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# Publications

## The latest publications from the Molecular Programming Project.

#### Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues

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...

#### A DNA nanoscope via auto-cycling proximity recording.

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...

#### A DNA nanoscope via auto-cycling proximity recording

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...

#### Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane.

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 ...

#### Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane

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 situ super-resolution imaging of genomic DNA with oligoSTORM and oligoDNA-PAINT

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 …

#### In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT.

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 ...

#### A cargo-sorting DNA robot

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...

#### Variant Interpretation: Functional Assays to the Rescue.

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...

#### Variant interpretation: functional assays to the rescue

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 …

#### A spatially localized architecture for fast and modular DNA computing

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...

#### A DNA Neural Network Constructed from Molecular Variable Gain Amplifiers

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 …

#### A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities

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) …

#### Learning-Based Abstractions for Nonlinear Constraint Solving

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...

#### Cell-free extract based optimization of biomolecular circuits with droplet microfluidics.

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...

#### Complex cellular logic computation using ribocomputing devices

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, ...

#### Synthetic genetic circuits in crop plants.

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...

#### Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA.

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...