeutic promise for treating bacterial pathogens including nontuberculous mycobacteria (NTM). A major impediment is the pau...

Genome synthesis, assembly, and rebooting of therapeutically useful high G+C% mycobacteriophages | PNAS www.pnas.org/doi/10.1073/...

High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria - Nature Structural & Molecular Biology Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...

www.nature.com/articles/s41...

Synthetic Rewiring of Virus-like Particles via Circular Permutation Enables Modular Peptide Display and Protein Encapsulation Virus-like particles (VLPs) are self-assembling nanoparticles derived from viruses with the potential as scaffolds for myriad applications. They are also excellent testbeds for engineering protein sup...

Synthetic Rewiring of Virus-like Particles via Circular Permutation Enables Modular Peptide Display and Protein Encapsulation | ACS Nano pubs.acs.org/doi/10.1021/...

Mapping the evolution of computationally designed protein binders Computational protein design enables the generation of binders that target specific epitopes on proteins. However, current approaches often require substantial screening from which hits require furthe...

www.biorxiv.org/content/10.1...

Modular generation of multispecific antibodies using protein trans-splicing Multispecific antibodies are exhibiting rapid growth in drug development due to their ability to engage multiple therapeutic targets and deliver unique functional properties inaccessible to convent...

www.tandfonline.com/doi/full/10....

QuantGUV: Quantifying Encapsulation Efficiency of Small Molecules in GUVs https://www.biorxiv.org/content/10.1101/2025.10.23.684161v1

Predicting the conformational flexibility of antibody and T cell receptor complementarity-determining regions - Nature Machine Intelligence ALL-conformations, a dataset capturing the full range of experimentally observed conformations of CDR loops, T cell and antibody regions interacting with antigen targets, is introduced. ITsFlexible—a ...

www.nature.com/articles/s42...

Automated Cell-free Protein Synthesis for Distributed Biomanufacturing Recombinant proteins are fundamental to modern medicine, enabling research, diagnostics, and drug discovery, yet their access is often restricted by centralized manufacturing and cold-chain distributi...

Automated Cell-free Protein Synthesis for Distributed Biomanufacturing
www.medrxiv.org/content/10.1...

Assembly and cell-free expression of a partial genome for the synthetic cell https://www.biorxiv.org/content/10.1101/2025.10.16.682769v1

Metabolomics-informed coarse-grained model enables prediction of cell-free protein expression dynamics Cell-free expression systems have gained considerable attention for their potential in biomanufac-turing, biosensing, and circuit prototyping. All these endeavors make use of the innate metabolic acti...

Metabolomics-informed coarse-grained model enables prediction of cell-free protein expression dynamics www.biorxiv.org/content/10.1...

Generative design of antibody Fc-variants with synthetic and programmable functional profiles Beyond antigen recognition, antibodies direct diverse immune effector functions through their constant (Fc) domain. While the Fc domain is central to antibody biology and therapeutic efficacy, our und...

Generative design of antibody Fc-variants with synthetic and programmable functional profiles
www.biorxiv.org/content/10.1...

A generative artificial intelligence approach for the discovery of antimicrobial peptides against multidrug-resistant bacteria - Nature Microbiology This study presents a generative artificial intelligence approach for the high-throughput discovery of antimicrobials against multidrug-resistant bacteria.

A generative artificial intelligence approach for the discovery of antimicrobial peptides against multidrug-resistant bacteria www.nature.com/articles/s41...

Split inteins for generating combinatorial non-ribosomal peptide libraries https://www.biorxiv.org/content/10.1101/2025.10.02.680031v1

Cell-free opens a unique test-bed to reconstituteand to explore alternative life possibilities.

Check our review (by Maud Hofmann, Farouk Abdo, @manishmicrobe and myself) :

Reconstituting alternative life using the test-bed of cell-free systems
doi.org/10.1098/rstb...

Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections - Nature Microbiology The Entelli-02 phage product containing five phages has frontline potential to address infections caused by the multidrug-resistant Enterobacter cloacae complex.

Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections www.nature.com/articles/s41...

Improved Therapeutic Antibody Reformatting through Multimodal Machine Learning Modern therapeutic antibody design often involves composing multi-part assemblages of individual functional domains, each of which may be derived from a different source or engineered independently. W...

Improved Therapeutic Antibody Reformatting through Multimodal Machine Learning
arxiv.org/abs/2509.196...

Cell-free recombinase-integrated Boolean output system Chen et al. present CRIBOS, a large-scale recombinase-based logic platform for cell-free systems. They define key circuit design rules, demonstrate portable paper-based logic devices, and enable long-...

Cell-free recombinase-integrated Boolean output system: Cell Systems www.cell.com/cell-systems...

An AI-driven Workflow for Accelerated Optimization of Cell-Free Protein Synthesis Cell-free protein synthesis (CFPS) is a versatile tool for rapid biological prototyping. However, exploring the large number of component combinations…

www.sciencedirect.com/science/arti...

Hollow-fibre biomanufacturing and cell-free engineering of HEK293 extracellular vesicles https://www.biorxiv.org/content/10.1101/2025.09.20.677537v1

Generative design of novel bacteriophages with genome language models Many important biological functions arise not from single genes, but from complex interactions encoded by entire genomes. Genome language models have emerged as a promising strategy for designing biol...

Generative design of novel bacteriophages with genome language models www.biorxiv.org/content/10.1...

Microsystem technologies for accelerating the discovery and translation of immunotherapies - Nature Reviews Drug Discovery The potential of microsystem technologies to accelerate the development and clinical translation of immunotherapies is now being realized. This Review discusses recent advances in microsystem technolo...

Microsystem technologies for accelerating the discovery and translation of immunotherapies www.nature.com/articles/s41...

The diversity of PET degrading enzymes: A systematic review of sequence, structure, and function Polyethylene terephthalate (PET) is one of the most significant plastic pollutants. Unlike other plastic polymers, PET can be degraded by PET-hydrolytic enzymes (PETases). Over the past two decades, ....

onlinelibrary.wiley.com/doi/full/10....

Characterizing Cell-Free Transcription and Translation Dynamics with Nucleic Acid-Based Assays https://www.biorxiv.org/content/10.1101/2025.09.10.675373v1

Development of a nonreplicative phage-based DNA delivery system and its application to antimicrobial therapies:

academic.oup.com/pnasnexus/ar...

How safe is your mind in a world flooded with junk information? Yuval Noah Harari warns that unlike past media, AI-driven networks never rest, blurring the boundaries between us and digital reality. He calls to preserve your autonomy as AI becomes more unpredictable  www.youtube.com/watch?v=K1Ov...

Cryo-EM structure of a cell-free synthesized full-length human β1-adrenergic receptor in complex with Gs Truncated derivatives of G protein coupled receptors are often studied to avoid recombinant production problems. Merino et al. implemented cell-free synthesis in E. coli lysates to obtain the full-len...

Cryo-EM structure of a cell-free synthesized full-length human β1-adrenergic receptor in complex with Gs: Structure www.cell.com/structure/fu...

Online monitoring of the mitochondrial respiration activity and protein formation in the Almost Living Cell-free Expression (ALiCE) system - BMC Biotechnology Cell-free protein synthesis (CFPS) is one approach to address the increasing demand for complex recombinant proteins in various applications, especially in the pharmaceutical sector. CFPS offers a var...

Online monitoring of the mitochondrial respiration activity and protein formation in the Almost Living Cell-free Expression (ALiCE) system
bmcbiotechnol.biomedcentral.com/articles/10....

Refinement of OnePot PURE and Crude Ribosome Production for Reproducible Cell-free Protein Synthesis

app.jove.com/t/68826/refi...