# Synthetic Biology & Genome Engineering Domain: Biotechnology & Life Sciences · 317 papers indexed · newest 2026-10-26 Synthetic genomes, genetic circuits, cell-free systems, genome writing and biomanufacturing, plus biosafety and governance considerations. Key concepts: synthetic biology, genetic circuit, cell-free, synthetic genome ## Most influential - **[Synthetic biology: applications come of age](https://space-kitty.com/papers/doi:10.1038/nrg2775)**. Ahmad S. Khalil, James J. Collins · 2010 · Nature Reviews Genetics (doi:10.1038/nrg2775 · 1,381 citations). Source: - **[A synchronized quorum of genetic clocks](https://space-kitty.com/papers/doi:10.1038/nature08753)**. Tal Danino, Octavio Mondragón-Palomino, Lev S. Tsimring et al. · 2010 · Nature (doi:10.1038/nature08753 · 995 citations). Source: - **[Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers](https://space-kitty.com/papers/doi:10.1186/s12951-021-00806-7)**. Nooraei S, Bahrulolum H, Hoseini ZS et al. · 2021 · Journal of nanobiotechnology (doi:10.1186/s12951-021-00806-7 · 623 citations). Source: > Virus-like particles (VLPs) are virus-derived structures made up of one or more different molecules with the ability to self-assemble, mimicking the form and size of a virus particle but lacking the genetic material so they are not capable of infecting the host cell. Expression and self-assembly of the viral structural proteins can take place in various living or cell-free expression systems after which the viral structures can be assembled and reconstructed. VLPs are gaining in popularity in the field of preventive medicine and to date, a wide range of VLP-based candidate vaccines have been d… > _Abstract excerpt by Nooraei S et al., CC-BY, https://doi.org/10.1186/s12951-021-00806-7; truncated._ - **[Protein-Sol: a web tool for predicting protein solubility from sequence](https://space-kitty.com/papers/doi:10.1093/bioinformatics/btx345)**. Hebditch M, Carballo-Amador MA, Charonis S et al. · 2017 · Bioinformatics (Oxford, England) (doi:10.1093/bioinformatics/btx345 · 641 citations). Source: > Motivation Protein solubility is an important property in industrial and therapeutic applications. Prediction is a challenge, despite a growing understanding of the relevant physicochemical properties. Results Protein-Sol is a web server for predicting protein solubility. Using available data for Escherichia coli protein solubility in a cell-free expression system, 35 sequence-based properties are calculated. Feature weights are determined from separation of low and high solubility subsets. The model returns a predicted solubility and an indication of the features which deviate most from avera… > _Abstract excerpt by Hebditch M et al., CC-BY, https://doi.org/10.1093/bioinformatics/btx345; truncated._ - **[Paper-Based Synthetic Gene Networks](https://space-kitty.com/papers/doi:10.1016/j.cell.2014.10.004)**. Keith Pardee, Alexander A. Green, Tom Ferrante et al. · 2014 · Cell (doi:10.1016/j.cell.2014.10.004 · 703 citations). Source: - **[Engineering bacteria as interactive cancer therapies](https://space-kitty.com/papers/doi:10.1126/science.add9667)**. Candice R. Gurbatri, Nicholas Arpaia, Tal Danino · 2022 · Science (doi:10.1126/science.add9667 · 456 citations). Source: - **[Genetic programs constructed from layered logic gates in single cells](https://space-kitty.com/papers/doi:10.1038/nature11516)**. Tae Seok Moon, Chunbo Lou, Alvin Tamsir et al. · 2012 · Nature (doi:10.1038/nature11516 · 581 citations). Source: - **[Synthetic biology to access and expand nature's chemical diversity](https://space-kitty.com/papers/doi:10.1038/nrmicro.2015.24)**. Michael J. Smanski, Hui Ling Zhou, Jan Claesen et al. · 2016 · Nature Reviews Microbiology (doi:10.1038/nrmicro.2015.24 · 483 citations). Source: - **[A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice](https://space-kitty.com/papers/doi:10.1126/science.1203535)**. Haifeng Ye, Marie Daoud‐El Baba, Ren‐Wang Peng et al. · 2011 · Science (doi:10.1126/science.1203535 · 469 citations). Source: - **[Gene-Expressing Liposomes as Synthetic Cells for Molecular Communication Studies](https://space-kitty.com/papers/doi:10.3389/fbioe.2019.00001)**. Giordano Rampioni, Francesca D’Angelo, Livia Leoni et al. · 2019 · Frontiers in Bioengineering and Biotechnology (doi:10.3389/fbioe.2019.00001 · 446 citations). Source: > The bottom-up branch of synthetic biology includes – among others – innovative studies that combine cell-free protein synthesis with liposome technology to generate cell-like systems of minimal complexity, often referred to as synthetic cells. The functions of this type of synthetic cell derive from gene expression, hence they can be programmed in a modular, progressive and customizable manner by means of ad hoc designed genetic circuits. This experimental scenario is rapidly expanding and synthetic cell research already counts numerous successes. Here we present a review focused on the exchan… > _Abstract excerpt by Giordano Rampioni et al., CC-BY, https://doi.org/10.3389/fbioe.2019.00001; truncated._ - **[Synthetic analog computation in living cells](https://space-kitty.com/papers/doi:10.1038/nature12148)**. Ramiz Daniel, Jacob R. Rubens, Rahul Sarpeshkar et al. · 2013 · Nature (doi:10.1038/nature12148 · 456 citations). Source: - **[Cell-free synthetic biology: Thinking outside the cell](https://space-kitty.com/papers/doi:10.1016/j.ymben.2011.09.002)**. C. Eric Hodgman, Michael C. Jewett · 2011 · Metabolic Engineering (doi:10.1016/j.ymben.2011.09.002 · 427 citations). Source: - **[Materials design by synthetic biology](https://space-kitty.com/papers/doi:10.1038/s41578-020-00265-w)**. Tzu‐Chieh Tang, Bolin An, Yuan‐Yuan Huang et al. · 2020 · Nature Reviews Materials (doi:10.1038/s41578-020-00265-w · 389 citations). Source: - **[Guidelines for Genome-Scale Analysis of Biological Rhythms](https://space-kitty.com/papers/doi:10.1177/0748730417728663)**. Hughes ME, Abruzzi KC, Allada R et al. · 2017 · Journal of biological rhythms (doi:10.1177/0748730417728663 · 237 citations). Source: > Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding "big data" that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical… > _Abstract excerpt by Hughes ME et al., CC-BY, https://doi.org/10.1177/0748730417728663; truncated._ - **[Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology](https://space-kitty.com/papers/doi:10.1038/ncomms1516)**. Baojun Wang, Richard Ian Kitney, Nicolas Joly et al. · 2011 · Nature Communications (doi:10.1038/ncomms1516 · 426 citations). Source: ## Newest - **[HELICS: Biobank-scale Conditional Synthetic Genome Generation via Latent Flow Matching](https://space-kitty.com/papers/arxiv:2610.36361)**. Ahmad Abdel-Azim, Xihong Lin · 2026 (arXiv:2610.36361). Source: - **[Proteoliposome Preparation and Functional Reconstitution of Human Mitochondrial Transporters Via Wheat Germ Cell-Free Expression System](https://space-kitty.com/papers/doi:10.1002/cpz1.70500)**. Kharaghani D, Deng H, Su X · 2026 · Current protocols (doi:10.1002/cpz1.70500). Source: - **[Quinoa and Peanut Extracts as Alternatives to Animal-Derived Extracellular Matrix Proteins in Cultured Meat Production](https://space-kitty.com/papers/doi:10.1111/1750-3841.71509)**. Mundt D, Chiu KH, Schillberg S et al. · 2026 · Journal of food science (doi:10.1111/1750-3841.71509). Source: - **[A proof-carrying architecture for synthetic genetic logic circuits under stochastic temporal contracts](https://space-kitty.com/papers/arxiv:2609.38218)**. Arman Ferdowsi, Laura Kovacs · 2026 (arXiv:2609.38218). Source: - **[Characterization of recombinase-based genetic parts and circuits using nanopore sequencing](https://space-kitty.com/papers/doi:10.1038/s41467-026-77605-x)**. Greco FV, Cameron SK, Joshi SH et al. · 2026 · Nature communications (doi:10.1038/s41467-026-77605-x). Source: - **[Let there be multifunctionality: Uncovering the dynamical zoo of the AC-DC genetic circuit](https://space-kitty.com/papers/doi:10.1016/j.cels.2026.101715)**. Maretvadakethope S, Aor I, Fischer MM et al. · 2026 · Cell systems (doi:10.1016/j.cels.2026.101715). Source: - **[From gibson assembly to cell-free expression: A guide to recombinant plasmid and toscana virus N protein production](https://space-kitty.com/papers/doi:10.1016/j.jviromet.2026.115455)**. Dionisi L, De Pascali AM, Ingletto L et al. · 2026 · Journal of virological methods (doi:10.1016/j.jviromet.2026.115455). Source: - **[Radiation-Triggered Chemokine-Secreting Probiotics for Boron Neutron Capture Therapy Based Radioimmunotherapy](https://space-kitty.com/papers/doi:10.1002/advs.77542)**. Liu Y, Qian Y, Huang S et al. · 2026 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) (doi:10.1002/advs.77542). Source: - **[Minimal organism JCVI-syn3.0, an engineered derivative of \Mycoplasma mycoides\, encodes an assortment of unrecognized membrane transporters and immunity factors](https://space-kitty.com/papers/doi:10.1128/msphere.00077-26)**. Mushegian AR, Yamamoto PK, Torikai N et al. · 2026 · mSphere (doi:10.1128/msphere.00077-26). Source: - **[Optimizing RNA yield using deep neural networks coupled to massively parallel screening](https://space-kitty.com/papers/arxiv:2608.23722)**. Dinghai Zheng, Justin Hong, Jun Wang et al. · 2026 (arXiv:2608.23722). Source: --- Space Kitty Archive · https://space-kitty.com · API: https://space-kitty.com/api/v1 · MCP: https://space-kitty.com/mcp · Premium: $0.20/request via x402 (Base Sepolia (testnet)). Metadata: arXiv (CC0), OpenAlex (CC0), Europe PMC (CC BY/CC0 works), ClinicalTrials.gov.