Filippo Caschera

Maria's paper on characterizing trans-properties of transcription factors and how they affect gene expression is out now!

www.biorxiv.org/content/10.6...

First preprint from my PhD work!

We changed the chemical composition of cell-free (PURE) gene expression reactions to support robust replication of linear DNA templates.

This system is based on the protein-primed Phi29 phage DNA replication machinery. We saw over 3000-fold amplification of DNA!

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

Combinatorial optimization of synthetic cells

www.biorxiv.org/content/10.6...

A portable orthogonal replication system enables continuous gene evolution near the biological speed limit

www.biorxiv.org/content/10.6...

The Role of Glycan Structures in Modulating GM-CSF Bioactivity: Insights from Glycoengineering www.biorxiv.org/content/10.6...

From cells to companies: Study shows how diversity scales within complex systems A new study in PNAS introduces a mathematical model that quantifies how different systems, from cells to organizations, diversify and specialize as they grow. The study finds that while systems vary i...

A new study by SFI and MIT researchers shows that as systems grow, from cells to governments, the pace of adding new functions steadily slows. Though they vary in how much they invest in novelty, once new functions exist, subsequent growth follows a universal pattern known as sublinear growth.

Programmable RNA detection generates DNA barcodes for multiplexed phage-host interaction screening https://www.biorxiv.org/content/10.64898/2026.02.13.705812v1

High-throughput methods leveraging robotics and computer vision for the development of therapeutic phage cocktails

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

Efficient Preparation of Homogenous Antibody Conjugates via Glycosite‐Specific Transglycosylation Enabled by Readily Available Glycosyl Donors A streamlined platform for glycosite-specific antibody conjugation is enabled by LacNAc-derived cyclic acetal donors, which can be prepared in only two steps and used directly in single-enzyme Endo S....

Efficient Preparation of Homogenous Antibody Conjugates via Glycosite‐Specific Transglycosylation Enabled by Readily Available Glycosyl Donors - onlinelibrary.wiley.com/doi/full/10....

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

Receptor Proteins: Lipids challenge ligands to control receptors The behaviour of a receptor protein can be influenced by the presence of certain lipids in the membrane it is embedded in.

doi.org/10.7554/eLif...

Structural ontogeny of protein-protein interactions Understanding how protein binding sites evolve interactions with other proteins could hold clues to targeting “undruggable” surfaces. We used synthetic coevolution to engineer new interactions between...

www.science.org/doi/10.1126/...

Artificial Recombination of Nonribosomal Peptide Synthetases Rapidly Evolves Natural Products https://www.biorxiv.org/content/10.64898/2026.02.09.704528v1

Integrated microdroplet workflow for high-throughput cell-free transcription in double emulsion picoreactors www.biorxiv.org/content/10.1...

Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT-2 and Flex In synthetic biology, DNA assembly is a routine process where increasing demands for standardization, high-throughput capacity, and error-free execution are driving the development of accessible, auto...

Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT-2 and Flex | ACS Synthetic Biology pubs.acs.org/doi/10.1021/...

Prototyping Minimal Extracellular Vesicle Mimetics Using Cell-Free Synthesis The many surface proteins on extracellular vesicles (EVs) allow them to target recipient cells and modulate cellular responses. Despite their importance, relating surface protein and EV function is ch...

Prototyping Minimal Extracellular Vesicle Mimetics Using Cell-Free Synthesis | ACS Nano pubs.acs.org/doi/10.1021/...

The status of extracellular vesicles as drug carriers and therapeutics - Nature Reviews Bioengineering Extracellular vesicles (EVs) are emerging as biocompatible carriers for targeted drug delivery, yet challenges in yield, cargo loading and biodistribution persist. In this Review, key trends from over...

www.nature.com/articles/s44...

An AI-Native Biofoundry for Autonomous Enzyme Engineering: Integrating Active Learning with Automated Experimentation

www.biorxiv.org/content/10.6...

Topological reprogramming transforms an integral membrane oligosaccharyltransferase into a water-soluble glycosylation catalyst https://www.biorxiv.org/content/10.64898/2026.01.30.702934v1

journals.plos.org/plosbiology/...

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

A continuous viral vaccine biomanufacturing platform utilizing multiple bioreactor configurations Scalable, continuous biomanufacturing processes have grown in importance to meet demand for smaller bioreactor sizes, lowered production costs, and improved quality attributes. The Sf9/recombinant bac...

www.biorxiv.org/content/10.6...

A Guide to Bayesian Optimization in Bioprocess Engineering Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small data sets, and provi...

analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...

Molecular systems engineering of synthetic cells

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

Enhanced tRNA array method version 2 for simultaneous in vitro synthesis of 21 tRNAs Transfer RNAs (tRNAs) play an essential role in translation, and their simultaneous in vitro synthesis remains a key challenge in bottom-up synthetic biology. We previously developed the tRNA array me...

www.biorxiv.org/content/10.6...

If you are looking to integrate your latest genetic creation into the genome of your favourite bug, you might find our latest review now out in OUP Synthetic Biology useful. 🧬⚒️ Work led by Riesa Rohmat with input from Thea Irvine and Shivang Joshi. #genome #synbio doi.org/10.1093/synb...

Harnessing protein-folding algorithms to drug intrinsically disordered epitopes Due to their lack of a specific structure and dynamical nature, targeting of epitopes that are part of an intrinsically disordered region of a protein is a notoriously difficult task. Here, we describ...

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

The Role of Intrinsically Disordered Domains in Regulating G Protein-Coupled Receptor Signaling The α2A adrenergic receptor (α2AAR) is a clinically important target for various diseases including hypertension, diabetes, and chronic pain. Here, using single-molecule fluorescence resonance energy ...

pubs.acs.org/doi/10.1021/...

Planning and scheduling biological experiments across multiple liquid handling robots https://www.biorxiv.org/content/10.64898/2025.12.26.696584v1