2024
Heonjoon Lee, Tian Xie, Byunghwa Kang, Xinjie Yu, Samuel W. Schaffter, Rebecca Schulman. Plug-and-play protein biosensors using aptamer-regulated in vitro transcription. Nature Communications, 2024.10.7281/T1/IRLoIE Link to Original
Ruohong Shi, Kuan-Lin Chen, Joshua Fern, Siming Deng, Yixin Liu, Dominic Scalise, Qi Huang, Noah J. Cowan, David H. Gracias, Rebecca Schulman. Programming gel automata shapes using DNA instructions. Nature Communications, 2024. 10.1038/s41467-024-51198-9Link to Original
Mingzhi Zhang, Colin Yancey, Chao Zhang, Junyan Wang, Qian Ma, Linlin Yang, Rebecca Schulman, Da Han, Weihong Tan. A DNA circuit that records molecular events. Science Advances, 2024.10.1126/sciadv.adn3329 Link to Original
Yanqi Jiang, Michael S. Pacella, Sojeong Lee, Jasen Zhang, Jonathan A. Gunn, Paul Vallejo, Pragya Singh, Tiffany Hou, Evan Liu, Rebecca Schulman. Hierarchical Assembly and Modeling of DNA Nanotube Networks using Y-shaped DNA. Nanoscale, 2024. Link to Original
Joshua Cole, Rebecca Schulman. Limiting the Broadcast Range of a Secreting Cell during Intercellular Signaling Using Protease-Mediated Degradation. ACS Synthetic Biology, 2024. 10.1021/acssynbio.4c00042 Link to Original
Samuel W. Schaffter, Eli Kengmana, Joshua Fern, Shane R. Byrne, Rebecca Schulman. Strategies to Reduce Promoter-Independent Transcription of DNA Nanostructures and Strand Displacement Complexes. ACS Synthetic Biology, 2024. 10.1021/acssynbio.3c00726 Link to Original
Colin Yancey, Rebecca Schulman. Distinguishing genlet circuit input pulses via a pulse detector. Natural Computing, 2024. 10.1007/s11047-024-09992-3 Link to Original
Moshe Rubanov, Joshua Cole, Heon-Joon Lee, Leandro G. Soto Cordova, Zachary Chen, Elia Gonzalez, Rebecca Schulman. Multi-domain automated patterning of DNA-functionalized hydrogels. PLoS ONE 19(2): e0295923. https://doi.org/10.1371/journal.pone.0295923, 2024 Link to Original Download
2023
Fern, J., Shi, R., Liu, Y., Xiong, Y., Gracias, D. H.*, Schulman, R*. Swelling characteristics of DNA polymerization gels. Soft Matter, DOI: 10.1039/D3SM00321C [3.2], 2023 Supplemental Materials Link to Original. Download
Helena Hall-Thomsen, Shavier Small, Momcilo Gavrilov, Taekjip Ha, Rebecca Schulman, and Pepijn Gerben Moerman. Directing Uphill Strand Displacement with an Engineered Superhelicase. ACS Synth. Biol. https://doi.org/10.1021/acssynbio.3c00452, 2023 Download Link to Original
Misha Rubanov, Josh Cole, Heon-Joon Lee. Rebecca Schulman. MAPDH Patterning Protocol. protocols.io, 10.17504/protocols.io.j8nlkw2ywl5r/v1, 2023 Download Link to Original
Heonjoon Lee, Tian Xie, Xinjie Yu, Samuel W. Schaffter, Rebecca Schulman. Plug-and-play protein biosensors using aptamer-regulated in vitro transcription. bioRxiv 2023.08.10.552680; doi: https://doi.org/10.1101/2023.08.10.552680, 2023 Download Link to Orginal Supplemental Materials
Pepijn G. Moerman, Huang Fang, Thomas E. Videbæk, W. Benjamin Rogers, Rebecca Schulman. A simple method to reprogram the binding specificity of DNA-coated colloids that crystallize. Soft Matter 10.1039/D3SM01105D 2023, 19, 8779-8789 Link to Original Download Supplemental Materials
2022
Liu, A.P.*, Appel, E.A., Ashby, P.D., Baker, B.M, Franco, E., Gu, L., Haynes K., Joshi, N.S., Kloxin, A.M., Kouwer, P.H.J., Mittal J., Morsut, L., Noireaux, V., Parekh, S., Schulman, R., Stephanopolous, N., Tang, S.K.Y., Valentine, M.T., Vega, S.L., Weber, W., Chauduri, O.* The living interface between synthetic biology and biomaterial design. Nature Materials, 21, 390–397. https://doi.org/10.1038/s41563-022-01231-3 [41.2] 2022 Link to Original Download
Kuan-Lin Chen, Rebecca Schulman.Exploring Material Design Space with a Deep-Learning Guided Genetic Algorithm. 28th International Conference on DNA Computing and Molecular Programming (DNA 28), 10.4230/LIPIcs.DNA.28.4 2022 Link to Original Download Supplemental Materials
Yi Li, Christopher Maffeo, Himanshu Joshi, Aleksei Aksimentiev, Brice Menardand, Rebecca Schulman. Leakless end-to-end transport of small molecules through micron-length DNA nanochannels. Science Advances Vol 8, Issue 36 10.1126/sciadv.abq4834 2022 Link to original Download Supplemental Materials 1 2
Phillip J. Dorsey, Dominic Scalise, Rebecca Schulman. A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides. R. Soc. open sci.9. 10.1098/rsos.220200 2022 Link to Original Download Supplemental Materials
Moshe Rubanov, Phillip J. Dorsey, Dominic Scalise, Rebecca Schulman. Sequential Activation of Spatially Localized Oligonucleotides. ACS Materials Letters 10.1021/acsmaterialslett.2c00286 2022 Link to Original Download Supplemental Materials Video 1 Video 2 Erratum Erratum Materials
Samuel W. Schaffter, Kuan-Lin Chen, Jackson O’Brien, Madeline Noble, Arvind Murugan & Rebecca Schulman. Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks. Nature Chemistry. 10.7281/T1/UBSZF1 2022 Link to Original Download Supplemental Materials
Pepijn Moerman, Momcilo Gavrilov, Taekjip Ha., Rebecca Schulman. Catalytic DNA Polymerization Can Be Expedited by Active Product Release. Angewandte Chemie, 10.26434/chemrxiv-2022-3k98v, 2022 Download Supplemental Materials Link to Original
Naresh Niranjan Dhanasekar, Yi Li and Rebecca Schulman. The ion permeability of DNA nanotube channels. bioRxiv, 10.1101/2022.03.04.482952, 2022 Link to Original Download Supplemental Materials
2021
Sisi Jia, Siew Cheng Phua, Yuta Nihongaki, Yizeng Li, Michael Pacella, Yi Li, Abdul Mohammed, Sean Sun, Takanari Inoue and Rebecca Schulman
Growth and site-specific organization of micron-scale biomolecular devices on living mammalian cells
Nature Communications, 12, pp 5729, 10.1038/s41467-021-25890, 2021 Download Link to Original Supplemental Materials
2020
Samuel Schaffter, Dominic Scalise, Terence Murphy, Anusha Patel and Rebecca Schulman
Feedback regulation of crystal growth by buffering monomer concentration
Nature Communications, 11(1) pp 6057,10.1038/241467-020-19882-8, 2020 Download Supplemental Material Link to Original Associated Data and Code
Samuel Schaffter, Joanna Schneider, Deepak Agrawal, Michael Pacella, Eric Rothchild, Terence Murphy and Rebecca Schulman
Reconfiguring DNA Nanotube Architectures via Selective Regulation of Terminating Structures
ACS Nano, 14, 10, pp 13451–13462, 10.1021/acsnano.0c05340, 2020. Download Supplemental Material Link to Original
Ruohong Shi, Joshua Fern, Weinan Xu, Sisi Jia, Qi Huang, Gayatri Pahapale, Rebecca Schulman and David H. Gracias
Multicomponent DNA Polymerization Motor Gels
Small, 16, 2002946, 10.1002/smll.202002946, 2020. Download Supplemental Material Link to Original
Philip Dorsey, Dominic Scalise and Rebecca Schulman
DNA Reaction-Diffusion Attractor Patterns
Angewandte Chemie, 60, pp 338,10.1002/anie.202009756, 2020. Download Supplemental Material Link to Original German Edition
Pepijn Moerman and Rebecca Schulman
DNA Computation Improves Diagnostic Workflows
Nature Nanotechnology, 15, pp 626–627,10.1038/241565-020-0710-9, 2020. Download Link to Original
Xinyu Cui, Dominic Scalise and Rebecca Schulman
Powering DNA Strand-displacement Reactions with a Continuous Flow Reactor
Natural Computing, 20, 4, pp 821–827, 10.1007/s11047-020-09795-2, 2020. Download Supplemental Material Link to Original
Deepak Agrawal and Rebecca Schulman
Modular protein-oligonucleotide signal exchange
Nucleic Acids Research, 48, 12, pp 6431-6444, 2020. Download Supplemental Material Link to Original
Dominic Scalise, Moshe Rubanov, Katherine Miller, Leo Potters, Madeline Noble and Rebecca Schulman
Programming the Sequential Release of DNA
ACS Synthetic Biology, 9(4), pp 749-755, 2020. Download Supplemental Materials Link to Original
Michael Pacella, Vahid Mardanlou, Siddhart Agarwal, Anusha Patel, Elizabeth Jelezniakov, Abdul Mohammed, Elisa Franco and Rebecca Schulman
Characterizing the Length-Dependence of DNA Nanotube End-to-End Joining Rates
Molecular Systems Design & Engineering, 5, pp 544-558, 2020. Download Link to Original
2019
Phillip Dorsey, Misha Rubanov, Wenlu Wang and Rebecca Schulman
Digital maskless photolithographic patterning of DNA-functionalized poly(ethylene glycol) diacrylate hydrogels with visible light enabling photo-directed release of oligonucleotides
ACS Macro Letters, 8, pp 1133-1140, 2019. Download Supplemental Materials Link to Original
Samuel Schaffter and Rebecca Schulman
Building in vitro transcriptional regulatory networks that integrate multiple functional circuit motifs
Nature Chemistry,11, pp 829-838, 2019. Download Link to Original Supplementary Materials
Yi Li and Rebecca Schulman
DNA Nanotubes that Self-Heal in Serum
Nano Letters, 19 (6), pp 3751-3760, 2019. Download Supplementary Material Link to Original Supplementary movies
Yi Li and Rebecca Schulman
Talking across the Membrane
Nature Chemistry, 11, pp 18-20, 2019. Download Link to Original
Dominic Scalise and Rebecca Schulman
Control of Matter at the Molecular Scale with DNA Circuits
Annual Review of Biomedical Engineering, 21, pp 469-493, 2019. Download Link to Original
2018
John Zenk, Matthew Billups and Rebecca Schulman
Optimizing Component-Component Interaction Energies in the Self-Assembly of Finite, Multicomponent Structures
ACS Omega, 3 (12), pp 18753 – 18761, 2018. Download Supplementary Material Link to Original
Dominic Scalise, Nisita Dutta and Rebecca Schulman
DNA Strand Buffers
Journal of the American Chemical Society, 140 (38), pp 12068-12076, 2018. Download Supplementary material Link to Original
Joshua Fern and Rebecca Schulman
Modular DNA strand-displacement controllers for directing material expansion
Nature Communications 9, Article 3766, 2018. Download Supplementary material Link to original
Samuel W. Schaffter, Leopold N. Green, Joanna Schneider, Hari KK Subramanian, Rebecca Schulman and Elisa Franco
T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures
Nucleic Acids Research, 46 (10), pp 5332-5343, 2018. Download Supplementary material Link to original
2017
Friedrich C. Simmel and Rebecca Schulman.
Self-organizing materials built with DNA
Materials Research Society (MRS) Bulletin, 42 (12), pp 913-919, 2017. Download Link to original
Angelo Cangialosi, ChangKyu Yoon, Jiayu Liu, Qi Huang, Jingkai Guo, Thao D. Nguyen, David H. Gracias and Rebecca Schulman.
DNA Sequence-Directed Shape Change of Photopatterned Hydrogels via High-Degree Swelling
Science 357, pp 1126-1130, 2017. Download Supplementary material Supplementary movies Link to original
Deepak K. Agrawal, Ruoyu Jiang, Seth Reinhart, Abdul M. Mohammed, Tyler D. Jorgenson and Rebecca Schulman.
Terminating DNA Tile Assembly with Nanostructured Caps
ACS Nano, 11 (10), pp 9770-9779, 2017. Download Supplementary material Supplementary movies Link to original Erratum
Joshua Fern and Rebecca Schulman.
Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium
ACS Synthetic Biology, 6 (9), pp 1774-1783, 2017. Download Supplementary material Link to original
Abdul M Mohammed, Petr Sulc, John Zenk and Rebecca Schulman.
Self-Assembling DNA Nanotubes to Connect Molecular Landmarks.
Nature Nanotechnology 12, pp 312-316, 2017. Download Supplementary material Supplementary movies Link to original
John Zenk, Dominic Scalise, Kai-Yuan Wang, Philip Dorsey, Joshua Fern, Ariana Cruz and Rebecca Schulman.
Stable DNA-Based Reaction-Diffusion Patterns
RSC Advances, 7, pp 18032-18040, 2017. Download Supplementary material Link to original
Tyler D. Jorgenson, Abdul M Mohammed, Deepak K. Agrawal and Rebecca Schulman.
Self-Assembly of Hierarchical DNA Nanotube Architectures with Well-Defined Geometries.
ACS Nano, 17, pp 1927-1936, 2017. Download Supplementary material Link to original
Abdul M Mohammed, Lourdes Velazquez, Allison Chisenhall, Daniel Schiffels, Deborah K Fygenson and Rebecca Schulman.
Self-Assembly of Precisely Defined DNA Nanotube Superstructures Using DNA Origami Seeds.
Nanoscale, 9, pp 522-526, 2017. Download Supplementary material Link to original
2016
Joshua Fern, Dominic Scalise, Angelo Cangialosi, Dylan Howie, Leo Potters and Rebecca Schulman.
DNA Strand-Displacement Timer Circuits.
ACS Synthetic Biology, 6, 190-193, 2016. Download Supplementary material Link to original
John Zenk, Chanon Tuntivate and Rebecca Schulman.
Kinetics and Thermodynamics of Watson-Crick Base Pairing Driven DNA Origami Dimerization.
Journal of the American Chemical Society, 138, 3346-3354, 2016. Download Supplementary materialLink to original
Joshua Fern, Jennifer Lu and Rebecca Schulman.
The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex.
ACS Nano, 10, 1836-1844, 2016. Download Supplementary material Link to original
2015
Deepak K. Agrawal, Elisa Franco and Rebecca Schulman.
A self-regulating biomolecular comparator for processing oscillatory signals
Journal of The Royal Society Interface 12.111, 20150586, 2015. Download Supplementary material Link to original
Rebecca Schulman, Christina Wright and Erik Winfree.
Increasing Redundancy Exponentially Reduces Error Rates during Algorithmic Self-Assembly
ACS Nano 9, 5760-5771, 2015. Download Supplementary material Link to original.
Rebecca Schulman and David Doty.
Designing Ordered Nucleic Acid Self-Assembly Processes.
Current Opinion in Structural Biology 31, 57-63, 2015. Download Link to original
2014
Dominic Scalise and Rebecca Schulman.
Emulating Cellular Automata in Chemical Reaction-Diffusion Networks.
In Proceedings of the 20th Annual Conference on DNA Computing and Molecular Programming, 2014. Download Link to original.
Natural Computing, online first Download Link to original.
John Zenk and Rebecca Schulman.
An Assembly Funnel Makes Biomolecular Complex Assembly Efficient.
PLoS One 9 (10): e11123, 2014. Download Link to original.
Dominic Scalise and Rebecca Schulman.
Designing modular reaction-diffusion programs for complex pattern formation.
Technology 02 55-66, 2014. Download Link to original.
2013
Abdul M. Mohammed and Rebecca Schulman.
Directing Self-Assembly of DNA Nanotubes Using Programmable Seeds.
Nano Letters 13 (9) 4006-4013, 2013. Download Supplementary Material Link to original
Simulation code (matlab scripts) (All files are collected into a single zip archive.)
2012
Stephen Whitelam, Rebecca Schulman and Lester O. Hedges.
Self-assembly of multicomponent structures in and out of equilibrium.
Physical Review Letters 109 (26) 265506, 2012. Download Supplementary Material Link to original
Rebecca Schulman, Bernard Yurke and Erik Winfree.
Robust Self-Replication of Combinatorial Information via Crystal Growth and Scission.
Proceedings of the National Academy of Science, 109 (17) 6405-6410, 2012.
Download Supplementary Material Link to original
Rebecca Schulman and Erik Winfree.
Simple Evolution of Complex Crystal Species.
Natural Computing, 11, 187-197, 2012. Link
2011 and Before
Rebecca Schulman.
Beyond Biology: Designing a New Mechanism for Self-Replication and Evolution at the Nanoscale.
In Proceedings of the Conference on Genetics and Evolutionary Computation (GECCO), 2011. Link
Rebecca Schulman and Bernard Yurke.
A Molecular Algorithm for Path Self-Assembly in 3 Dimensions.
In Proceedings of Robotics: Science and Systems, 2010. Link
Rebecca Schulman and Erik Winfree.
Simple Evolution of Complex Crystal Species.
In Proceedings of the 16th Annual Conference on DNA Computing and Molecular Programming, 2010. Link
Rebecca Schulman and Erik Winfree.
Programmable control of nucleation for algorithmic self-assembly.
SIAM Journal of Scientific Computing , 39 (4) 1581-1616, 2009. Link or ArXiv version
Robert Barish, Rebecca Schulman, Paul Rothemund and Erik Winfree.
An Information-Bearing Seed for Algorithmic Self-Assembly.
Proceedings of the National Academy of Sciences USA, 106 (15), 6054-–6059, 2009. Link
Rebecca Schulman and Erik Winfree.
How Crystals that Sense and Respond to Their Environments Could Evolve.
Natural Computing, 7 (2) 219-237, 2008. Link
Rebecca Schulman and Erik Winfree.
Synthesis of Crystals with a Programmable Barrier to Nucleation.
Proceedings of the National Academy of Sciences USA, 104 (39), 15236-15241, 2007. Link
Ho-Lin Chen, Rebecca Schulman, Ashish Goel and Erik Winfree.
Reducing Facet Nucleation During Algorithmic Self-Assembly.
Nano Letters, 7 (9), 2913-2919, 2007. Link
Rebecca Schulman and Erik Winfree.
Self-Replication and Evolution of DNA Crystals.
In Proceedings of the VIIIth European Conference on Artificial Life, 2005. Link
Rebecca Schulman and Erik Winfree.
Programmable Control of Nucleation for Algorithmic Self-Assembly (Extended Abstract).
In Proceedings of the 10th Annual Conference on DNA-Based Computation, 2004. Link
Rebecca Schulman, Shaun Lee, Nick Papadakis and Erik Winfree.
One-dimensional boundaries for DNA tile self-assembly.
In Proceedings of the 9th Annual Conference on DNA-Based Computation, 2003. Link