synthetic biology papers

Behavioral, Physiological, and Transcriptional Mechanisms of Memory in a Synthetic Living Construct

This study demonstrates that basal Xenobots, synthetic living constructs derived from Xenopus embryonic cells, can exhibit distinct, long-term, stimulus-specific memories through coordinated ciliary activity, calcium signaling, and transcriptional changes following exposure to specific chemical stimuli, thereby establishing a foundation for understanding non-neural information processing in synthetic cellular collectives.

Pai, V. P., Traer, J. A., Sperry, M. M. + 2 more2026-03-17📄 synthetic biology

De novo design of metalloproteases for targeted amyloid-β cleavage

This study demonstrates the successful de novo design of highly specific zinc metalloproteases using the Proteus2 generative model to precisely cleave amyloid-β peptides at targeted sites, offering a promising therapeutic strategy for Alzheimer's disease.

Qu, Y., Wang, C., Zhu, H. + 2 more2026-03-16📄 synthetic biology

Robust Multiplicative Control in Chemical Reaction Networks -Extended Version

This paper proposes a robust chemical reaction network control architecture that achieves steady-state tracking of multiplicative combinations of biomolecular species concentrations, extending the framework to regulate arbitrary monomial outputs and validating the approach through stability analysis and numerical simulations.

Alexis, E., Rowley, C. W., Avalos, J. L.2026-03-16📄 synthetic biology

Programmable bacterial adhesion to plastic surfaces for enhanced biodegradation

This study demonstrates that engineering *Escherichia coli* to overexpress curli or Antigen 43 enables programmable adhesion to various plastic surfaces, which, when combined with the secretion of the PET depolymerase PHL7, significantly enhances the biodegradation of polyethylene terephthalate (PET).

Schneier, A., Armijo-Galdames, B. O., Lau, E. C. H. T. + 1 more2026-03-16📄 synthetic biology

Generative AI-based design of hybrid transcriptional activator proteins with new DNA-binding specificity

This study demonstrates that a variational autoencoder trained on LuxR-family DNA-binding domains can successfully generate hybrid transcriptional activator proteins with novel, dual-promoter recognition capabilities, offering a data-driven strategy to expand the design space of synthetic genetic circuits.

Okuda, S. L., Minami, A., Aiko, M. + 4 more2026-03-13📄 synthetic biology

Continuous hypermutation and evolution of noncanonical amino acid synthases

This study establishes an end-to-end in vivo framework for the continuous evolution of amino acid synthases using OrthoRep and aaRS-based biosensors, enabling yeast to efficiently biosynthesize diverse noncanonical tyrosine analogs from simple precursors to support scalable genetic code expansion.

Furuhata, Y., Rix, G., Almhjell, P. J. + 1 more2026-03-12📄 synthetic biology

Built-in integrated living electronics: from biosynthesis tomodulation of neuronal function

This paper reports a transformative approach where bionic neurons autonomously synthesize integrated fluorescent fibrils that function as neuromodulators, offering a pathway to engineer natural electroactive systems and write connections directly into living brains.

Tommasini, G., Iencharelli, M., Santillo, S. + 13 more2026-03-12📄 synthetic biology

Optimization of the glucosinolate core pathway for production of simple glucosinolates in Escherichia coli

This study demonstrates the optimized microbial biosynthesis of defined glucosinolates in *Escherichia coli* by engineering P450 expression and sulfate assimilation, achieving a 37-fold titer increase for benzyl glucosinolate and establishing the first production of tyrosine-derived glucosinolates with a record 1250 μM yield of indolyl-3-methyl glucosinolate.

Poborsky, M., Crocoll, C., Halkier, B. A.2026-03-12📄 synthetic biology

Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

This study presents Fung-AI, an AI/ML-driven pipeline that successfully generated and experimentally validated novel de novo antifungal peptides with activity against *Fusarium graminearum* and *Candida albicans* and low cytotoxicity, demonstrating a proof-of-concept for rapid antifungal discovery.

Berman, D. S., Lewis, L. M., Curtis, T. D. + 4 more2026-03-10📄 synthetic biology

Reaction-Conditioned Enzyme Discovery with Multimodal Deep Learning

This paper introduces VenusRXN, a multimodal deep learning framework that enables zero-shot discovery of novel enzymes for unreported chemical reactions by directly mapping reaction conditions to protein sequences, successfully identifying active biocatalysts from vast protein spaces where traditional homology-based methods fail.

Tan, P.2026-03-10📄 synthetic biology

Hydration-dehydration cycles drive compartment dynamics in minimal protocells

This study demonstrates that periodic hydration-dehydration cycles alone can drive the growth, division, and content organization of minimal, single-component membrane compartments, proving that complex chemical reactions are not strictly necessary to generate sustained, cell-like dynamics in early protocells.

Zdanowicz, R., Chandramowli, D., De Franceschi, N.2026-03-10📄 synthetic biology

Impact of retroactivity on information flows in engineered synthetic biological circuits

This paper combines stochastic modeling and information theory to demonstrate that while retroactivity in synthetic biological circuits generally constrains information flow and limits the efficacy of gain-based mitigation under noise, it can also be strategically exploited as a functional mechanism to enable controllable state transitions and programmable cellular decision-making.

Moirangthem, S. S., Raman, K.2026-03-06📄 synthetic biology

Automated mini-bioreactors reveal the temporal dynamics and multi-omics responses of CRISPRi knockdowns in Pseudomonas putida

By integrating a tightly regulated CRISPRi system with an automated turbidostat platform in *Pseudomonas putida*, this study establishes a scalable framework that overcomes the temporal limitations of batch cultures to precisely map the physiological dynamics and multi-omics responses of essential gene knockdowns before escaper mutants emerge.

Saavedra, M. A., Grassi, S., Jespersen, M. G. + 5 more2026-03-06📄 synthetic biology

Synthetic Genome Shuffling of Poxviruses through Yeast for Next-Generation Oncolytic Platforms

This study establishes a novel synthetic virology platform using transformation-associated recombination (TAR) in yeast to generate infectious chimeric poxviruses with enhanced and diverse oncolytic properties through the genome shuffling of Vaccinia, Cowpox, Rabbitpox, and Modified Vaccinia Ankara viruses.

Agaoua, A., Rey, C., Hortelano, J. + 3 more2026-03-06📄 synthetic biology

Engineering S. cerevisiae extracellular vesicles using synthetic biology

This study establishes a synthetic biology framework for engineering *Saccharomyces cerevisiae* extracellular vesicles as therapeutic delivery vehicles by developing a modular cloning strategy to identify and validate protein scaffolds, such as the yeast ortholog Bro1, that efficiently sort cargo into yeast EVs.

Bouffard, J., Trani, J., Pawelczak, A. C. + 3 more2026-03-06📄 synthetic biology

Synergistic Multi-Enzyme Cascades Assembled on Modular Protein Scaffolds for Efficient PET Biorecycling

This study presents a modular protein scaffold-based multi-enzyme cascade that synergistically assembles PETase, MHETase, and ICCG to efficiently convert PET waste into monomers while overcoming kinetic limitations and intermediate inhibition, with further applications demonstrated through MOF immobilization, product valorization, and whole-cell biocatalysis.

Zhang, Y., Li, C., Hashemi, E. + 5 more2026-03-04📄 synthetic biology

Fundamental limitations of genomic language models for realistic sequence generation

This study demonstrates that current genomic language models fail to generate realistic synthetic genomes because they capture local sequence statistics but fundamentally lack the ability to preserve essential long-range organization, repetitive elements, and evolutionary constraints, making synthetic sequences easily distinguishable from natural ones.

Tzanakakis, A., Mouratidis, I., Georgakopoulos-Soares, I.2026-03-02📄 synthetic biology

High Diversity Gene Libraries Facilitate Machine Learning Guided Exploration of Fluorescent Protein Sequence Space

This study demonstrates that experimentally expanding training data diversity through large-scale gene synthesis and DNA shuffling enables machine learning models to overcome extrapolation limitations, successfully guiding the discovery of novel functional fluorescent proteins in previously unexplored regions of sequence space.

Benabbas, A., Kearns, P., Billo, A. + 2 more2026-03-02📄 synthetic biology

CADGE 2.0, Transcription-Translation-Coupled DNA Replication is Improved in a Chemically Modified Cell-Free System

The paper demonstrates that the CADGE 2.0 platform achieves robust and efficient clonal amplification of linear DNA in a chemically modified cell-free system by replacing standard energy mixes with optimized, homemade counterparts, thereby overcoming previous limitations in in vitro directed evolution.

Nagai, R., Ramirez, C. C., Abil, Z.2026-03-01📄 synthetic biology

Evaluating AI-Assisted Customer Verification for Synthetic Nucleic Acid Screening

This study demonstrates that AI-assisted verification, specifically using the Gemini 2.5 Pro model integrated with external APIs, can achieve accuracy comparable to human experts in screening synthetic nucleic acid orders while reducing costs by up to 50-fold, supporting a hybrid approach where AI handles information gathering and humans retain final decision-making authority.

Acelas, A., Palya, H., Flyangolts, K. + 2 more2026-03-01📄 synthetic biology

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