Search Results - "Pierce, Niles A."

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust by Choi, Harry M T, Schwarzkopf, Maayan, Fornace, Mark E, Acharya, Aneesh, Artavanis, Georgios, Stegmaier, Johannes, Cunha, Alexandre, Pierce, Niles A

“…hybridization based on the mechanism of the hybridization chain reaction (HCR) has addressed multi-decade challenges that impeded imaging of mRNA expression in…”
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Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability by Choi, Harry M. T, Beck, Victor A, Pierce, Niles A

“…Hybridization chain reaction (HCR) provides multiplexed, isothermal, enzyme-free, molecular signal amplification in diverse settings. Within intact vertebrate…”
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Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing by Shah, Sheel, Lubeck, Eric, Schwarzkopf, Maayan, He, Ting-Fang, Greenbaum, Alon, Sohn, Chang Ho, Lignell, Antti, Choi, Harry M T, Gradinaru, Viviana, Pierce, Niles A, Cai, Long

“…Accurate and robust detection of mRNA molecules in thick tissue samples can reveal gene expression patterns in single cells within their native environment…”
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Programmable in situ amplification for multiplexed imaging of mRNA expression by Pierce, Niles A, Choi, Harry M T, Chang, Joann Y, Trinh, Le A, Padilla, Jennifer E, Fraser, Scott E

“…In situ hybridization methods enable the mapping of mRNA expression within intact biological samples. With current approaches, it is challenging to…”
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Programming biomolecular self-assembly pathways by Pierce, Niles A, Yin, Peng, Choi, Harry M. T, Calvert, Colby R

“…In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic…”
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Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering by Wolfe, Brian R, Porubsky, Nicholas J, Zadeh, Joseph N, Dirks, Robert M, Pierce, Niles A

“…We describe a framework for designing the sequences of multiple nucleic acid strands intended to hybridize in solution via a prescribed reaction pathway…”
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Nucleic acid sequence design via efficient ensemble defect optimization by Zadeh, Joseph N., Wolfe, Brian R., Pierce, Niles A.

“…We describe an algorithm for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at…”
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Triggered Amplification by Hybridization Chain Reaction by Dirks, Robert M., Pierce, Niles A., Mayo, Stephen L.

“…We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the…”
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Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology by Hanewich-Hollatz, Mikhail H, Chen, Zhewei, Hochrein, Lisa M, Huang, Jining, Pierce, Niles A

“…A guide RNA (gRNA) directs the function of a CRISPR protein effector to a target gene of choice, providing a versatile programmable platform for engineering…”
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A Synthetic DNA Walker for Molecular Transport by Shin, Jong-Shik, Pierce, Niles A

“…Inspired by kinesin movement along a microtubule, we demonstrate a processive bipedal DNA walker. Powered by externally controlled DNA fuel strands, the walker…”
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Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos by Trivedi, Vikas, Choi, Harry M T, Fraser, Scott E, Pierce, Niles A

“…For decades, hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA…”
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An autonomous polymerization motor powered by DNA hybridization by Pierce, Niles A, Venkataraman, Suvir, Dirks, Robert M, Rothemund, Paul W. K, Winfree, Erik

“…We present a synthetic molecular motor capable of autonomous nanoscale transport in solution. Inspired by bacterial pathogens such as Rickettsia rickettsii,…”
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Thermodynamic Analysis of Interacting Nucleic Acid Strands by Dirks, Robert M., Bois, Justin S., Schaeffer, Joseph M., Winfree, Erik, Pierce, Niles A.

“…Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an…”
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A partition function algorithm for nucleic acid secondary structure including pseudoknots by Dirks, Robert M., Pierce, Niles A.

“…Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure…”
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Selective cell death mediated by small conditional RNAs by Venkataraman, Suvir, Dirks, Robert M., Ueda, Christine T., Pierce, Niles A.

“…Cancer cells are characterized by genetic mutations that deregulate cell proliferation and suppress cell death. To arrest the uncontrolled replication of…”
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Multiplexed miRNA northern blots via hybridization chain reaction by Schwarzkopf, Maayan, Pierce, Niles A

“…Northern blots enable detection of a target RNA of interest in a biological sample using standard benchtop equipment. miRNAs are the most challenging targets…”
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Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology by Hochrein, Lisa M, Ge, Tianjia J, Schwarzkopf, Maayan, Pierce, Niles A

“…Dynamic RNA nanotechnology with small conditional RNAs (scRNAs) offers a promising conceptual approach to introducing synthetic regulatory links into…”
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An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots by Dirks, Robert M., Pierce, Niles A.

“…Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of…”
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An introduction to the adjoint approach to design by GILES, Michael B, PIERCE, Niles A

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Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy by Rosenthal, Adam Z., Zhang, Xinning, Lucey, Kaitlyn S., Ottesen, Elizabeth A., Trivedi, Vikas, Choi, Harry M. T., Pierce, Niles A., Leadbetter, Jared R.

“…Identifying microbes responsible for particular environmental functions is challenging, given that most environments contain an uncultivated microbial…”
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