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Publications and Impact

List of Publications

Journal Publications

2025

  • Engineering a custom-sized DNA scaffold for more efficient DNA origami-based nucleic acid data storage
    Sarah E. Kobernat, Maryna Lazouskaya, Benjamin C. Balzer, Amanda Wolf, Golam M Mortuza, George D. Dickinson, Tim Andersen, William L. Hughes, Luca Piantanida & Eric J. Hayden, Synthetic Biology, (2025). doi.org/10.1093/synbio/ysaf008

2024

  • DNA-PAINT Probe Modifications Support High-Resolution Imaging with Shorter Binding Domains
    Luca Piantanida, George D. Dickinson, Jacob M. Majikes, William Clay, J. Alexander Liddle, Tim Andersen, Eric J. Hayden, Wan Kuang & William L. Hughes, ACS NANO, 18:33, (2024). doi.org/10.1021/acsnano.4c06886

2023

  • Generation of DNA oligomers with similar chemical kinetics via in-silico optimization
    Michael D. Tobiason, Bernard Yurke & William L. Hughes, Communications Chemistry, 6:226 (2023). doi.org/10.1038/s42004-023-01026-w
  • A method for storing information in DNA with improved dropout tolerance
    Golam Md Mortuza, Michael D. Tobiason, Kelsey Suyehira, , William L. Hughes, Tim Andersen & Reza Zadegan, bioRxiv, 2023.06.20.545769 (2023). doi.org/10.1101/2023.06.20.545769
  • In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)
    Golam Md Mortuza, Jorge Guerrero, Shoshanna Llewellyn,  Michael D. Tobiason, George D. Dickinson, William L. Hughes, Reza Zadegan & Tim Andersen, BMC Bioinformatics, 24:160,(2023). doi.org/10.1186/s12859-023-05264-6

2022

  • An 80MHz frame-rate 17.4% fill-factor 16×16 SPAD image array with event-based multiplexing for super-resolution microscopy
    Mehdi Bandali, Ximing Ren, Fnu Tala, William Clay, William L. Hughes, Wan Kuang & Benjamin Johnson, Proceedings Volume 12089, Advanced Photon Counting Techniques XVI; 1208902 (2022). doi.org/10.1038/s41467-021-22277-y

2021

  • An alternative approach to nucleic acid memory
    George D. Dickinson, Golam Md Mortuza, William Clay, Luca Piantanida, Christopher M. Green, Chad Watson, Eric J. Hayden, Tim Andersen, Wan Kuang, Elton Graugnard, Reza Zadegan & William L. Hughes, Nature Communications, 12:2371, (2021). doi.org/10.1038/s41467-021-22277-y
  • A PCR-free approach to random access in DNA
    Luca Piantanida, & William L. Hughes, Nature Materials, 1172:1178, (2021). doi.org/10.1038/s41563-021-01089-x
  • Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects
    Christopher M. Green, William L. Hughes, Elton Graugnard, and Wan Kuang, ACS Nano, 15, 11597:11606, (2021). doi.org/10.1021/acsnano.1c01976

2017

  • Metrology of DNA arrays by super-resolution microscopy
    Christopher M. Green, Kelly Schutt, Noah Morris, Reza M. Zadegan,
    William L. Hughes, Wan Kuang and Elton Graugnard, Nanoscale, 9, 10205, (2017). doi.org/10.1039/c7nr00928c.
  • CAGE: Chromatin Analogous Gene Expression
    Reza M. Zadegan and William L. Hughes, ACS Synthetic Biology, 6, 1800:1806, (2017). doi.org/10.1021/acssynbio.7b00045.

2016

  • Nucleic acid memory
    Victor Zhirnov, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church and William L. Hughes, Nature Materials, 15, (2016). doi.org/10.1038/nmat4594.

Conference Publications

  • 3D Nucleic Acid Memory Readout Using SPAD-Enabled Fluorescent Lifetime Imaging Microscopy
    Francis N. Mokogwu, Trevor Pratt, Mehdi Bandali, Benjamin C. Johnson, 2024 IEEE Workshop on Microelectronics and Electron Devices (WMED), 2024, doi.org/10.1109/WMED61554.2024.10534142
  • A Coding Scheme for Nucleic Acid Memory (NAM)
    Kelsey Suyehira, Simon Llewellyn, William Clay, Reza Zadegan, William L. Hughes and Tim Andersen, 2017 IEEE WORKSHOP ON MICROELECTRONICS AND ELECTRON DEVICES (WMED), 2017, pp. 1-3, doi.org/10.1109/WMED.2017.7916922

Conference Presentations

Talk contributions

  • Luca Piantanida, NanoInBio 2022 Nucleic Acid Memory: Super Resolution Microscopy enhances novel approach to DNA data storage, Le Gosier-Guadeloupe.
  • Luca Piantanida (invited), ASU Center of Molecular Design & Biomimetics Annual Symposium 2021, Digital Nucleic Acid Memory. Online event.
  • Christopher M. Green,  FNANO 2021, Correlative DNA-PAINT/AFM Microscopy of DNA Nanostructures and Characterization of Addressable Sites, Online event.
  • George D. Dickinson, FNANO 2021, Digital Nucleic AcidMemory: A New Approach to DNA-based Data Storage. Online event.

Poster contributions

  • Benjamin C. Balzer, FNANO 2025, Random Access in DNA origami for Digital Nucleic Acid Memory. Snowbird, UT.
  • Maryna Lazouskaya, FNANO 2025, Improving Large DNA Origami (11 kbp) for Enhanced Digital Nucleic Acid Memory (dNAM). Snowbird, UT.
  • Michael Tobiason, DNA30 2024. Generation of DNA oligomers with similar chemical kinetics via in-silico optimization. Maryland, NY.
  • Michael Tobiason, FNANO 2024. Generation of DNA oligomers with similar chemical kinetics via in-silico optimization. Snowbird, UT.
  • Luca Piantanida, DNA28 (2022), Nucleic Acid Memory: Super Resolution Microscopy enhances novel approach to DNA data storage. Albuquerque, NM.
  • Sarah Kobernat, DNA28 (2022), Digital Nucleic Acid Memory 2.0: Advances in storage capacity and ease-of-use. Albuquerque, NM.
  • Luca Piantanida, FNANO 2022, A DNA-PAINT approach for Nucleic Acid Memory. Online event.
  • Michael Tobiason, FNANO 2019, Engineering Kinetically Reproducible DNA Devices. Snowbird, UT.
  • Michael Tobiason, DNA25 (2019), Engineering Kinetically Uniform Sets of DNA sequences. Seattle, WA.

Dissertations/Theses

  • Optical and Electrical Interfaces for Biological Structures (PhD in Electrical and Computer Engineering)
    Mehdi Bandali, (2023). Boise State University Theses and Dissertations. doi.org/10.18122/td.2147.boisestate
  • Robust Digital Nucleic Acid Memory (PhD in Computing)
    Goalm M Mortuza, (2023). Boise State University Theses and Dissertations. doi.org/10.18122/td.2118.boisestate
  • DNA Origami Scaffold Development for Digital Nucleic Acid Memory (PhD in Biomolecular Sciences)
    Sarah E. Kobernat, (2022). Boise State University Theses and Dissertations. doi.org/10.18122/td.2025.boisestate
  • Structure Aware Smart Encoding and Decoding of Information in DNA (MSc in Computer Science)
    Llewellyn, Shoshana,  (2022). Boise State University Theses and Dissertations. doi.org/10.18122/td.2008.boisestate
  • In Silico Sequence Optimization for the Reproducible Generation of DNA Structures (PhD in Material Science and Engineering)
    Tobiason Michael D.,  (2019). Boise State University Theses and Dissertations. 1614. doi.10.18122/td/1614/boisestate
  • Nanoscale Optical and Correlative Microscopies for Quantitative Characterization of DNA Nanostructures (PhD in Material Science and Engineering)
    Green Christopher M., (2019). Boise State University Theses and Dissertations. 1639 doi.10.18122/td/1639/boisestate
  • The Development of Nucleic Acid Biosensors with Allosteric Fluorescence Signals (PhD in Biomolecular Sciences)
    Burden Steven J., (2019). Boise State University Theses and Dissertations. 1627 doi.10.18122/td/1627/boisestate
  • Using DNA For Data Storage: Encoding and Decoding Algorithm Development (MSc in Computer Science)
    Suyehira Kelsey,  (2018). Boise State University Theses and Dissertations. 1500 doi.10.18122/td/1500/boisestate

Patents

  • William L. Hughes, Elton Graugnard, Wan Kuang, Tim Andersen, Eric J. Hayden, Reza Zadegan, George D. Dickinson, Luca Piantanida, William Clay, Christopher M. Green, Golam Md Mortuza, US Patent, 17/443312, “NUCLEIC ACID MEMORY (NAM) / DIGITAL NUCLEIC ACID MEMORY (DNAM)”, 2021, US 20220025428 A1.

Undergraduate programs contributions

  • Lillian Massie, Undergraduate Research Showcase (2025), Digital Nucleic Acid Memory (dNAM) Folding Condition Optimization, Boise ID.
  • Holly Morrison, Undergraduate Research Showcase (2025), Creation of Long-term Bacterial Storage for the Digital Nucleic Acid Memory Project (dNAM), Boise ID.
  • Emily Schlothauer, Audrey Thompson, Ivan Markevych, Undergraduate Research Showcase (2025), Digital Nucleic Acid Memory: Synthesizing DNA Scaffold and Electrophoresis Optimization, Boise, ID.
  • Jeremy Naftzger, Holly Morrison, Audrey Thompson, Chloe Day, Lillian Massie, Emily Schlothauer,  Boise State Vertically Integrated Projects Showcase (2024). Digital Nucleic Acid Memory: Revolutionizing Data Storage. Boise, ID.
  • Jeremy Naftzger, Chloe Day, Audrey Thompson, Idaho Conference on Undergraduate Research (2024). Digital Nucleic Acid Memory: Up-Scaling ssDNA Synthesis of Novel P11453.1 Scaffold for DNA Origami.  Boise, ID.
  • Jeremy Naftzger, Idaho INBRE Statewide Research Conference (2024). Digital Nucleic Acid Memory: Up-Scaling ssDNA Synthesis of Novel P11453.1 Scaffold for DNA Origami. Moscow, ID.
  • Trevor Pratt, Idaho Conference on Undergraduate Research (2024). Picosecond Precision: Time-to-Digital Conversion for DNA Memory and Micro-scale Implants. Boise, ID.
  • Benjamin Balzer, Graduate Research Showcase at Boise State University (2024). Random Access and One-Pot Synthesis of DNA Origami for Digital Nucleic Acid Memory, Boise, ID.
  • Francis Mokogwu, Graduate Research Showcase at Boise State University (2024). A Single Photon Avalanche Diode (SPAD) Array for Fluorescent Lifetime Imaging Microscopy (FLIM) Applications. Boise, ID.
  • Amanda Wolf,  Idaho Conference on Undergraduate Research (2022), The efficiency of Pooled vs. Unpooled Staple Strands for Folding DNA Nanostructures. Online event.
  • Benjamin Balzer,  Idaho Conference on Undergraduate Research (2022), Custom DNA origami Scaffolds for Digital Nucleic Acid Memory. Online event.
  • Amanda Wolf,  Idaho Conference on Undergraduate Research (2021), DNA origami FRET Ruler for Nucleic Acid Memory. Online event.
  • Benjamin Balzer,  Idaho Conference on Undergraduate Research (2021), Enhancement of Digital Nucleic Acid Memory by Customizing DNA Origami Scaffolds. Online event.

Outreach