[83] N. Gopalkrishnan, S. Punthambaker, T. E. Schaus, G. M. Church and P. Yin*
A DNA nanoscope that identifies and precisely localizes over a hundred unique molecular features with nanometer accuracy
bioRxiv, DOI: 10.1101/2020.08.27.271072. Posted August 28, 2020. [PDF] [Supplementary Materials]

[82] F. Hong, J. Y. Kishi, R. N. Delgado, J. Jeong, S. K. Saka, H. Su, C. L. Cepko & P. Yin*
Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels
Nature Methods (2023), Published: 27 December 2023
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[81] C. M. Wintersinger, D. Minev, A. Ershova, H. M. Sasaki, G. Gowri, J. F. Berengut, F. E. Corea-Dilbert, P. Yin, W. M. Shih
Multi-micron crisscross structures grown from DNA-origami slats
Nature Nanotechnology (2022), Published: 21 December 2022
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[80] J. Y. Kishi^†*, N. Liu^†, E. R. West^†, K. Sheng, J. J. Jordanides, M. Serrata, C. L. Cepko*, S. K. Saka* & P. Yin*
Light-Seq: Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing
Nature Methods 19, 1393-1402 (2022), Published: 10 October 2022
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[79] I. M. Schaefer, M. L. Hemming, M. Z. Lundberg, M. P. Serrata, I. Goldaracena, N. Liu, P. Yin, J. A. Paulo, S. P. Gygi, S. George, J. A. Morgan, M. M. Bertagnolli, E. T. Sicinska, C. Chu, S. Zheng, A. Mariño-Enríquez, J. L. Hornick, C.P. Raut, W. B. Ou, G. D. Demetri, S. K. Saka, J. A. Fletcher
Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST
British Journal of Cancer 127, 2072-2085 (2022), Published: 29 September 2022
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[78] D. Liu^†, F. A. Thélot^†, J. A. Piccirilli, M. Liao* & P. Yin*
Sub-3 Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly
Nature Methods 19, 576-585 (2022), Published: 02 May 2022
DOI: 10.1038/s41592-022-01455-w [PDF] [Supplementary Materials]

[77] J. A. Alfaro*^†, P. Bohländer^†, M. Dai^†, M. Filius^†, C. J. Howard^†, X. F. van Kooten^†, S. Ohayon^†, A. Pomorski^†, S. Schmid^†, A. Aksimentiev, E. V. Anslyn, G. Bedran, C. Cao, M. Chinappi, E. Coyaud, C. Dekker, G. Dittmar, N. Drachman, R. Eelkema, D. Goodlett, S. Hentz, U. Kalathiya, N. L. Kelleher, R. T. Kelly, Z. Kelman, S. Hyun Kim, B. Kuster, D. Rodriguez-Larrea, S. Lindsay, G. Maglia, E. M. Marcotte, J. P. Marino, C. Masselon, M. Mayer, P. Samaras, K. Sarthak, L. Sepiashvili, D. Stein, M. Wanunu, M. Wilhelm, P. Yin, A. Meller* & C. Joo*
The emerging landscape of single-molecule protein sequencing technologies
Nature Methods 18, 604-617 (2021), Published: 7 June 2021
DOI: 10.1038/s41592-021-01143-1 [PDF]

[76] J. Shen, W. Sun, D. Liu, T. Schaus and P. Yin*
Three-dimensional nanolithography guided by DNA modular epitaxy
Nature Materials 20, 683-690 (2021), Published: 10 April 2021
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[75] L. R. Robinson-Mccarrthy, A. J. Mijalis, G. T. Filsinger, H. de Puig, N. M. Donghia, T. E. Schaus, R. A. Rasmussen, L. Raphael, J. E. Lunshof, G. Chao, D. Ter-Ovanesyan, O. Dodd, E. Kuru, A. M. Sesay, J. Rainbow, A. C. Pawlowski, T. M. Wannier, P. Yin, J. J. Collins, D. E. Ingber, G. M. Church & J. M. Tam
Anomalous COVID-19 tests hinder researchers
Science 371:6526, 244-245 (2021), Published: 15 January 2021
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[74] S. F. J. Wickham, A. Auer, J. Min, N. Ponnuswamy, J. B. Woehrstein, F. Schueder, M. T. Strauss, J. Schnitzbauer, B. Nathwani, Z. Zhao, S. D. Perrault, J. Hahn, S. Lee, M. M. Bastings, S. W. Helmig, A. L. Kodal, P. Yin, R. Jungmann* & W. M. Shih*
Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard
Nature Communications, 11, Article number: 5768 (2020)
DOI: 10.1038/s41467-020-18910-x [PDF] [Supplementary Information] [Supplementary Software] [Supplementary Data] [Supplementary Movies] [Reporting Summary] [Description of Supplementary Files]

[73] F. Schueder, J. Lara-Gutierrez, D. Haas, K. S. Beckwith, P. Yin, J. Ellenberg and R. Jungmann*
Super-resolution spatial proximity detection with proximity-PAINT
Angewandte Chemie, Published: 16 September 2020
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[72] W. Sun*^†, J. Shen^†, Z. Zhao^†, N. Arellano, C. Rettner, J. Tang, T. Cao, Z. Zhou, T. Ta, J. K. Streit, J. A. Fagan, T. Schaus, M. Zheng, S. Han, W. M. Shih, H. T. Maune and P. Yin*
Precise pitch-scaling of carbon nanotube arrays within three-dimensional DNA nanotrenches
Science, Vol. 368, Issue 6493, pp. 874-877 (2020)
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[71] F. Xu, D. Ma, K. P. MacPherson, S. Liu, Y. Bu, Y. Wang, Y. Tang, C. Bi, T. Kwok, A. A. Chubykin, P. Yin, S. Calve, G. E. Landreth and F. Huang
Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval
Nature Methods, 17, pages531-540(2020)
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[Supplementary Information] [Supplementary Video1] [Supplementary Video2] [Supplementary Video3] [Supplementary Video4] [Supplementary Video5] [Supplementary Video6] [Supplementary Video7] [Supplementary Video8] [Supplementary Video9] [Supplementary Software1] [Supplementary Software2]

[70] F. Zhou, W. Sun, C. Zhang, J. Shen, P. Yin* and H. Liu*
3D freestanding DNA nanostructure hybrid as a low-density high-strength material
ACS Nano, Publication Date: 1 May 2020
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[69] S. An, K. F. Ziegler, P. Zhang, Y. Wang, T. Kwok, F. Xu, C. Bi, S. Matosevic, P. Yin, T. Li, and F. Huang
Axial plane single-molecule super-resolution microscopy of whole cells
Biomedical Optics Express, Vol. 11, Issue 1, pp. 461-479 (2020)
DOI: 10.1364/BOE.377890 [PDF]

[68] D. Minev^†, R. Guerra^†, J. Y. Kishi^‡, C. Smith^‡, E. Krieg, K. Said, A. Hornick, H. M Sasaki, G. Filsinger, B. J. Beliveau, P. Yin, G. M. Church, W. M. Shih
Rapid in vitro production of single-stranded DNA
Nucleic Acids Research, gkz998, Published: 12 November 2019
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[67] J. Kim^†, Y. Zhou^†, P. D. Carlson, M. Teichmann, S. Chaudhary, F. C. Simmel, P. A. Silver, J. J. Collins, J. B. Lucks, P. Yin* & A. A. Green*
De novo-designed translation-repressing riboregulators for multi-input cellular logic
Nature Chemical Biology, Published 04 November 2019
DOI: 10.1038/s41589-019-0388-1 [PDF] [Supplementary Information]

• See media coverage: Wyss Press Release, ASU Press Release, Phys.org, Technology Networks, ScienceDaily

[66] Y. Kim & P. Yin
Enhancing biocompatible stability of DNA nanostructures using dendritic oligonucleotides and brick motifs
Angewandte Chemie, Accepted Articles, First published: 09 October 2019
DOI: 10.1002/anie.201911664 [PDF] [Supplementary Information]

[65] HuBMAP Consortium
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
Nature, volume 574, pages 187-192 (2019) DOI: 10.1038/s41586-019-1629-x [PDF]

[64] P. Anikeeva, E. Boyden, [...], P Yin, [...], X. Zhuang
Voices in methods development
Nature Methods, volume 16, pages 945-951 (2019) DOI: 10.1038/s41592-019-0585-6 [PDF]

[63] Ninning Liu^†, Mingjie Dai^†,*, Sinem K. Saka & Peng Yin*
Super-resolution labelling with Action-PAINT
Nature Chemistry, Published: 16 September 2019.
DOI: 10.1038/s41557-019-0325-7 [PDF] [Supplementary Information]

• Highlighted in Nature Research Highlights.
• See media coverage: Wyss Press Release, Phys.org, Technology Networks

[62] S. K. Saka^†,*, Y. Wang^†,*, J. Y. Kishi, A. Zhu, Y. Zeng, W. Xie, K. Kirli, C. Yapp, M. Cicconet, B. J. Beliveau, S. W. Lapan, S. Yin, M. Lin, E. S. Boyden, P. S. Kaeser, G. Pihan, G. M. Church, and P. Yin*
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues
Nature Biotechnology, published 19 August 2019. DOI: 10.1038/s41587-019-0207-y [PDF]
[Website: http://immuno-saber.net/]
[Supplementary Information] [Supplementary Protocols]

• See media coverage: Wyss Press Release, Phys.org, ScienceDaily, Biocompare, Science Codex
• See video:

  Lighting up proteins with Immuno-SABER

[61] P. Kosuri, B. D. Altheimer, M. Dai, P. Yin, X. Zhuang*
Rotation tracking of genome-processing enzymes using DNA origami rotors
Nature, published 17 July 2019. DOI: 10.1038/s41586-019-1397-7 [PDF]
[Supplementary Information] [Reporting Summary] [Supplementary Table1] [Supplementary Table2] [Supplementary Video1] [Supplementary Video2]

• See media coverage: Harvard Press Release

[60] M. Jin^†, N. Garreau de Loubresse^†, Y. Kim, J. Kim*, P. Yin*
Programmable CRISPR-Cas repression, activation, and computation with sequence-independent targets and triggers
ACS Synth. Biol., 2019, 8, 7, 1583-1589 published 10 July 2019. DOI: 10.1021/acssynbio.9b00141 [PDF]
[Supplementary Information]

[59] J. Y. Kishi^†, S. W. Lapan^†, B. J. Beliveau^†*, E. R. West^†, A. Zhu, H. M. Sasaki, S. K. Saka, Y. Wang, C. L. Cepko*, P. Yin*
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues
Nature Methods, published 20 May 2019. DOI: 10.1038/s41592-019-0404-0 [PDF]
[Website: http://saber.fish]
[Supplementary Information] [Reporting Summary] [Supplementary Protocols] [Supplementary Table1: SABER sequences] [Supplementary Table2: SABER simulated parameters] [Supplementary Table3: SABER experimental conditions] [Supplementary Table4: SABER puncta counts]

• See media coverage: Wyss Press Release, Technology Networks, Phys.org, Nanowerk, ScienceDaily, 7thSpace
• See video:

  SABER-FISH: Enabling the sensitive and multiplexed detection of nucleic acids within thick tissues

[58] D. Woods^†,*, D. Doty^†,*, C. Myhrvold, J. Hui, F. Zhou, P. Yin, and E. Winfree*
Diverse and robust molecular algorithms using reprogrammable DNA self-assembly
Nature, 567, 366-372 (2019)
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• See media coverage: Caltech Press Release

[57] O.K. Wade^†, J.B. Woehrstein^†, P. C. Nockels^†, S. Strauss^†, F. Stehr, J. Stein, F. Schueder, M.T. Strauss, M. Ganji, J. Schnitzbauer, H. Grabmayr, P. Yin, P. Schwille, R. Jungmann*
124-color super-resolution imaging by engineering DNA-PAINT blinking kinetics
Nano Lett., Article ASAP
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• See media coverage: ScienceDaily

[56] G. Nir^†, I. Farabella^†, C. Perez Estrada^†, C.G. Ebeling^†, B.J. Beliveau, H.M. Sasaki, S.H. Lee, S. Nguyen, R.B. McCole, S. Chattoraj, J. Erceg, J. AlHaj Abed, N.C. Martins, H.Q. Nguyen, M.A. Hannan, S. Russell, N.C. Durand, S.P. Rao, J.Y. Kishi, P. Soler-Vila, M. Di Pierro, J.N. Onuchic, S. Callahan, J. Schreiner, J. Stuckey*, P. Yin*, E. Lieberman Aiden*, M.A. Marti-Renom*, C.T. Wu*
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
PLoS Genet, 14(12): e1007872
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• See media coverage: Wyss Press Release

[55] X. Qi, F. Zhang, Z. Su, S. Jiang, D. Han, B. Ding, Y. Liu, W. Chiu, P. Yin, H. Yan
Programming molecular topologies from single-stranded nucleic acids
Nature Communications, 9, Article number: 4579 (2018)
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[54] W. Xu, P. Yin*, M. Dai*
Super-resolution geometric barcoding for multiplexed miRNA profiling
Angewandte Chemie, Accepted Article, September 5, 2018.
DOI: 10.1002/ange.201807956 [PDF] [Supplementary Information]

[53] T. Lin, J. Yan, L. L. Ong, J. Robaszewski, H. D. Lu, Y. Mi, P. Yin*, and B. Wei*
Hierarchical assembly of DNA nanostructures based on four-way toehold-mediated strand displacement
Nano Lett., 2018, 18 (8), pp 4791-4795
DOI: 10.1021/acs.nanolett.8b01355 [PDF] [Supplementary Information]

[52] K. Ye*, D. L. Kaplan, G. Bao, C. Bettinger, G. Forgacs, C. Dong, A. Khademhosseini, Y. Ke , K. Leong, A. Sambanis, W. Sun, and P. Yin
Advanced Cell and Tissue Biomanufacturing
ACS Biomater. Sci. Eng., 2018, 4, 7, 2292-2307
DOI: 10.1021/acsbiomaterials.8b00650 [PDF]

[51] G. Sachdeva, C. Myhrvold, P. Yin and P. A. Silver
Synthetic RNA scaffolds for spatial engineering in cells
Synthetic Biology: Parts, Devices and Applications (Book Chapter), Editor(s): C. Smolke, S. Y. Lee, J. Nielsen, G. Stephanopoulos
First published: 30 March 2018, Print ISBN:9783527330751 | Online ISBN:9783527688104
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[50] B. J. Beliveau*, J. Y. Kishi, G. Nir, H. M. Sasaki, S. K. Saka, S. C. Nguyen, C.-t. Wu, and P. Yin*
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
Proc Natl Acad Sci USA, March 6, 2018. 115 (10) E2183-E2192
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[49] J. Kim, P. Yin*, and A. A. Green*
Ribocomputing: Cellular Logic Computation Using RNA Devices
Biochemistry, 2018, 57 (6), pp 883-885
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[48] D. Han^†, X. Qi^†, C. Myhrvold, B. Wang, M. Dai, S. Jiang, M. Bates, Y. Liu, B. An^*, F. Zhang^*, H. Yan^* and P. Yin^*
Single-stranded DNA and RNA origami
Science Vol. 358, Issue 6369, eaao2648 (2017) DOI: 10.1126/science.aao2648 [PDF] [Supplementary Materials] [Supplementary Movies]

• Highlighted in MRS Bulletin.
• See media coverage: Wyss Press Release, Harvard Gazette, Phys.Org, ScienceDaily, Scicasts, Nanowerk, ScienceNewsline, AZoNano, Technology Networks, IEEE GlobalSpec
• See video:

  Illustration of single-stranded origami

[47] L. L. Ong, N. Hanikel, O. K. Yaghi, C. Grun, M. T. Strauss, P. Bron, J. Lai-Kee-Him, F. Schueder, B. Wang, P. Wang, J. Y. Kishi, C.A. Myhrvold, A. Zhu, R. Jungmann, G. Bellot^*, Y. Ke^*, and P. Yin^*
Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components
Nature 552, 72 (2017) doi: 10.1038/nature24648, PMID: 29219968 [PDF] [Supplementary Materials] [Supplementary Data] [Supplementary Movies: SV1, SV2, SV3] [Software: info page, software link] [PhD Thesis: Luvena Ong, 2016]

• Highlighted in Nature News and Views [PDF], Nature Reviews Materials [PDF], Science News, Science Podcast.
• See media coverage: Wyss Press Release, HMS News, C&EN, CHEMISTRY WORLD, The Scientist, Phys.Org, Phys.Org 2, ScienceDaily, Nanowerk, nanotechweb, ZME Science, Medical Design Technology, Controlled Environments, Innovations Report, FutureTimeline, Infosurhoy, Sciworthy, welt der physik, Wissenschaft aktuell, DNASpeaking, hsmap.com
• See video:

  Illustration of a self-assembled structure with a teddy bear shape cavity

[46] F. Schueder, J. Lara-Guiterrez, B. Beliveau, S. Saka, H. Sasaki, J. Woehrstein, M. Strauss, H. Grabmayr, P. Yin^*, and R. Jungmann^*
Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT
Nature Communications 8, Article number: 2090 (2017) doi: 10.1038/s41467-017-02028-8, PMID: 29233999 [PDF] [Supplementary Materials] [Peer Review File] [Description of Additional Supplementary Files] [Supplementary Movies: 1, 2, 3] [Supplementary Data: 1, 2, 3, 4]

• See media coverage: Wyss Press Release, ScienceDaily, GEN, Phys.Org, ebiotrade.com

[45] J. Kishi, T. Schaus, N. Gopalkrishnan, F. Xuan, and P. Yin
Programmable autonomous synthesis of single-stranded DNA
Nature Chemistry Advanced Online Publication (2017) doi: 10.1038/nchem.2872, PMID: 29359755 [PDF] [Supplementary Materials]

• See media coverage: Wyss Press Release, HMS News, Nanowerk News, ScienceDaily, Phys.org , Technology Networks, eBiotrade.com
• See video:

  Primer Exchange Reactions

[44] T. E. Schaus, S. Woo, F. Xuan, X. Chen and P. Yin
A DNA nanoscope via auto-cycling proximity recording
Nature Communications 8, Article number: 696 (2017) doi: 10.1038/s41467-017-00542-3, PMID: 28947733 [PDF] [Supplementary Materials]

• See media coverage: Wyss Press Release, Nanowerk News, AZoNano, BioTecNika, Phys.Org, Gears Of Biz, R & D Magazine, HiTechDays, ScienceDaily, eBiotrade.com
• See an animation video:

  Auto-cycling Proximity Recording

[43] B. J. Beliveau, A. N. Boettiger, G. Nir, B. Bintu, P. Yin^*, X. Zhuang^*, C.-t Wu^*
In situ super-resolution imaging of genomic DNA with OligoSTORM and OligoDNA-PAINT
In: Erfle H. (eds) Super-Resolution Microscopy.
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[42] J. L. Werbin, M. S. Avendano, V. Becker, R. Jungmann, P. Yin^*, G. Danuser^* and P. K. Sorger^*
Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane
Scientific Reports 7, Article number: 12150 (2017) doi: 10.1038/s41598-017-12257-y, PMID: 28939861 [PDF] [Supplementary Materials]

[41] A. A. Green^†, J. Kim^†, D. Ma, P. A. Silver, J. J. Collins and P. Yin
Complex cellular logic computation using ribocomputing devices
Nature (2017) doi: 10.1038/nature23271, PMID: 28746304 [PDF] [Supplementary Materials]

• See media coverage: Wyss Press Release, ASU Press Release, IEEE Spectrum, Kurzweil Accelerating Intelligence, Tonic, DigitalJournal.com, MOTHERBOARD, Technology Networks, ScienceDaily 1, ScienceDaily 2, Scientific Computing, Nanotechnology Now, New big future, Phys.org, Biocompare, Nanowerk 1, Nanowerk 2, Newswise, R&D Magazine, Controlled Environments, Spektrum.de, Le Scienze
• See an illustration:

[40] J. B. Woehrstein, M. T. Strauss, L. L. Ong, B. Wei, D. Y. Zhang, R. Jungmann^* and P. Yin^*
Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA
Science Advances Vol. 3, no. 6, e1602128, doi: 10.1126/sciadv.1602128, PMID: 28691083 [PDF] [Supplementary Materials]

• See media coverage: Wyss Press Release, MPI Press Release, Phys.org, nanotechweb.org, Nanowerk, Controlled Environments, Informationsdienst Wissenschaft, JuraForum, innovations report, NeoDoc, MEDIZIN ASPEKTE, scinexx

[39] Y. Wang, J. B. Woehrstein, N. Donoghue, M. Dai, M. S. Avendano, R. C.J. Schackmann, J. Zoeller, S. S. H. Wang, P. W. Tillberg, D. Park, S. W. Lapan, E. S. Boyden, J. S. Brugge, P. S. Kaeser, G. M. Church, S. S. Agasti^*, R. Jungmann^*, P. Yin^*
Rapid sequential in situ multiplexing with DNA-Exchange-Imaging in Neuronal Cells and Tissues
Nano Letters Article ASAP, DOI: 10.1021/acs.nanolett.7b02716, PMID: 28933153 [PDF] [bioRxiv] [Supplementary Materials] [Supplementary Movie] [Supplementary Movie Caption]

• See a data video:

[38] F. Schueder, M. T. Strauss, D. Hoerl, J. Schnitzbauer, T. Schlichthaerle, S. Strauss, P. Yin, H. Harz, H. Leonhardt and R. Jungmann
Universal super-resolution multiplexing by DNA exchange
Angewandte Chemie 2017, Early View, doi: 10.1002/anie.201611729, PMID: 28256790 [PDF] [Supplementary Materials] [Supplementary Movie]

[37] S. S. Agasti, Y. Wang, F. Schueder, A. Sukumar, R. Jungmann^* and P. Yin^*
DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging
Chem. Sci. 2017, Advance Article, doi: 10.1039/c6sc05420j, PMID: 28451377 [PDF] [Supplementary Materials]

[36] C. Myhrvold, M. Baym, N. Hanikel, L. L. Ong, J. S. Gootenberg and P. Yin
Barcode extension for analysis and reconstruction of structures
Nature Communications 8, Article number: 14698 (2017) doi: 10.1038/ncomms14698, PMID: 28287117 [PDF] [Supplementary Materials] [Supplementary Data]

[35] P. Zhan, P. K. Dutta, P. Wang, G. Song, M. Dai, S-X Zhao, Z-G Wang, P. Yin, W. Zhang, B. Ding, and Y. Ke
Reconfigurable three-dimensional gold nanorod plasmonic nanostructures organized on DNA origami tripod
ACS Nano 2017, 11 (2), pp 1172-1179 [PDF] [Supplementary Materials]

[34] C. Tian, H. Kim, W. Sun, Y. Kim, P. Yin, and H. Liu
DNA nanostructures-mediated molecular imprinting lithography
ACS Nano 2017, 11 (1), pp 227-238. [PDF] [Supplementary Materials]

[33] M. Dai, R. Jungmann and P. Yin
Optical imaging of individual biomolecules in densely packed clusters
Nature Nanotechnology, 11, 798-807 (2016), doi: 10.1038/nnano.2016.95, PMID: 27376244 [PDF]
[Supplementary Information: S1, Supplementary Table: S2]

• Highlighted in Nature Review Materials [PDF], Nature Nanotechnology News and Views [PDF]
  
• See media coverage: Wyss Press Release, Harvard Gazette, NIH NIBIB, Phys.org, Laboratory Network, Science Newsline, ScienceDaily, GeekJournal, Controlled Environments, BestTheNews, AZoNano, American Laboratory, Nanowerk, Photonics Online, Science Codex, Nanotechnology Now, Next Big Future, ChemEurope.com, Microscopy and Analysis.
• See videos:

  Discrete Molecular Imaging	Super Resolution DMI

[32] R. Jungmann^†, M. S. Avendano^†, M. Dai, J. B. Woehrstein, S. S. Agasti, Z. Feiger, A. Rodal and P. Yin
Quantitative super-resolution imaging with qPAINT
Nature Methods, 13, 439-442 (2016), doi: 10.1038/nmeth.3804, PMID: 27018580 [PDF]
[Supplementary Materials: S1, Supplementary Videos: V1, V2]

• See media coverage: Wyss Press Release, Nanowerk, Phys.org, ScienceNewline, Weekly Hot News, Mountain Dreams News, ScienceDaily, NIH NIBIB, ScienceDaily 2, News Medical

[31] J. Elbaz, P. Yin, and C. Voigt
Genetic encoding of DNA nanostructures and their self-assembly in living bacteria
Nature Communications, 7, Article number: 11179 doi: 10.1038/ncomms11179, PMID: 27091073 [PDF] [Supplementary Materials]

[30] F. Zhou, W. Sun, K. B. Ricardo, D. Wang, J. Shen, P. Yin, and H. Liu
Programmably-shaped carbon nanostructure from shape-conserving carbonization of DNA
ACS Nano, 2016, 10 (3), pp 3069-3077, DOI: 10.1021/acsnano.5b05159. [PDF] [Supplementary Materials]

[29] J. B. Knudsen, L. Liu, A. L. B. Kodal, M. Madsen, Q. Li, J. Song, J. B. Woehrstein, S. F. Wickham, M. T. Strauss, F. Schueder, J. Vinther, A. Krissanaprasit, D. Gudnason, A. A. A. Smith, R. Ogaki, A. N. Zelikin, F. Besenbacher, V. Birkedal, P. Yin, W. M. Shih, R. Jungmann, M. Dong and K. V. Gothelf
Routing of individual polymers in designed patterns
Nature Nanotechnology 10, 892-898 (2015). [PDF] [Supplementary Materials]

[28] M. B. Scheible, L. L. Ong, J. B. Woehrstein, R. Jungmann, P. Yin and F. C. Simmel
A compact DNA cube with side length 10 nm
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[27] C. Grun, J. Werfel, D. Y. Zhang, and P. Yin
DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology
J. R. Soc. Interface 12: 20150580 (2015). [PDF] [Supplementary Materials]

[26] B. J. Beliveau, A. N. Boettiger, M. S. Avendano, R. Jungmann, R. B. McCole, E. F. Joyce, C. Kim-Kiselak, F. Bantignies, C. Y. Fonseka, J. Erceg, M. A. Hannan, H. G. Hoang, D. Colognori, J. T. Lee, W. M. Shih, P. Yin, X. Zhuang & C. Wu
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
Nature Communications 6, 7147 (2015). [PDF] [Supplementary Materials]

[25] B. Wei, M. K. Vhudzijena, J. Robaszewski, P. Yin
Self-assembly of complex two-dimensional shapes from single-stranded DNA tiles
J. Vis. Exp. 99, e52486, doi: 10.3791/52486, PMID: 25993048 (2015). [link] [Materials List]

[24] W. Sun, E. Boulais, Y. Hakobyan, W. Wang, A. Guan, M. Bathe^*, P. Yin^*
Casting inorganic structures with DNA molds
Science 346:1258361 (2014). [PDF] [Supplementary Materials]

• See media coverage: Wyss News Release, Phys.org, The Science Times, Nanotechnology Now, Nanowerk, ars technica, AZO Materials

[23] K. Pardee, A.A. Green, T. Ferrante, E. Cameron, A. DaleyKeyser, P. Yin, and J.J. Collins
Paper-based synthetic gene networks
Cell159:940-954 (2014). [PDF], [Supplementary Materials: S1, Supplementary Data: S1, S2]

[22] A.A. Green, P.A. Silver, J.J. Collins, P. Yin
Toehold switches: de-novo-designed regulators of gene expression
Cell 159: 925-939 (2014). [PDF], [Supplementary Materials: S1, S2, Supplementary Tables: S1, S2, S3, S4, S5, S6, S7]

• See media coverage for [22] and [23]: Wyss News Release, BBC News, Laboratory Equipment, Nanowerk, Medical News Today, Red Orbit, CNET, TheScientist, Phys.org, IEEE Spectrum, Medical Daily, MIT Technology Review, heise online, Next Big Future, Design & Trend, Newsweek, io9, Headlines & Global News, Digital Trends, (e) Science News, R&D Magazine
• See videos:

  Programmable Paper	Toehold Switches

[21] Y. Ke^†, L.L. Ong^†, W. Sun^†, J. Song, M. Dong, W.M. Shih, P. Yin
DNA brick crystals with prescribed depths
Nature Chemistry 6:994-1002 (2014). [PDF], [Supplementary Materials: S1, S2, S3]

• See media coverage: Wyss News Release, R&D Magazine, Phys.org, gizmag, Tech Times, ZME Science, Headlines & Global News, Next Big Future

[20] Z. Jin, W. Sun, P. Yin, M. Strano
Nanolithography based on metalized DNA templates for graphene patterning
Current Protocols in Chemical Biology 6:53-64 (2014).

[19] B. Wei, L.L. Ong, J. Chen, A. Jaffe, P. Yin
Complex reconfiguration of DNA nanostructures
Angewandte Chemie 126:7605-7609 (2014). [PDF] [Supplementary Materials]

[18] R. Iinuma^†, Y. Ke^†, R. Jungmann^†, T. Schlichthaerle, J.B. Woehrstein, P. Yin
Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT
Science 344:65-69 (2014). [PDF] [Supplementary Materials] [Movie 1] [Movie 2]

• See media coverage: Wyss News Release, Nanotechnology Now, Veooz, Brunch News, Science Daily, Machines Like Us, Nanowerk, Harvard Gazette, Phys.org, Biomedicine, Science Codex, The Emory Health Sciences Research Blog, Tech Times, e! Science News, Microscopy and Analysis, HNGN, USA News, Newsfiber, Fierce Drug Delivery, Nolet, w8.ns, Design News
• See an animation video:

  Spotting DNA cages with blinking DNA

[17] J. Sadowski, C.R. Calvert, D.Y. Zhang, N.A. Pierce, P. Yin
Developmental self-assembly of a DNA tetrahedron
ACS Nano DOI: 10.1021/nn4038223, PMID: 24720462 (2014). [PDF] [Supplementary Materials]

[16] J. Wu, D. Zhang, P. Yin, F. Vollmer
Ultraspecific and highly sensitive nucleic acid detection by integrating a DNA catalytic network with a label-free microcavity
Small DOI: 10.1002/smll.201303558, PMID: 24585636 (2014).[PDF] [Supplementary Materials]

[15] R. Jungmann^†, M.S. Avendano^†, J.B. Woehrstein^†, M. Dai, W.M. Shih, P. Yin
Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT
Nature Methods11(3):313-318 (2014). [PDF] [Supplementary Materials]

• See abstract and summary figure here.
• See media coverage: Wyss News Release, Harvard Gazette, Gizmodo, The Daily Mail, Wired, R&D Magazine, Phys.org, Updated News, News Medical, Nanowerk, e! Science News, Bioscience Technology, redOrbit, Softpedia, Worldess Tech, Hematology Times, Antibody Review, SOTT, Nanotech Etc., Qstorm, Biomedicine, The Engineer, Genome Web, Epoch Times, Bubblews, Scicasts, Kurzweil

[14] B. Wei, M. Dai, C. Myhrvold, Y. Ke, R. Jungmann, P. Yin
Design space for complex DNA structures
J. Am. Chem. Soc. 135 (48):18080-8 (2013). [PDF], [Supplementary Materials: S1, S2]

[13] L. Hochrein, M. Schwarzkopf, M. Shahgholi, P. Yin, N. Pierce
Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs
J. Am. Chem. Soc. 135 (46):17322-30, (2013). [PDF], [Supplementary Materials]

[12] H. Qi, M. Ghodousi, Y. Du, C. Grun, H. Bae, P. Yin^*, A. Khademhosseini^*.
DNA-directed self-assembly of shape-controlled hydrogels
Nature Communications 4, 2275 (2013). [PDF], [Supplementary Materials]

• See abstract and summary figure here.
• See media coverage: Wyss Institute's press release, Design News, Harvard Gazette, The Harvard Crimson, Wired, Discovery News, BostonInno, Harvard Systems Biology, Mashable, Science Daily, Las Vegas Guardian Express, Popular Mechanics

[11] C. Myhrvold, M. Dai, P.A. Silver, P. Yin.
Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions
Nano Letters 13(9): 4242-8 (2013). [PDF], [Supplementary Materials: S1, S2]

• See abstract and summary figure here.

[10] T.E. Schaus, P. Yin.
Molecular computing: In situ computation of cell identity (News and Views)
Nature Nanotechnolgy 155, 546-8 (2013). [PDF]

[9] S. Surwade, F. Zhou, B. Wei, W. Sun, A. Powell, C. O'Donnell, P. Yin^*, H. Liu^*
Nanoscale growth and patterning of inorganic oxides using DNA nanostructure templates
J. Am. Chem. Soc. 135, 6778-6781 (2013). [PDF] [Supporting Material]

• See abstract and summary figure here.

[8] Z. Jin, W. Sun, Y. Ke, C.-J. Shih, G. L.C. Paulus, Q. H. Wang, B. Mu, P. Yin^*, M. S. Strano^*
Metalized DNA nanolithography for encoding and transferring spatial information for graphene patterning
Nature Communications 4, 1663 (2013). [PDF] [Supporting Material]

• See abstract and summary figure here.
• See media coverage: MIT new release, SciTech Daily, Electronic News, ExtremeTech, Paste Magazine, Physics Buzz, The Verge, Digital Manufacturing Report

[7] D. Woods, H.L. Chen, S. Goodfriend, N. Dabby, E. Winfree, P. Yin
Active self-assembly of algorithmic shapes and patterns in polylogarithmic time
Proceedings of the 4th conference on Innovations in Theoretical Computer Science (ITCS) 353-354 (2013). [PDF]. Full article preprint on arXiv arXiv:1301.2626v1. [PDF]

• See abstract and summary figure here.

[6] Y. Ke, L. Ong, W. Shih, P. Yin
Three-dimensional structures self-assembled from DNA bricks
Science 338, 1177-1183 (2012). [PDF] [Supporting Material]

• See abstract and summary figure here.
• See perpective article by K. Gothelf: "LEGO-like DNA structures".
• See media coverage: Wyss Institute's press release, Harvard Gazette, NBC News Video, NBC News, LA Times, Boston.com, Discover Magazine, Discovery News, CBS42.com, The Scientist, Space.com, BioTechniques, Bio-Medicine, Genetic Engineering & Biotechnology News, Popular Mechanics, R&D Magazine, Chemistry World, Phys.org, TechNewsDaily, Science Daily, Extreme Tech, e! Science News, Science Codex, Lab Spaces, Genome Web, IvanHoe.com, Lukor.com, Terra Brasil, French Tribune, Spanish Scientific News Agency, Medindia, Wissenslogs, stdaily.com
• See photo slideshow here.
• See animation videos:

  Building 3D Structures with DNA Bricks	DNA Bricks -- Molecular Animation

[5] C. Lin, R. Jungmann, A.M. Leifer, C. Li, D. Levner, G.M. Church, W. Shih^*, P. Yin^*
Sub-micrometer geometrically encoded fluorescent barcodes self-assembled from DNA
Nature Chemistry 4, 832-839 (2012). [PDF] [Supporting Material]

• See abstract and summary figure here.
• See media coverage: Wyss Institute's press release, Harvard Crimson, NSF, Phys.org, R & D magazine, Materials Today, BioOpticsWorld, DarkDaily, TechNewsDaily, Laboratory Talk

[4] B. Wei, M. Dai and P. Yin
Complex shapes self-assembled from single-stranded DNA tiles
Nature 485, 623-626 (2012). [PDF] [Supporting material: S1-5, S6, S7, S8]

• See abstract and summary figure here.
• See News and Views by P. Rothemund and E.S. Anderson: "The importance of being modular".
• See media coverage: Wyss Institute's press release, Nature, Discover Magazine, Harvard Gazette, MSNBC, Los Angeles Times, Daily Mail (UK), MSN, NewScientist, BioTechniques, Foresight Institute, The China Post, Science Illustrated, PCWorld, Gizmodo, Azonano, Radio Australia News, iOL Scitech, World News Australia, Asian Age, Physics World, Phys.org, R & D Magazine, Arabs Today, Fast Code Design
• See an animation video:

  Making Structures with DNA "Building Blocks"

[3] D.Y. Zhang, S.X. Chen, and P. Yin
Optimizing the specificity of nucleic acid hybridization
Nature Chemistry 4, 208-14 (2012). [PDF] [Supporting material]

• See abstract and summary figure here.
  
• See News and Views by G. Altan-Bonnet and F.R. Kramer: "Robust sequence discrimination".
• See Wyss Institute's news story

[2] P. Yin, R.F. Hariadi, S. Sahu, H.M.T. Choi, S.H. Park, T.H. LaBean, J.H. Reif
Programming DNA tube circumferences
Science 321, 824-826 (2008). [PDF] [Supporting material]

• See abstract and summary figure here.
  
• Highlighted in Nature Nanotechnology
  
• See Caltech's news release

[1] P. Yin, H.M.T. Choi, C.R. Calvert, N.A. Pierce
Programming biomolecular self-assembly pathways
Nature 451, 318-322 (2008). [PDF] [Supporting material]

• See abstract and summary figure here.
  
• Highlighted in "The year in Nature", which features Nature manuscript editors' 22 favorites in 2008
  
• See Caltech's news release and NSF's news release
  
• See commentaries: "Biomolecular assembly: Dynamic DNA" by W. Shih in Nature Materials, "Rational engineering of dynamic DNA systems" by U. Feldkamp and C.M. Niemeyer in Angew Chemie, and "Tying new knots in synthetic biology" by D.K. Karig and M.L. Simpson in HFSP Journal