To decipher the molecular mechanisms of biological function, it is critical to map the molecular composition of individual cells or even more importantly tissue samples in the context of their biological environment in situ. Immunofluorescence (IF) provides specific labeling for molecular prof... Read more
Analysis of the spatial arrangement of molecular features enables the engineering of synthetic nanostructures and the understanding of natural ones. The ability to acquire a comprehensive set of pairwise proximities between components would satisfy an increasing interest in investigating indiv... Read more
Analysis of the spatial arrangement of molecular features enables the engineering of synthetic nanostructures and the understanding of natural ones. The ability to acquire a comprehensive set of pairwise proximities between components would satisfy an increasing interest in investigating indiv... Read more
Signal transduction by receptor tyrosine kinases (RTKs) involves complex ligand- and time-dependent changes in conformation and modification state. High resolution structures are available for individual receptors dimers, but less is known about receptor clusters that form in plasma membranes ... Read more
Signal transduction by receptor tyrosine kinases (RTKs) involves complex ligand-and time- dependent changes in conformation and modification state. High resolution structures are available for individual receptors dimers, but less is known about receptor clusters that form …
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OligoSTORM and OligoDNA-PAINT meld the Oligopaint technology for fluorescent in situ hybridization (FISH) with, respectively, Stochastic Optical Reconstruction Microscopy (STORM) and DNA-based Point Accumulation for Imaging in Nanoscale Topography (DNA …
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OligoSTORM and OligoDNA-PAINT meld the Oligopaint technology for fluorescent in situ hybridization (FISH) with, respectively, Stochastic Optical Reconstruction Microscopy (STORM) and DNA-based Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) to enable in situ single-molecule ... Read more
Two critical challenges in the design and synthesis of molecular robots are modularity and algorithm simplicity. We demonstrate three modular building blocks for a DNA robot that performs cargo sorting at the molecular level. A simple algorithm encoding recognition between cargos and their des... Read more
Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has clear limits. Fully realizing the... Read more
Classical genetic approaches for interpreting variants, such as case-control or co- segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has …
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Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signalling networks. Synthetic silicon-based circuitry similarly relies on spatial constraints to process information. Here, we show that spatial organization can be a similarly powerful desi... Read more
Biological nucleic acids have important roles as diagnostic markers for disease. The detection of just one molecular marker, such as a DNA sequence carrying a single nucleotide variant (SNV), can sometimes be indicative of a disease state. However, a …
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The mathematical formalism of mass-action chemical reaction networks (CRNs) has been proposed as a mid-level programming language for dynamic molecular systems. Several systematic methods for translating CRNs into domain-level strand displacement (DSD) …
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We propose a new abstraction refinement procedure based on machine learning to improve the performance of nonlinear constraint solving algorithms on large-scale problems. The proposed approach decomposes the original set of constraints into smaller subsets, and uses learning algorithms to prop... Read more
Engineering an efficient biomolecular circuit often requires time-consuming iterations of optimization. Cell-free protein expression systems allow rapid testing of biocircuits in vitro, speeding the design-build-test cycle of synthetic biology. In this paper, we combine this with droplet micro... Read more
Synthetic biology aims to develop engineering-driven approaches to the programming of cellular functions that could yield transformative technologies. Synthetic gene circuits that combine DNA, protein, and RNA components have demonstrated a range of functions such as bistability, oscillation, ... Read more
The love affair between crop breeding and genetics began over a century ago and has continued unabated, from mass selection programs to targeted genome modifications. Synthetic genetic circuits, a recent development, are combinations of regulatory and coding DNA introduced into a crop plant to... Read more
We study the tandem duplication distance between binary sequences and their roots. In other words, the quantity of interest is the number of tandem duplication operations of the form ${x} _ {}={a} _ {}{b} _ {}{c} _ {}\to {y} _ {}={a} _ {}{b} _ {}{b} _ {}{c} _ {} $, where ${x} _ {} …
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Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signalling networks. Synthetic silicon-based circuitry similarly relies on spatial constraints to process information. Here, we show that spatial organization can be a similarly powerful desi... Read more
Synthetic gene expression is highly sensitive to intragenic compositional context (promoter structure, spacing regions between promoter and coding sequences, and ribosome binding sites). However, much less is known about the effects of intergenic compositional context (spatial arrangement and ... Read more
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemical reaction networks sample? We begin tackling these questions by showing three ways in …
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The majority of the human genome consists of repeated sequences. An important type of repeated sequences common in the human genome are tandem repeats, where identical copies appear next to each other. For example, in the sequence $ AGTC\underline {TGTG} …
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Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluo... Read more
The love affair between crop breeding and genetics began over a century ago and has continued unabated, from mass selection programs to targeted genome modifications. Synthetic genetic circuits, a recent development, are combinations of regulatory and coding …
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In the context of the ESA M5 (medium mission) call we proposed a new satellite mission, Theia, based on relative astrometry and extreme precision to study the motion of very faint objects in the Universe. Theia is primarily designed to study the local dark matter properties, the existence of E... Read more
