Publications from the Molecular Systems Lab    Dept. Systems Biology Harvard Medical School Wyss Institute for Biologically Inspired Engineering


2025

[97] Gokul Gowri, Xiaokang Lun, Allon M Klein*, Peng Yin*
Approximating mutual information of high-dimensional variables using learned representations.
NIPS '24: Proceedings of the 38th International Conference on Neural Information Processing Systems 4223, 132843-132875 (2025), Published: June 5 2025
DOI: 10.5555/3737916.3742139, [PDF]

[96] Hehai Jiang*, Logan A Walker*, Ye Li*, Bin Duan, Xiaoman Niu, Jung-Chien Hsieh, Mou-Chi Cheng, Hanquan Su, Kuanwei Sheng, Jessica P Tang, Kenneth Athukorala, Stacey Greene, Ruby Pan, Arya Parlapalli, Peng Yin, Meng Cui#, Dawen Cai#
A parallelly distributed microscope and software system for scalable high-throughput multispectral 3D imaging.
bioRxiv (2025), Published: June 3 2025
DOI: 10.1101/2025.05.31.657163, [PDF]

[95] Nic Fishman*, Gokul Gowri*, Peng Yin, Jonathan Gootenberg, Omar Abudayyeh
Generative Distribution Embeddings.
arXiv (2025), Published: May 23 2025
DOI: arXiv.2505.18150, [PDF]

[94] Gokul Gowri, Peng Yin, Allon M Klein
Measurement noise scaling laws for cellular representation learning.
arXiv (2025), Published: March 3 2025
DOI: 10.48550/arXiv.2503.02726, [PDF]

[93] Johannes Stein*, Maria Ericsson, Michel Nofal, Lorenzo Magni, Sarah Aufmkolk, Ryan B McMillan, Laura Breimann, Conor P Herlihy, S Dean Lee, Andréa Willemin, Jens Wohlmann, Laura Arguedas-Jimenez, Peng Yin, Ana Pombo, George M Church*, Chao-ting Wu*
Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.
bioRxiv (2025), Published: February 13 2025
DOI: 10.1101/2024.02.05.576943, [PDF]


2024

[92] Shen T*, Hu Z*, Sun S*, Liu D*, Wong F, Wang J, Chen J, Wang Y, Hong L, Xiao J, Zheng L, Krishnamoorthi T, King I, Wang S*, Yin P*, Collins JJ*, Li Y*
Accurate RNA 3D structure prediction using a language model-based deep learning approach.
Nature Methods (2024), Published: 21 November 2024
DOI: 10.1038/s41592-024-02487-0, [PDF]

[91] Wang S, Shin TW, Yoder HB 2nd, McMillan RB, Su H, Liu Y, Zhang C, Leung KS, Yin P, Kiessling LL*, Boyden ES*
Single-shot 20-fold expansion microscopy.
Nature Methods (2024), Published: 11 October 2024
DOI: 10.1038/s41592-024-02454-9, [PDF]

[90] Wang Y*, Liu X, Zeng Y, Saka SK, Xie W, Goldaracena I, Kohman RE, Yin P, Church GM*
Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions.
Nucleic Acids Research (2024), Published: 22 August 2024
DOI: 10.1093/nar/gkae592, [PDF]

[89] Lun XK, Sheng K, Yu X, Lam CY, Gowri G, Serrata M, Zhai Y, Su H, Luan J, Kim Y, Ingber DE, Jackson HW, Yaffe MB, Yin P*
Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry.
Nature Biotechnology (2024), Published: 29 July 2024
DOI: 10.1038/s41587-024-02316-x, [PDF]

  • See media coverage: Wyss Press Release
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  • [88] Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA*
    Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches.
    Chem (2024), Published: 11 July 2024
    DOI: 10.1016/j.chempr.2024.03.015, [PDF]

    [87] Gowri G*, Sheng K, Yin P*
    Scalable design of orthogonal DNA barcode libraries.
    Nature Computational Science (2024), Published: 7 June 2024
    DOI: 10.1038/s43588-024-00646-z, [PDF]

    [86] Woo S, Saka SK, Xuan F, Yin P
    Molecular robotic agents that survey molecular landscapes for information retrieval.
    Nature Communications (2024), Published: 17 April 2024
    DOI: 10.1038/s41467-024-46978-2, [PDF]

    [85] Stein J*, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM*, Wu CK*
    Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level.
    bioRxiv (2024), Published: 5 February 2024 [Preprint]
    DOI: 10.1101/2024.02.05.576943, [PDF]


    2023

    [84] 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 Methods21, 331–341 (2024), Published: 27 December 2023
    DOI: 10.1038/s41592-023-02115-3, [PDF] [Supplementary Materials]


    2022

    [83] 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
    DOI: 10.1038/s41565-022-01283-1 [PDF]

    [82] 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
    DOI: 10.1038/s41592-022-01604-1 [PDF] [Supplementary Materials]

    [81] 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
    DOI: 10.1038/s41416-022-01990-5 [PDF]

    [80] Hiroshi M. Sasaki, Jocelyn Y. Kishi, Chao-ting Wu, Brian J. Beliveau*, Peng Yin*
    Quantitative multiplexed imaging of chromatin ultrastructure with Decode-PAINT
    bioRxiv 2022.08.01.502089, Published: 03 August 2022
    DOI: 10.1101/2022.08.01.502089 [PDF]

    [79] 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]


    2021

    [78] 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]

    [77] 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
    DOI:10.1038/s41563-021-00930-7 [PDF] [Supplementary materials]

    [76] 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
    DOI: 10.1126/science.abf8873 [PDF]


    2020

    [75] 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]

    [75] Kim Y, Yaseen AB, Kishi JY, Hong F, Saka SK, Sheng K, Gopalkrishnan N, Schaus TE*, Yin P*
    Single-strand RPA for rapid and sensitive detection of SARS-CoV-2 RNA
    medRxiv, Published: 25 October 2020
    DOI:10.1101/2020.08.17.20177006 [PDF]

    [74] 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
    DOI:10.1002/anie.202009031 [PDF] [Supplementary Materials]

    [73] 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]

    [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)
    DOI: 10.1126/science.aaz7440 [PDF] [Supplementary Materials]

    [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)
    DOI: 10.1038/s41592-020-0816-x [PDF]
    [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
    DOI: 10.1021/acsnano.0c00178 [PDF] [Supplementary Materials]

    [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]


    2019

    [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
    DOI: 10.1093/nar/gkz998 [PDF] [Supplementary Information]

    [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]

    [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]

    [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]

    [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]

    [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]

    [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)
    DOI: 10.1038/s41586-019-1014-9 [PDF] [Supplementary Information] [Supplementary Data] [Supplementary Figure]

    [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
    DOI: 10.1021/acs.nanolett.9b00508 [PDF] [Supplementary Information]


    2018

    [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
    DOI: 10.1371/journal.pgen.1007872, PMID: 30586358 [PDF] [Supplementary Movie1] [Supplementary Movie2]

    [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)
    DOI: 10.1038/s41467-018-07039-7, PMID: 30389935 [PDF] [Supplementary Information]

    [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
    DOI: 10.1002/9783527688104 [PDF]

    [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
    DOI: 10.1073/pnas.1714530115, PMID: 29463736 [PDF] [Supplementary Information] [Supplementary Dataset1] [Supplementary Dataset2]

    [49] J. Kim, P. Yin*, and A. A. Green*
    Ribocomputing: Cellular Logic Computation Using RNA Devices
    Biochemistry, 2018, 57 (6), pp 883-885
    DOI: 10.1021/acs.biochem.7b01072, PMID: 29256603 [PDF]


    2017

    [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]

    [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]

    [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]

    [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]

    [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]

    [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.
    Methods in Molecular Biology, vol 1663. Humana Press, New York, NY doi: 10.1007/978-1-4939-7265-4_19, PMID: 28924672 [PDF]

    [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]

    [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]

    [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]


    2016

    [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]

    [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]

    [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]


    2015

    [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
    Small 11: 5200-5205 (2015). [PDF] [Supplementary Materials]

    [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]


    2014

    [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]

    [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]

    [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]

    [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]

    [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]


    2013

    [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]

    [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]

    [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.

    2012

    [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]

    [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]

    [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]

    [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]


    2008

    [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]

    [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]


    Old publications (2005 and before) can be found here.