Biology subjects

Rothemund, P. W. K.

Publications and source records attributed to Rothemund, P. W. K..

4 recordsLinked to original sources

bioRxiv2025

Guided multi-agent AI invents highly accurate, uncertainty-aware transcriptomic aging clocks

Scientific discovery has long relied on human creativity, with computation limited to analysis. Here we report an AI-guided system, K-Dense, that accelerates hypothesis testing and delivers robust scientific discoveries. Trained on ARCHS4 (57,584 samples, 28 tissues, 1,039 cohorts, ages 1-114), the unified ensemble clock achieved R2 = 0.854 and MAE = 4.26 years--while uniquely providing calibrated confidence intervals. This self-aware design flags predictions made at transitional or extreme ages, where biological heterogeneity peaks, suggesting clinical utility for uncertainty itself. Development revealed stage-specific markers, including CDKN2A/p16 (senescence), AMPD3 (muscle wasting), MIR29B2CHG (progeroid traits), and SEPTIN3 (neurodegeneration resistance). Sliding-window analysis across 85 overlapping ranges uncovered wave-like shifts in gene importance, showing that transcriptomic aging signatures evolve continuously, not discretely. By transforming biological age assessment from static point estimates to calibrated predictions with explicit uncertainty, this approach establishes reliable and interpretable clocks. Beyond the clock itself, K-Dense demonstrates how guided AI can compress months of exploration into weeks, pointing toward a scalable framework for accelerated scientific discovery.

systems biology↗

bioRxiv2023

Modular RNA motifs for orthogonal phase separated compartments

Recent discoveries in biology have highlighted the importance of protein and RNA-based condensates as an alternative to classical membrane-bound organelles for the task of compartmentalizing molecules and biochemical reactions. Here, we demonstrate the rational design of pure RNA condensates from star-shaped RNA motifs. We generate condensates using two different RNA nanostar architectures: multi-stranded nanostars whose binding interactions are programmed via single-stranded overhangs, and single-stranded nanostars whose interactions are programmed via kissing loops. Through rational design of the nanostar interaction sequences, we demonstrate that both architectures can produce orthogonal (distinct and immiscible) condensates, which can be individually tracked via fluorogenic aptamers. We also show that aptamers make it possible to recruit peptides and proteins to the condensates with high specificity. Successful cotranscriptional formation of condensates from single-stranded nanostars suggests that they may be genetically encoded and produced in living cells. We provide a library of orthogonal RNA condensates that can be modularly customized and offer a route toward creating systems of functional artificial organelles.

synthetic biology↗

bioRxiv2023

Co-transcriptional production of programmable RNA condensates and synthetic organelles

Condensation of RNA and proteins is central to cellular functions, and the ability to program it would be valuable in synthetic biology and synthetic cell science. Here we introduce a modular platform for engineering synthetic RNA condensates from tailor-made, branched RNA nanostructures that fold and assemble co-transcriptionally. Up to three orthogonal condensates can form simultaneously and selectively accumulate guest molecules. The RNA condensates can be expressed within synthetic cells to produce membrane-less organelles with controlled number, size, morphology and composition, and that display the ability to selectively capture proteins. The in situ expression of programmable RNA condensates could underpin spatial organisation of functionalities in both biological and synthetic cells.

synthetic biology↗

bioRxiv2022

Digital nanoreactors for control over absolute stoichiometry and spatiotemporal behavior of receptors within lipid bilayers

Interactions between membrane proteins are essential for cell survival and proper function, but the structural and mechanistic details of these interactions are often poorly understood. Even the biologically functional ratio of protein components within a multi-subunit membrane complex--the native stoichiometry--is difficult to establish. We have demonstrated digital nanoreactors that can control interactions between lipid-bound molecular receptors along three key dimensions: stoichiometric, spatial, and temporal. Each nanoreactor is based on a DNA origami ring, which both templates the synthesis of a liposome and provides tethering sites for DNA-based receptors. Receptors are released into the liposomal membrane using strand displacement and a DNA logic gate measures receptor heterodimer formation. High-efficiency tethering of receptors enables the kinetics of receptors in 1:1 and 2:2 absolute stoichiometries to be observed by bulk fluorescence in a plate reader which in principle is generalizable to any ratio. Similar single molecule in bulk experiments using DNA-linked membrane proteins could determine native stoichiometry and the kinetics of membrane protein interactions for applications ranging from signalling research to drug discovery.

bioengineering↗