DNA 보존과 Random Access 참고 논문

9주차는 보존 재료의 형성·회수와 가속 열화 평가를, 10주차는 주소 선택·분자 표본화·원본 재사용·입자 검색을 다룹니다. 각 강의의 그림에는 논문과 패널을 표시하였습니다.

9주차 강의 · 10주차 강의 · 전체 강의

DNA 장기 보존

1. Robert N. Grass, Reinhard Heckel, Michela Puddu, Daniela Paunescu, Wendelin J. Stark (2015). Robust Chemical Preservation of Digital Information on DNA in Silica with Error‐Correcting Codes.
2. Lee Organick, Bichlien H. Nguyen, Rachel McAmis, Weida D. Chen, A. Xavier Kohll, Siena Dumas Ang, Robert N. Grass, Luis Ceze, Karin Strauss (2021). An Empirical Comparison of Preservation Methods for Synthetic DNA Data Storage.
3. Elisabeth Prince, Ho Fung Cheng, James L. Banal, Jeremiah A. Johnson (2024). Reversible Nucleic Acid Storage in Deconstructable Glassy Polymer Networks.
4. Tomas Lindahl (1993). Instability and decay of the primary structure of DNA.
5. Daniela Paunescu, Michela Puddu, Justus O B Soellner, Philipp R Stoessel, Robert N Grass (2013). Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA 'fossils'.
6. Karishma Matange, James M. Tuck, Albert J. Keung (2021). DNA stability: a central design consideration for DNA data storage systems.
7. A. Xavier Kohll, Philipp L. Antkowiak, Weida D. Chen, Bichlien H. Nguyen, Wendelin J. Stark, Luis Ceze, Karin Strauss, Robert N. Grass (2020). Stabilizing synthetic DNA for long-term data storage with earth alkaline salts.
8. Jacques Bonnet, Marthe Colotte, Delphine Coudy, Vincent Couallier, Joseph Portier, Bénédicte Morin, Sophie Tuffet (2009). Chain and conformation stability of solid-state DNA: implications for room temperature storage.
9. Yi Zhang, Yangyi Liu, Li Miao, Huaxia Zhu, Yubin Ren, Kelu Zhao, Sikang Wan, Yawei Liu, Yang Yang, Chunhua Lu, Fan Wang, Xingyu Jiang, Hongjie Zhang, Chunhai Fan, Kai Liu (2025). Liquid crystal–guided DNA information storage: Nondestructive recovery and long-term preservation.
10. Qiu-Jun Liu, Qian Liu, Jie Zhang, Cheng Zhang, Long Qian, Hao Qi, Yue-Sheng Li, Dong-Po Song (2025). Photonic microspheres for high-capacity DNA data storage: Robust, straightforward, and scalable random access via nonfading indexes.
11. Alexis Ferrasse, Rodrigo Mendez, John E. Gorzynski, Chloe Reuter, Jennefer N. Carter, Michael Blas, , Alyssa A. Tran, Arjun Tarakad, Ashok Balasubramanyam, Brendan H. Lee, Carlos A. Bacino, Daryl A. Scott, Elaine Seto, Gary D. Clark, Hongzheng Dai, Hsiao-Tuan Chao, Ivan Chinn, James P. Orengo, Jill A. Rosenfeld, Kim Worley, Lindsay C. Burrage, Lisa T. Emrick, Lorraine Potocki, Monika Weisz Hubshman, Richard A. Lewis, Ronit Marom, Seema R. Lalani, Shamika Ketkar, Tiphanie P. Vogel, William J. Craigen, Jared Sninsky, Lauren Blieden, Sandesh Nagamani, Hugo J. Bellen, Michael F. Wangler, Oguz Kanca, Shinya Yamamoto, Christine M. Eng, Patricia A. Ward, Pengfei Liu, Adeline Vanderver, Cara Skraban, Edward Behrens, Gonench Kilich, Kathleen Sullivan, Kelly Hassey, Ramakrishnan Rajagopalan, Rebecca Ganetzky, Vishnu Cuddapah, Anna Raper, Daniel J. Rader, Giorgio Sirugo, Anne Slavotinek, Christopher Mayhew, Eneida Mendonca, Ziyuan Guo, Allyn McConkie-Rosell, Kelly Schoch, Mohamad Mikati, Nicole M. Walley, Rebecca C. Spillmann, Vandana Shashi, Alan H. Beggs, Calum A. MacRae, David A. Sweetser, Deepak A. Rao, Edwin K. Silverman, Elizabeth L. Fieg, Frances High, Gerard T. Berry, Ingrid A. Holm, J. Carl Pallais, Joan M. Stoler, Joseph Loscalzo, Lance H. Rodan, Laurel A. Cobban, Lauren C. Briere, Matthew Coggins, Melissa Walker, Richard L. Maas, Susan Korrick, Jessica Douglas, Cecilia Esteves, Emily Glanton, Isaac S. Kohane, Kimberly LeBlanc, Shamil R. Sunyaev, Shilpa N. Kobren, Brett H. Graham, Erin Conboy, Francesco Vetrini, Kayla M. Treat, Khurram Liaqat, Lili Mantcheva, Stephanie M. Ware, Kathleen Page, Paul Auwaerter, Yuka Manabe, Carlos A. Pardo-Villamizar, Julie Hoover-Fong, Philip Dane Witmer, Winston Timp, Matthew Robinson, Zackary Dov Berger, Elizabeth Wohler, Nara Sobreira, Arian Nouraee, Carlos Prada, Erica Davis, Kai Lee Yap, Kelly Regan-Fendt, María Paula Silva, Patrick McMullen, Breanna Mitchell, Brendan C. Lanpher, Devin Oglesbee, Eric Klee, Filippo Pinto e Vairo, Ian R. Lanza, Kahlen Darr, Lindsay Mulvihill, Lisa Schimmenti, Queenie Tan, Surendra Dasari, Abdul Elkadri, Brett Bordini, Donald Basel, James Verbsky, Julie McCarrier, Michael Muriello, Michael T. Zimmermann, Adriana Rebelo, Carson A. Smith, Deborah Barbouth, Guney Bademci, Joanna M. Gonzalez, Kumarie Latchman, LéShon Peart, Mustafa Tekin, Nicholas Borja, Stephan Zuchner, Stephanie Bivona, Willa Thorson, Herman Taylor, Rakale C. Quarells, Ayuko Iverson, Bruce Gelb, Charlotte Cunningham-Rundles, Eric Gayle, Joanna Jen, Louise Bier, Mafalda Barbosa, Manisha Balwani, Mariya Shadrina, Rachel Evard, Saskia Shuman, Susan Shin, Vaidehi Jobanputra, Andrea Gropman, Barbara N. Pusey Swerdzewski, Camilo Toro, Colleen E. Wahl, Donna Novacic, Ellen F. Macnamara, John J. Mulvihill, Maria T. Acosta, Precilla D’Souza, Valerie V. Maduro, Ben Afzali, Ben Solomon, Cynthia J. Tifft, David R. Adams, Elizabeth A. Burke, Francis Rossignol, Heidi Wood, Jiayu Fu, Joie Davis, Leoyklang Petcharet, Lynne A. Wolfe, Margaret Delgado, Marie Morimoto, Marla Sabaii, MayChristine V. Malicdan, Neil Hanchard, Orpa Jean-Marie, Wendy Introne, William A. Gahl, Yan Huang, Andrew Stergachis, Danny E. Miller, Elisabeth Rosenthal, Elizabeth Blue, Elsa Balton, Emily Shelkowitz, Eric Allenspach, Fuki M. Hisama, Gail P. Jarvik, Ghayda Mirzaa, Ian Glass, Kathleen A. Leppig, Katrina Dipple, Mark Wener, Martha Horike-Pyne, Michael Bamshad, Peter Byers, Runjun Kumar, Seth Perlman, Sirisak Chanprasert, Virginia Sybert, Wendy Raskind, Nitsuh K. Dargie, Chun-Hung Chan, Francisco Bustos velasq, Isum Ward, Jason Schend, Jennifer Morgan, Megan Bell, Miranda Leitheiser, Mohamad Saifeddine, Paul Berger, Rachel Li, Taylor Beagle, Alexander Miller, Beatriz Anguiano, Beth A. Martin, Brianna Tucker, Devon Bonner, Elijah Kravets, Hector Rodrigo Mendez, Holly K. Tabor, Jacinda B. Sampson, Jason Hom, Jennefer N. Kohler, Jennifer Schymick, Kevin S. Smith, Laura Keehan, Laurens Wiel, Meghan C. Halley, Mia Levanto, Page C. Goddard, Paul G. Fisher, Rachel A. Ungar, Raquel L. Alvarez, Sara Emami, Shruti Marwaha, Stephen B. Montgomery, Suha Bachir, Tanner D. Jensen, Taylor Maurer, Terra R. Coakley, Anna Hurst, Brandon M. Wilk, Bruce Korf, Elizabeth A. Worthey, Kaitlin Callaway, Martin Rodriguez, Pongtawat Lertwilaiwittaya, Reaford Blackburn, Tammi Skelton, Tarun K. K. Mamidi, Teneasha Washington, Andrew B. Crouse, Jordan Whitlock, Mariko Nakano-Okuno, Matthew Might, William E. Byrd, Albert R. La Spada, Changrui Xiao, Elizabeth C. Chao, Eric Vilain, Jose Abdenur, Kirsten Blanco, Maija-Rikka Steenari, Rebekah Barrick, Richard Chang, Sanaz Attaripour, Suzanne Sandmeyer, Tahseen Mozaffar, Alden Huang, Andres Vargas, Bianca E. Russell, Brent L. Fogel, Esteban C. Dell’Angelica, George Carvalho, Julian A. Martínez-Agosto, Layal F. Abi Farraj, Manish J. Butte, Martin G. Martin, Naghmeh Dorrani, Neil H. Parker, Rosario I. Corona, Stanley F. Nelson, Yigit Karasozen, Dana Sayer, Jennifer Tousseau, Aaron Quinlan, Alistair Ward, Ashley Andrews, Corrine K. Welt, Dave Viskochil, Erin E. Baldwin, John Carey, Justin Alvey, Lorenzo Botto, Nicola Longo, Paolo Moretti, Rebecca Overbury, Russell Butterfield, Steven Boyden, Thomas J. Nicholas, Matt Velinder, Gabor Marth, Pinar Bayrak-Toydemir, Rong Mao, Monte Westerfield, John A. Phillips, Kimberly Ezell, Lynette Rives, Rizwan Hamid, Alyson Krokosky, Ashley McMinn, Cathy Shyr, Eric Gamazon, Joy D. Cogan, Lakshitha Perera, Lisa Bastarache, Mary Koziura, Thomas Cassini, Alex Paul, Dana Kiley, Daniel Wegner, Erin McRoy, Jennifer Wambach, Kathy Sisco, Patricia Dickson, F. Sessions Cole, Dustin Baldridge, Jimann Shin, Lilianna Solnica-Krezel, Stephen C. Pak, Timothy Schedl, Allen Bale, Carol Oladele, Caroline Hendry, Emily Wang, Hua Xu, Hui Zhang, Lauren Jeffries, María José Ortuño Romero, Mark Gerstein, Michele Spencer-Manzon, Monkol Lek, Nada Derar, Odelya Kaufman, Shrikant Mane, Teodoro Jerves Serrano, Vasilis Vasiliou, Winston Halstead, Yong-Hui Jiang, Jonathan A. Bernstein, Matthew T. Wheeler, James L. Banal, Euan A. Ashley (2026). Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing.
12. Delphine Coudy, Marthe Colotte, Aurélie Luis, Sophie Tuffet, Jacques Bonnet (2021). Long term conservation of DNA at ambient temperature. Implications for DNA data storage.

DNA Random Access

1. Lee Organick, Siena Dumas Ang, Yuan-Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher N Takahashi, Sharon Newman, Hsing-Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, Georg Seelig, Luis Ceze, Karin Strauss (2018). Random access in large-scale DNA data storage.
2. Lee Organick, Yuan-Jyue Chen, Siena Dumas Ang, Randolph Lopez, Xiaomeng Liu, Karin Strauss, Luis Ceze (2020). Probing the physical limits of reliable DNA data retrieval.
3. Kevin N. Lin, Kevin Volkel, James M. Tuck, Albert J. Keung (2020). Dynamic and scalable DNA-based information storage.
4. Carina Imburgia, Lee Organick, Karen Zhang, Nicolas Cardozo, Jeff McBride, Callista Bee, Delaney Wilde, Gwendolin Roote, Sofia Jorgensen, David Ward, Charlie Anderson, Karin Strauss, Luis Ceze, Jeff Nivala (2025). Random access and semantic search in DNA data storage enabled by Cas9 and machine-guided design.
5. Junyao Li, Xuyang Zhao, Qingyuan Fan, Yanping Long, Ronghui Liu, Jixian Zhai, Qing Pan, Yi Li (2025). Empowering low-crosstalk, dynamic-decision random access of DNA storage via 384-multiplexed nanopore signatures.
6. James L. Banal, Tyson R. Shepherd, Joseph Berleant, Hellen Huang, Miguel Reyes, Cheri M. Ackerman, Paul C. Blainey, Mark Bathe (2021). Random access DNA memory using Boolean search in an archival file storage system.
7. Bas W. A. Bögels, Bichlien H. Nguyen, David Ward, Levena Gascoigne, David P. Schrijver, Anna-Maria Makri Pistikou, Alex Joesaar, Shuo Yang, Ilja K. Voets, Willem J. M. Mulder, Andrew Phillips, Stephen Mann, Georg Seelig, Karin Strauss, Yuan-Jyue Chen, Tom F. A. de Greef (2023). DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access.
8. Billy Lau, Shubham Chandak, Sharmili Roy, Kedar Tatwawadi, Mary Wootters, Tsachy Weissman, Hanlee P. Ji (2023). Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing.
9. S. M. Hossein Tabatabaei Yazdi, Yongbo Yuan, Jian Ma, Huimin Zhao, Olgica Milenkovic (2015). A Rewritable, Random-Access DNA-Based Storage System.
10. Qiu-Jun Liu, Qian Liu, Jie Zhang, Cheng Zhang, Long Qian, Hao Qi, Yue-Sheng Li, Dong-Po Song (2025). Photonic microspheres for high-capacity DNA data storage: Robust, straightforward, and scalable random access via nonfading indexes.
11. Jiankai Li, Cuiping Mao, Shuchen Wang, Xingjian Li, Xueqing Luo, Dou Wang, Shuo Zheng, Jialin Shao, Rui Wang, Chunhai Fan, Xingyu Jiang (2025). A compact cassette tape for DNA-based data storage.

그림 출처

원문 그림 전체 또는 표시한 패널을 사용하였으며, 부분 확대는 그림 아래에 표기하였습니다. 원본 파일은 그림 링크로 열 수 있습니다. 연구에서 측정한 값과 장기 외삽값은 구분하여 설명합니다.

• Organick et al., Nature Communications 11, 616 (2020), Fig. 1 — CC BY 4.0. 출처
• Organick et al., Nature Communications 11, 616 (2020), Fig. 2 — CC BY 4.0. 출처
• MIT researchers / MIT News — CC BY-NC-ND, 원그림 그대로. 출처
• Bonnet et al., Nucleic Acids Research (2010), Fig. 10 — CC BY-NC 2.5. 출처
• Bonnet et al., Nucleic Acids Research (2010), Fig. 6 — CC BY-NC 2.5. 출처
• MIT researchers / MIT News — CC BY-NC-ND, 원그림 그대로. 출처
• Imburgia et al., Nature Communications (2025), Fig. 1 — CC BY-NC-ND 4.0; whole figure unchanged. 출처
• Coudy et al., PLOS ONE (2021), Fig. 1 — CC BY 4.0. 출처
• Lin et al., Nature Communications (2020), Fig. 2 — CC BY 4.0. 출처
• Lin et al., Nature Communications (2020), Fig. 3a (부분 확대) — CC BY 4.0. 출처
• Lin et al., Nature Communications (2020), Fig. 3b–c (부분 확대) — CC BY 4.0. 출처
• Zhang et al., Science Advances (2025), Fig. 2A–D (부분 확대) — CC BY-NC 4.0. 출처
• Zhang et al., Science Advances (2025), Fig. 3A (부분 확대) — CC BY-NC 4.0. 출처
• Lau et al., Scientific Reports (2023), Fig. 4A (부분 확대) — CC BY 4.0. 출처
• Lau et al., Scientific Reports (2023), Fig. 1 — CC BY 4.0. 출처
• Lau et al., Scientific Reports (2023), Fig. 2D (부분 확대) — CC BY 4.0. 출처
• Poisson 분주 모형 / 교육용 모형, 측정 데이터 아님 — 강의 제작 그래프. 분자정보공학 강의용 수학·회로 모형
• NHGRI — 미국 정부 교육 그림. 출처
• Liu et al., Science Advances (2025), Fig. 4B (부분 확대) — CC BY-NC 4.0. 출처
• Liu et al., Science Advances (2025), Fig. 5E–G (부분 확대) — CC BY-NC 4.0. 출처
• Liu et al., Science Advances (2025), Fig. 5A–D (부분 확대) — CC BY-NC 4.0. 출처
• Liu et al., Science Advances (2025), Fig. 4C–F (부분 확대) — CC BY-NC 4.0. 출처
• Liu et al., Science Advances (2025), Fig. 2C–H (부분 확대) — CC BY-NC 4.0. 출처
• Organick et al., Small Methods (2021), Fig. 1 (저자 공개본) — CC BY-ND 4.0; whole figure unchanged. 출처
• Organick et al., Small Methods (2021), Fig. 2 (저자 공개본) — CC BY-ND 4.0; whole figure unchanged. 출처
• Organick et al., Small Methods (2021), Fig. 4 (저자 공개본) — CC BY-ND 4.0; whole figure unchanged. 출처
• Organick et al., Small Methods (2021), Fig. 5 (저자 공개본) — CC BY-ND 4.0; whole figure unchanged. 출처
• Matange et al., Nature Communications (2021), Fig. 1 — CC BY 4.0. 출처
• Li et al., Science Advances (2025), Fig. 6A–C (부분 확대) — CC BY-NC 4.0. 출처
• Li et al., Science Advances (2025), Fig. 2 — CC BY-NC 4.0. 출처
• Bögels et al., Nature Nanotechnology (2023), Fig. 5D (부분 확대) — CC BY 4.0. 출처
• Bögels et al., Nature Nanotechnology (2023), Fig. 1 — CC BY 4.0. 출처

강의 개편 2026년 10월 27일. 이전 강의 보관본