@article{https://authors.library.caltech.edu/records/5tqf9-jve59, title = "Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction", journal = "ACS Chemical Biology", year = "2024", url = "https://authors.library.caltech.edu/records/5tqf9-jve59", id = "record", issn = "1554-8929", doi = "10.1021/acschembio.3c00431", volume = "19", pmcid = "PMC10877569" } @article{https://authors.library.caltech.edu/records/hncah-g5h50, title = "HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples", journal = "Development", year = "2024", url = "https://authors.library.caltech.edu/records/hncah-g5h50", id = "record", issn = "0950-1991", doi = "10.1242/dev.202307", volume = "151", pmcid = "PMC10941662" } @other{https://resolver.caltech.edu/CaltechAUTHORS:20230324-864239000.6, title = "NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems", year = "2023", url = "https://resolver.caltech.edu/CaltechAUTHORS:20230324-864239000.6", id = "record", doi = "10.26434/chemrxiv-2022-xv98l" } @other{https://resolver.caltech.edu/CaltechAUTHORS:20230322-367067000.13, title = "HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing", year = "2023", url = "https://resolver.caltech.edu/CaltechAUTHORS:20230322-367067000.13", id = "record", doi = "10.1101/2022.09.18.508442" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20230227-258668000.1, title = "Hybridization Chain Reaction Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing", journal = "ACS Infectious Diseases", year = "2023", url = "https://resolver.caltech.edu/CaltechAUTHORS:20230227-258668000.1", id = "record", issn = "2373-8227", doi = "10.1021/acsinfecdis.2c00472", volume = "9", pmcid = "PMC9924079" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20220808-223919000, title = "Looking on the Horizon; Potential and Unique Approaches to Developing Radiation Countermeasures for Deep Space Travel", journal = "Life Sciences in Space Research", year = "2022", url = "https://resolver.caltech.edu/CaltechAUTHORS:20220808-223919000", id = "record", issn = "2214-5524", doi = "10.1016/j.lssr.2022.08.003", volume = "35" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20210604-111535359, title = "Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization", journal = "Development", year = "2021", url = "https://resolver.caltech.edu/CaltechAUTHORS:20210604-111535359", id = "record", issn = "0950-1991", doi = "10.1242/dev.199847", volume = "148", pmcid = "PMC8645210" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20210503-115702708, title = "High-Performance Allosteric Conditional Guide RNAs for Mammalian Cell-Selective Regulation of CRISPR/Cas", journal = "ACS Synthetic Biology", year = "2021", url = "https://resolver.caltech.edu/CaltechAUTHORS:20210503-115702708", id = "record", issn = "2161-5063", doi = "10.1021/acssynbio.1c00037", volume = "10" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20200911-133138429, title = "A Unified Dynamic Programming Framework for the Analysis of Interacting Nucleic Acid Strands: Enhanced Models, Scalability, and Speed", journal = "ACS Synthetic Biology", year = "2020", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200911-133138429", id = "record", issn = "2161-5063", doi = "10.1021/acssynbio.9b00523", volume = "9" } @inbook{https://resolver.caltech.edu/CaltechAUTHORS:20200518-144322691, title = "In Situ Hybridization Protocols", chapter = "Multiplexed Quantitative In Situ Hybridization for Mammalian or Bacterial Cells in Suspension: qHCR Flow Cytometry (v3.0)", year = "2020", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200518-144322691", id = "record", isbn = "978-1-0716-0622-3", doi = "10.1007/978-1-0716-0623-0\_8" } @inbook{https://resolver.caltech.edu/CaltechAUTHORS:20200518-142723478, title = "In Situ Hybridization Protocols", chapter = "Multiplexed Quantitative In Situ Hybridization with Subcellular or Single-Molecule Resolution Within Whole-Mount Vertebrate Embryos: qHCR and dHCR Imaging (v3.0)", year = "2020", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200518-142723478", id = "record", isbn = "978-1-0716-0622-3", doi = "10.1007/978-1-0716-0623-0\_10" } @inbook{https://resolver.caltech.edu/CaltechAUTHORS:20200518-143331174, title = "In Situ Hybridization Protocols", chapter = "Multiplexed Quantitative In Situ Hybridization for Mammalian Cells on a Slide: qHCR and dHCR Imaging (v3.0)", year = "2020", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200518-143331174", id = "record", isbn = "978-1-0716-0622-3", doi = "10.1007/978-1-0716-0623-0\_9" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20190123-124341981, title = "Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology", journal = "ACS Central Science", year = "2019", url = "https://resolver.caltech.edu/CaltechAUTHORS:20190123-124341981", id = "record", issn = "2374-7943", doi = "10.1021/acscentsci.9b00340", volume = "5", pmcid = "PMC6661866" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20181030-075958683, title = "Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology", journal = "ACS Synthetic Biology", year = "2018", url = "https://resolver.caltech.edu/CaltechAUTHORS:20181030-075958683", id = "record", issn = "2161-5063", doi = "10.1021/acssynbio.8b00424", volume = "7", pmcid = "PMC6305621" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20180702-084055324, title = "Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust", journal = "Development", year = "2018", url = "https://resolver.caltech.edu/CaltechAUTHORS:20180702-084055324", id = "record", issn = "0950-1991", doi = "10.1242/dev.165753", volume = "145", pmcid = "PMC6031405" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20180110-083122477, title = "Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos", journal = "Development", year = "2018", url = "https://resolver.caltech.edu/CaltechAUTHORS:20180110-083122477", id = "record", issn = "0950-1991", doi = "10.1242/dev.156869", volume = "145", pmcid = "PMC5825878" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170213-164458132, title = "Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering", journal = "Journal of the American Chemical Society", year = "2017", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170213-164458132", id = "record", issn = "0002-7863", doi = "10.1021/jacs.6b12693", volume = "139" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20161011-070233463, title = "Mapping a multiplexed zoo of mRNA expression", journal = "Development", year = "2016", url = "https://resolver.caltech.edu/CaltechAUTHORS:20161011-070233463", id = "record", issn = "0950-1991", doi = "10.1242/dev.140137", volume = "143", pmcid = "PMC5087610" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20160610-141528257, title = "Multiplexed miRNA northern blots via hybridization chain reaction", journal = "Nucleic Acids Research", year = "2016", url = "https://resolver.caltech.edu/CaltechAUTHORS:20160610-141528257", id = "record", issn = "0305-1048", doi = "10.1093/nar/gkw503", volume = "44", pmcid = "PMC5009741" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20160628-085406782, title = "Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing", journal = "Development", year = "2016", url = "https://resolver.caltech.edu/CaltechAUTHORS:20160628-085406782", id = "record", issn = "0950-1991", doi = "10.1242/dev.138560", volume = "143", pmcid = "PMC5004914" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20141027-090434819, title = "Sequence Design for a Test Tube of Interacting Nucleic Acid Strands", journal = "ACS Synthetic Biology", year = "2015", url = "https://resolver.caltech.edu/CaltechAUTHORS:20141027-090434819", id = "record", issn = "2161-5063", doi = "10.1021/sb5002196", volume = "4" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20150311-133810360, title = "Combinatorial Analysis of mRNA Expression Patterns in Mouse Embryos Using Hybridization Chain Reaction", journal = "Cold Spring Harbor Protocols", year = "2015", url = "https://resolver.caltech.edu/CaltechAUTHORS:20150311-133810360", id = "record", issn = "1940-3402", doi = "10.1101/pdb.prot083832", volume = "2015" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20141013-100900538, title = "Multiplexed In Situ Hybridization Using Hybridization Chain Reaction", journal = "Zebrafish", year = "2014", url = "https://resolver.caltech.edu/CaltechAUTHORS:20141013-100900538", id = "record", issn = "1557-8542", doi = "10.1089/zeb.2014.1501", volume = "11" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140919-101701968, title = "Exquisite Sequence Selectivity with Small Conditional RNAs", journal = "Nano Letters", year = "2014", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140919-101701968", id = "record", issn = "1530-6984", doi = "10.1021/nl501593r", volume = "14", pmcid = "PMC4134187" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140414-095156294, title = "Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability", journal = "ACS Nano", year = "2014", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140414-095156294", id = "record", issn = "1936-0851", doi = "10.1021/nn405717p", volume = "8", pmcid = "PMC4046802" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140603-072449619, title = "Developmental Self-Assembly of a DNA Tetrahedron", journal = "ACS Nano", year = "2014", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140603-072449619", id = "record", issn = "1936-0851", doi = "10.1021/nn4038223", volume = "8", pmcid = "PMC4004324" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20140710-084440757, title = "Selective Nucleic Acid Capture with Shielded Covalent Probes", journal = "Biophysical Journal", year = "2014", url = "https://resolver.caltech.edu/CaltechAUTHORS:20140710-084440757", id = "record", issn = "0006-3495", doi = "10.1016/j.bpj.2013.11.3412", volume = "106" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20131205-083955291, title = "Conditional Dicer Substrate Formation via Shape and Sequence Transduction with Small Conditional RNAs", journal = "Journal of the American Chemical Society", year = "2013", url = "https://resolver.caltech.edu/CaltechAUTHORS:20131205-083955291", id = "record", issn = "0002-7863", doi = "10.1021/ja404676x", volume = "135", pmcid = "PMC3842090" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20130930-102728287, title = "Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy", journal = "Proceedings of the National Academy of Sciences of the United States of America", year = "2013", url = "https://resolver.caltech.edu/CaltechAUTHORS:20130930-102728287", id = "record", issn = "0027-8424", doi = "10.1073/pnas.1307876110", volume = "110", pmcid = "PMC3791709" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20130905-155148025, title = "Selective Nucleic Acid Capture with Shielded Covalent Probes", journal = "Journal of the American Chemical Society", year = "2013", url = "https://resolver.caltech.edu/CaltechAUTHORS:20130905-155148025", id = "record", issn = "0002-7863", doi = "10.1021/ja4009216", volume = "135", pmcid = "PMC3703666" } @other{https://resolver.caltech.edu/CaltechAUTHORS:20130801-081334911, title = "Selective oligonucleotide and mRNA pull-down with shielded covalent probes", year = "2013", url = "https://resolver.caltech.edu/CaltechAUTHORS:20130801-081334911", id = "record" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20130501-084442039, title = "Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes", journal = "Biophysical Journal", year = "2013", url = "https://resolver.caltech.edu/CaltechAUTHORS:20130501-084442039", id = "record", issn = "0006-3495", doi = "10.1016/j.bpj.2012.11.2761", volume = "104" } @other{https://resolver.caltech.edu/CaltechAUTHORS:20120822-154455462, title = "Sensitive and selective nucleic acid capture with shielded covalent probes", year = "2012", url = "https://resolver.caltech.edu/CaltechAUTHORS:20120822-154455462", id = "record" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20110202-095344276, title = "Nucleic Acid Sequence Design via Efficient Ensemble Defect Optimization", journal = "Journal of Computational Chemistry", year = "2011", url = "https://resolver.caltech.edu/CaltechAUTHORS:20110202-095344276", id = "record", issn = "0192-8651", doi = "10.1002/jcc.21633", volume = "32" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170224-152102280, title = "NUPACK: Analysis and design of nucleic acid systems", journal = "Journal of Computational Chemistry", year = "2011", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170224-152102280", id = "record", issn = "0192-8651", doi = "10.1002/jcc.21596", volume = "32" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20160112-090928317, title = "Programmable in situ amplification for multiplexed imaging of mRNA expression", journal = "Nature Biotechnology", year = "2010", url = "https://resolver.caltech.edu/CaltechAUTHORS:20160112-090928317", id = "record", issn = "1087-0156", doi = "10.1038/nbt.1692", volume = "28", pmcid = "PMC3058322" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170224-143742507, title = "Programming biomolecular self-assembly pathways", journal = "Nature", year = "2008", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170224-143742507", id = "record", issn = "0028-0836", doi = "10.1038/nature06451", volume = "451" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20110216-154211699, title = "An autonomous polymerization motor powered by DNA hybridization", journal = "Nature Nanotechnology", year = "2007", url = "https://resolver.caltech.edu/CaltechAUTHORS:20110216-154211699", id = "record", issn = "1748-3387", doi = "10.1038/nnano.2007.225", volume = "2" } @article{https://resolver.caltech.edu/CaltechAUTHORS:DIRsiamrev07, title = "Thermodynamic Analysis of Interacting Nucleic Acid Strands", journal = "SIAM Review", year = "2007", url = "https://resolver.caltech.edu/CaltechAUTHORS:DIRsiamrev07", id = "record", issn = "0036-1445", doi = "10.1137/060651100", volume = "49" } @inbook{https://resolver.caltech.edu/CaltechAUTHORS:20191015-134801443, title = "Nanotechnology: Science and Computation", chapter = "Nanoscale Molecular Transport by Synthetic DNA Machines", year = "2006", url = "https://resolver.caltech.edu/CaltechAUTHORS:20191015-134801443", id = "record", isbn = "978-3-540-30295-7", doi = "10.1007/3-540-30296-4\_11" } @article{https://resolver.caltech.edu/CaltechAUTHORS:BOInar05, title = "Topological constraints in nucleic acid hybridization kinetics", journal = "Nucleic Acids Research", year = "2005", url = "https://resolver.caltech.edu/CaltechAUTHORS:BOInar05", id = "record", issn = "0305-1048", doi = "10.1093/nar/gki721", volume = "33", pmcid = "PMC1180668" } @article{https://resolver.caltech.edu/CaltechAUTHORS:DIRpnas04, title = "Triggered amplification by hybridization chain reaction", journal = "Proceedings of the National Academy of Sciences of the United States of America", year = "2004", url = "https://resolver.caltech.edu/CaltechAUTHORS:DIRpnas04", id = "record", issn = "0027-8424", doi = "10.1073/pnas.0407024101", volume = "101", pmcid = "PMC524468" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170224-152823096, title = "A Synthetic DNA Walker for Molecular Transport", journal = "Journal of the American Chemical Society", year = "2004", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170224-152823096", id = "record", issn = "0002-7863", doi = "10.1021/ja047543j", volume = "126" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20190503-151608000, title = "An algorithm for computing nucleic acid baseā€pairing probabilities including pseudoknots", journal = "Journal of Computational Chemistry", year = "2004", url = "https://resolver.caltech.edu/CaltechAUTHORS:20190503-151608000", id = "record", issn = "0192-8651", doi = "10.1002/jcc.20057", volume = "25" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170802-102130134, title = "Rewritable Memory by Controllable Nanopatterning of DNA", journal = "Nano Letters", year = "2004", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170802-102130134", id = "record", issn = "1530-6984", doi = "10.1021/nl049658r", volume = "4" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20200221-132333124, title = "Progress in adjoint error correction for integral functionals", journal = "Computing and Visualization in Science", year = "2004", url = "https://resolver.caltech.edu/CaltechAUTHORS:20200221-132333124", id = "record", issn = "1432-9360", doi = "10.1007/s00791-003-0115-y", volume = "6" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203820, title = "Paradigms for computational nucleic acid design", journal = "Nucleic Acids Research", year = "2004", url = "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203820", id = "record", issn = "0305-1048", doi = "10.1093/nar/gkh291", volume = "32", pmcid = "PMC390280" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20170227-084204047, title = "A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots", journal = "Journal of Computational Chemistry", year = "2003", url = "https://resolver.caltech.edu/CaltechAUTHORS:20170227-084204047", id = "record", issn = "0192-8651", doi = "10.1002/jcc.10296", volume = "24" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20110913-173425474, title = "Exact rotamer optimization for protein design", journal = "Journal of Computational Chemistry", year = "2003", url = "https://resolver.caltech.edu/CaltechAUTHORS:20110913-173425474", id = "record", issn = "0192-8651", doi = "10.1002/jcc.10121", volume = "24" } @article{https://resolver.caltech.edu/CaltechAUTHORS:PIEpeds02.939, title = "Protein Design is NP-hard", journal = "Protein Engineering", year = "2002", url = "https://resolver.caltech.edu/CaltechAUTHORS:PIEpeds02.939", id = "record", issn = "0269-2139", doi = "10.1093/protein/15.10.779", volume = "15" } @article{https://resolver.caltech.edu/CaltechAUTHORS:GILjfm01, title = "Analytic adjoint solutions for the quasi-one-dimensional Euler equations", journal = "Journal of Fluid Mechanics", year = "2001", url = "https://resolver.caltech.edu/CaltechAUTHORS:GILjfm01", id = "record", issn = "0022-1120", doi = "10.1017/S0022112000002366", volume = "426" } @article{https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432187, title = "Conformational splitting: a more powerful criterion for dead-end elimination", journal = "Journal of Computational Chemistry", year = "2000", url = "https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432187", id = "record", issn = "0192-8651", doi = "10.1002/1096-987X(200008)21:11<999::AID-JCC9>3.0.CO;2-A", volume = "21" } @article{https://resolver.caltech.edu/CaltechAUTHORS:PIEsiamrev00, title = "Adjoint recovery of superconvergent functionals from PDE approximations", journal = "SIAM Review", year = "2000", url = "https://resolver.caltech.edu/CaltechAUTHORS:PIEsiamrev00", id = "record", issn = "0036-1445", doi = "10.1137/S0036144598349423", volume = "42" }