Junhong Choi: Publications

Preprints

*Equal contribution #Co-corresponding authors

Jihye Park*, Yoojin Chang*, Joshua Schiffman, Divya Koyyalagunta, Hrishikesh Somayaji, Caden N. McQuillen, Joseph Chan, Quaid Morris, Dan A. Landau, Hyongbum Henry Kim#, Junhong Choi#. “Time-resolved lineage recording reveals a pre-existing, heritable cell state underlying metastatic potential” bioRxiv (2026) doi.org/10.64898/2026.08.10.744013v2

Yunzheng Liu, Jihye Park, Laura Amaya, Sergi Junyent, Xiangkai Sun, Jiabao Sean Xiao, Yuqi Wang, Hao Wang, Yunrui Lu, Shoma Nakagawa, Sung-Eun Park, Wenqi Hu, Shichen Liu, Jiangbo Wei, Hyongbum Henry Kim, Matthew Thomson, Cheng-Wei Ju, Marianne E. Bronner, Junhong Choi#, Magdalena Zernicka-Goetz#. “Lineage recording across mouse embryogenesis reveals asynchronous fate restriction and plasticity at the embryonic-extraembryonic boundary” bioRxiv (2026) doi.org/10.64898/2026.10.06.756974v1

 

Publications (Peer reviewed)

*Equal contribution #Co-corresponding authors

  • Samuel G. Regalado*, Chengxiang Qiu*,#, Sanjay Kottapalli, Chau Huynh, Riza M. Daza, Aidan Keith, Jihye Park, Beth K. Martin, Wei Chen, Hanna Liao, Haedong Kim, Xiaoyi Li, Jean-Benoît Lalanne, Nobuhiko Hamazaki, Silvia Domcke, Junhong Choi#, Jay Shendure#. “A fluctuation test for gastruloid heterogeneity” Cell (2026) doi.org/10.1016/j.cell.2026.09.057
  • Qi Yu*, Haedong Kim*, Sophie Seidel*, James F. Acosta-Clark, Beth K. Martin, Kyle O’Connor, Riza M. Daza, Molly Gasperini, Jenny F. Nathans, Maggie Lam, Elena Gamo, Shruthi V. Kumar, Lauren Kuo, Jean-Benoît Lalanne, Kamen Simeonov, Marion Pepper, Cole Trapnell, Jesse M. Gray, Junhong Choi, Chengxiang Qiu#, Jay Shendure#. “A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis” Science (2026) doi.org/10.1126/science.ael0508
  • Sophie Seidel*, Antoine Zwaans*, Samuel Regalado, Junhong Choi, Jay Shendure, Tanja Stadler#. “SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data” Nature Communications 17, 7398 (2026) doi.org/10.1038/s41467-026-73377-6
  • Sung-Eun Park and Junhong Choi#. “Lineage tracing in gastruloids to understand determinants of early fate decisions” Current Opinion in Genetics and Development 99, 102498 (2026)
  • Troy A. McDiarmid*,#, Megan L. Taylor*, Florence M. Chardon, Junhong Choi, Hanna Liao, Xiaoyi Li, Haedong Kim, Jean-Benoit Lalanne, Tony Li, Jenny F. Nathans, Beth K. Martin, Jordan Knuth, Alessandro L.V. Coradini, Jesse M. Gray, Sudarshan Pinglay, Jay Shendure#. “A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording” Nature Biotechnology (2025) doi.org/10.1038/s41587-025-02896-2
  • Wei Chen# and Junhong Choi#. “Molecular circuits for genomic recording of cellular events” Trends in Genetics 41, 647-659 (2025)
  • Junhong Choi#, Wei Chen, Hanna Liao, Xiaoyi Li, Jay Shendure#. “A molecular proximity sensor based on an engineered, dual-component guide RNA” eLife (2025)
  • Amjad Askary*, Wei Chen*, Junhong Choi*, Lucia Y. Du*, Michael B. Elowitz#, James A. Gagnon#, Alexander F. Schier#, Sophie Seidel*, Jay Shendure#, Tanja Stadler#, Martin Tran*. “The lives of cells, recorded” Nature Reviews Genetics (2024)
  • Wei Chen*,#, Junhong Choi*, Xiaoyi Li, Jenny F. Nathans, Beth Martin, Wei Yang, Nobuhiko Hamazai, Chengxiang Qiu, Jean-Benoit Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure#. “Symbolic recording of signalling and cis-regulatory element activity to DNA” Nature (2024) doi.org/10.1038/s41586-024-07706-4
  • Hanna Liao*, Junhong Choi*,#, Jay Shendure#. “Molecular recording using DNA Typewriter” Nature Protocol (2024)
  • Xiaoyi Li, Wei Chen, Beth K. Martin, Diego Calderon, Choli Lee, Junhong Choi, Florence M. Chardon, Troy McDiarmid, Haedong Kim, Jean-Benoit Lalanne, Jenny F. Nathans, Jay Shendure. “Chromatin context-dependent regulation and epigenetic manipulation of prime editing” Cell 187, 10, P2411-2427.E25 (2024)
  • Tianhan Huang, Junhong Choi, Arjun Prabhakar, Joseph D. Puglisi, Alexey N. Petrov. “Partial spontaneous intersubunit rotations in actively translating ribosome” Proceedings of the National Academy of Sciences of the United States of America 120 (41), e2114979120 (2023)
  • Jendrik Hentschel, Mareike Badstuebner, Junhong Choi, Clive R. Bagshaw, Christopher P. Lapointe, Jinfan Wang, Linnea I. Jansson, Joseph D. Puglisi, Michael D. Stone. “Multiplexed single-molecule analysis of human telomerase synthesizing DNA” Biophysical Journal (2023)
  • Arjun Prabhakar*, Natalie Krahn*, Jingji Zhang*, Oscar Vargas-Rodriguez, Miri Krupkin, Ziao Fu, Francisco J Acosta-Reyes, Xueliang Ge, Junhong Choi, Ana Crnković, Måns Ehrenberg, Elisabetta Viani Puglisi, Dieter Söll#, Joseph Puglisi#. “Uncovering translation roadblocks during the development of a synthetic tRNA” Nucleic Acid Research (2022)
  • Junhong Choi#, Wei Chen, Anna Minkina, Florence M. Chardon, Chase C. Suiter, Samuel G. Regalado, Silvia Domcke, Nobuhiko Hamazaki, Choli Lee, Beth Martin, Riza M. Daza, Jay Shendure#. “A time-resolved, multi-symbol molecular recorder via sequential genome editing” Nature 608, 98-107 (2022)
  • Junhong Choi*,#, Wei Chen*, Chase C. Suiter, Choli Lee, Florence M. Chardon, Wei Yang, Anh Leith, Riza M. Daza, Beth Martin, Jay Shendure#. “Precise genome deletions using paired prime editing” Nature Biotechnology 40, 218-226 (2021)
  • Kevin P. Larsen*, Junhong Choi*, Lynnette N. Jackson*, Kalli Kappel, Jingji Zhang, Betty Ha, Dong-Hua Chen, Elisabetta Viani Puglisi. “Distinct conformational states underlie pausing during initiation of HIV-1 reverse transcription” Journal of Molecular Biology 432, 4499-4522 (2020)
  • Junhong Choi, Sinead O’Loughlin, John F. Atkins, Joseph D. Puglisi. “The energy landscape of the -1 ribosomal frameshifting” Science Advances 6, eaax6969 (2020)
  • Junhong Choi*, James Marks*, Jingji Zhang, Dong-Hua Chen, Jinfan Wang, Nora Vazquez-Laslop#, Alexander S. Mankin#, Joseph D. Puglisi#. “Dynamics of the context-specific translation arrest by chloramphenicol and linezolid” Nature Chemical Biology 16, 310-317 (2019)
  • Manasvi Verma*, Junhong Choi*, Kyle A. Cottrell*, Erica N. Thomas, Zeno Lavagnino, Pawel Szczesny, David W. Piston, Slavica Pavlovic-Djuranovic, Hani Zaher, Joseph D. Puglisi, Sergej Djuranovic. “Short translational ramp determines efficiency of protein synthesis” Nature Communication 10, 5774 (2019)
  • Viswanathan Chandrasekaran*, Szymon Juszkiewicz*, Junhong Choi, Joseph D. Puglisi, Alan Brown, Sichen Shao, Venki Ramakrishnan, Ramanujan S. Hedge. “Mechanism of ribosome stalling during translation of a poly(A) tail” Nature Structural and Molecular Biology 26, 1132-1140 (2019)
  • Jinfan Wang, Alex G. Johnson, Christopher P. Lapointe, Junhong Choi, Arjun Prabhakar, Dong-Hua Chen, Alexey Petrov, Joseph D. Puglisi. “eIF5B gates the transition from translation initiation to elongation” Nature 573, 605-608 (2019)
  • Kevin P. Larsen*, Junhong Choi*, Arjun Prabhakar, Elisabetta Puglisi, Joseph D. Puglisi. “Relating structure and dynamics in RNA biology” Cold Spring Harbor Perspectives in Biology 11, a032474 (2019)
  • Junhong Choi, Rosslyn Grosely, Elisabetta Viani Puglisi, Joseph D. Puglisi. “Expanding single-molecule fluorescence spectroscopy to capture complexity in biology” Current Opinion in Structural Biology 58, 233-240 (2019)
  • Alex G. Johnson*, Christopher P. Lapointe*, Jinfan Wang, Nicholas C. Corsepius, Junhong Choi, Gabriele Fuchs, Joseph D. Puglisi. “RACK1 on and off the ribosome” RNA 25, 881-895 (2019)
  • Aaron T. Coey, Kevin P. Larsen, Junhong Choi, Daniel J. Barrero, Joseph D. Puglisi, Elisabetta Puglisi. “Dynamic Interplay of RNA and Protein in the Human Immunodeficiency Virus-1 Reverse Transcription Initiation Complex” Journal of Molecular Biology 430, 5137-5150 (2018)
  • Junhong Choi, Rosslyn Grosely, Arjun Prabhakar, Jinfan Wang, Christopher P. Lapointe, Joseph D. Puglisi. “How messenger RNA and nascent chain sequences regulate translation elongation” Annual Review of Biochemistry 87, 421-449 (2018)
  • Junhong Choi, Gabriele Indrisiunaite, Hasan Demirci, Ka-Weng Ieong, Jinfan Wang, Arjun Prabhakar, Dan Dominissini, Gideon Rechavi, Chuan He, Måns Ehrenberg, Joseph D. Puglisi. “2’-O-methylation in mRNA disrupts tRNA decoding during translation elongation” Nature Structural and Molecular Biology 25, 208-216 (2018)
  • Junhong Choi and Joseph D. Puglisi. “Three tRNAs on the ribosome slow translation elongation” Proceedings of the National Academy of Sciences of the United States of America 114, 13691–13696 (2017)
  • Alex G. Johnson, Alexey Petrov, Gabriele Fuchs, Karim Majzoub, Rosslyn Grosely, Junhong Choi, Joseph D. Puglisi. “Fluorescently-tagged human eIF3 for single-molecule spectroscopy” Nucleic Acids Research 46, e8 (2017)
  • Arjun Prabhakar, Mark C. Capece, Alexey Petrov, Junhong Choi, Joseph D. Puglisi. “Post-termination ribosome intermediate acts as the gateway to ribosome recycling” Cell Reports 20, 161-172 (2017)
  • Arjun Prabhakar, Junhong Choi, Alexey Petrov, Jinfan Wang, Joseph D. Puglisi. “Dynamic basis of fidelity and speed in translation: coordinated multi-step mechanisms of elongation and termination” Protein Science 26, 1352-1362 (2017)
  • Jin Chen*, Junhong Choi*, Sean O’Leary*, Arjun Prabhakar, Alexey Petrov, Rosslyn Grosely, Elizabetta Viani Puglisi, Joseph D. Puglisi. “The molecular choreography of protein synthesis: translational control, regulation, pathways” Quarterly Review of Biophysics 49, e11 (2016)
  • Junhong Choi, Ka-Weng Ieong, Hasan Demirci, Jin Chen, Alexey Petrov, Arjun Prabhakar, Sean O’Leary, Dan Dominissini, Gideon Rechavi, S Michael Soltis, Måns Ehrenberg, Joseph D. Puglisi. “N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics” Nature Structural and Molecular Biology 23, 110-115 (2016)