Honglue Shi - Publications, H-index & Citations

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Honglue Shi

University of California, Berkeley

22H-index

70Paper Count

1.5KCitation Count

Published Papers 29

Publication Date

Structure and evolution-guided design of minimal RNA-guided nucleases

Science

IF45.8

2026-07-16

PREAI

Petr Skopintsev; Isabel Esain-Garcia; Evan C. DeTurk; Peter H. Yoon; Zehan Zhou; Trevor Weiss; Maris Kamalu; Ajit Chamraj; Kenneth J. Loi; Conner J. Langeberg; Ron S. Boger; Hunter Nisonoff; Hannah M. Karp; Lin-Xing Chen; Honglue Shi; Kamakshi Vohra; Jillian F. Banfield; Jamie H. D. Cate; Steven E. Jacobsen; Jennifer A. Doudna

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Efficient Transgene-Free Multiplexed Germline Editing via Viral Delivery of an Engineered TnpB

Plant Biotechnology Journal

IF10.5

2026-03-17

OAAI

Trevor Weiss; Maris Kamalu; Honglue Shi; Gabriel Wirnowski; Alice Ingelsson; Jasmine Amerasekera; Kamakshi Vohra; Marena I. Trinidad; Zheng Li; Emily Freitas; Noah Steinmetz; Charlie Ambrose; Kerry Chen; Jennifer A. Doudna; Steven E. Jacobsen

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Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing

MOLECULAR CELL

IF16.6

2025-05-01

OAAI

Shi, Honglue; Al-Sayyad, Noor; Wasko, Kevin M.; Trinidad, Marena I.; Doherty, Erin E.; Vohra, Kamakshi; Boger, Ron S.; Colognori, David; Cofsky, Joshua C.; Skopintsev, Petr; Bryant, Zev; Doudna, Jennifer A.

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Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis

NATURE PLANTS

IF13.6

2025-04-22

OAAI

Weiss, Trevor; Kamalu, Maris; Shi, Honglue; Li, Zheng; Amerasekera, Jasmine; Zhong, Zhenhui; Adler, Benjamin A.; Song, Michelle M.; Vohra, Kamakshi; Wirnowski, Gabriel; Chitkara, Sidharth; Ambrose, Charlie; Steinmetz, Noah; Sridharan, Ananya; Sahagun, Diego; Banfield, Jillian F.; Doudna, Jennifer A.; Jacobsen, Steven E.

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Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates

NATURE COMMUNICATIONS

IF15.7

2025-03-26

OAAI

Aris, Kevin D. P.; Cofsky, Joshua C.; Shi, Honglue; Al-Sayyad, Noor; Ivanov, Ivan E.; Balaji, Ashwin; Doudna, Jennifer A.

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CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

NUCLEIC ACIDS RESEARCH

IF13.1

2024-12-19

OAAI

Soczek, Katarzyna M.; Cofsky, Joshua C.; Tuck, Owen T.; Shi, Honglue; Doudna, Jennifer A.

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RNA language models predict mutations that improve RNA function

NATURE COMMUNICATIONS

IF15.7

2024-12-05

OAAI

Shulgina, Yekaterina; Trinidad, Marena I.; Langeberg, Conner J.; Nisonoff, Hunter; Chithrananda, Seyone; Skopintsev, Petr; Nissley, Amos J.; Patel, Jaymin; Boger, Ron S.; Shi, Honglue; Yoon, Peter H.; Doherty, Erin E.; Pande, Tara; Iyer, Aditya M.; Doudna, Jennifer A.; Cate, Jamie H. D.

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An RNA excited conformational state at atomic resolution

NATURE COMMUNICATIONS

IF15.7

2023-12-19

OAAI

Geng, Ainan; Ganser, Laura; Roy, Rohit; Shi, Honglue; Pratihar, Supriya; Case, David A.; Al-Hashimi, Hashim M.

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Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

NUCLEIC ACIDS RESEARCH

IF13.1

2023-11-16

OAAI

Yoon, Peter H.; Skopintsev, Petr; Shi, Honglue; Chen, LinXing; Adler, Benjamin A.; Al-Shimary, Muntathar; Craig, Rory J.; Loi, Kenneth J.; DeTurk, Evan C.; Li, Zheng; Amerasekera, Jasmine; Trinidad, Marena; Nisonoff, Hunter; Chen, Kai; Lahiri, Arushi; Boger, Ron; Jacobsen, Steve; Banfield, Jillian F.; Doudna, Jennifer A.

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CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

NUCLEIC ACIDS RESEARCH

IF13.1

2023-10-27

OAAI

Adler, Benjamin A.; Trinidad, Marena, I; Bellieny-Rabelo, Daniel; Zhang, Elaine; Karp, Hannah M.; Skopintsev, Petr; Thornton, Brittney W.; Weissman, Rachel F.; Yoon, Peter H.; Chen, Linxing; Hessler, Tomas; Eggers, Amy R.; Colognori, David; Boger, Ron; Doherty, Erin E.; Tsuchida, Connor A.; Tran, Ryan, V; Hofman, Laura; Shi, Honglue; Wasko, Kevin M.; Zhou, Zehan; Xia, Chenglong; Al-Shimary, Muntathar J.; Patel, Jaymin R.; Thomas, Vienna C. J. X.; Pattali, Rithu; Kan, Matthew J.; Vardapetyan, Anna; Yang, Alana; Lahiri, Arushi; Maxwell, Michaela F.; Murdock, Andrew G.; Ramit, Glenn C.; Henderson, Hope R.; Calvert, Roland W.; Bamert, Rebecca S.; Knott, Gavin J.; Lapinaite, Audrone; Pausch, Patrick; Cofsky, Joshua C.; Sontheimer, Erik J.; Wiedenheft, Blake; Fineran, Peter C.; Brouns, Stan J. J.; Sashital, Dipali G.; Thomas, Brian C.; Brown, Christopher T.; Goltsman, Daniela S. A.; Barrangou, Rodolphe; Siksnys, Virginius; Banfield, Jillian F.; Savage, David F.; Doudna, Jennifer A.

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Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

IF15.6

2023-10-13

OAAI

Roy, Rohit; Geng, Ainan; Shi, Honglue; Merriman, Dawn K.; Dethoff, Elizabeth A.; Salmon, Loic; Al-Hashimi, Hashim M.

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Dynamic basis for dA○dGTP and dA○d8OGTP misincorporation via Hoogsteen base pairs

NATURE CHEMICAL BIOLOGY

IF13.7

2023-04-24

OAAI

Gu, Stephanie; Szymanski, Eric S.; Rangadurai, Atul K.; Shi, Honglue; Liu, Bei; Manghrani, Akanksha; Al-Hashimi, Hashim M.

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Improved genome editing by an engineered CRISPR-Cas12a

NUCLEIC ACIDS RESEARCH

IF13.1

2022-12-20

OAAI

Ma, Enbo; Chen, Kai; Shi, Honglue; Stahl, Elizabeth C.; Adler, Ben; Trinidad, Marena; Liu, Junjie; Zhou, Kaihong; Ye, Jinjuan; Doudna, Jennifer A.

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Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2022-07-20

OAAI

Conroy, Daniel W.; Xu, Yu; Shi, Honglue; Salguero, Nicole Gonzalez; Purusottam, Rudra N.; Shannon, Matthew D.; Al-Hashimi, Hashim M.; Jaroniec, Christopher P.

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Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2022-06-07

OAAI

Rangadurai, Atul; Shi, Honglue; Xu, Yu; Liu, Bei; Abou Assi, Hala; Boom, John D.; Zhou, Huiqing; Kimsey, Isaac J.; Al-Hashimi, Hashim M.

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Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA

NUCLEIC ACIDS RESEARCH

IF13.1

2021-11-18

OAAI

Shi, Honglue; Kimsey, Isaac J.; Gu, Stephanie; Liu, Hsuan-Fu; Pham, Uyen; Schumacher, Maria A.; Al-Hashimi, Hashim M.

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Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids

CURRENT OPINION IN STRUCTURAL BIOLOGY

IF7

2021-10-01

OAAI

Liu, Bei; Shi, Honglue; Al-Hashimi, Hashim M.

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A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions

NATURE COMMUNICATIONS

IF15.7

2021-08-31

OAAI

Liu, Bei; Shi, Honglue; Rangadurai, Atul; Nussbaumer, Felix; Chu, Chia-Chieh; Erharter, Kevin Andreas; Case, David A.; Kreutz, Christoph; Al-Hashimi, Hashim M.

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Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction

NATURE COMMUNICATIONS

IF15.7

2020-11-02

OAAI

Shi, Honglue; Rangadurai, Atul; Abou Assi, Hala; Roy, Rohit; Case, David A.; Herschlag, Daniel; Yesselman, Joseph D.; Al-Hashimi, Hashim M.

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Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage

JOURNAL OF BIOLOGICAL CHEMISTRY

IF3.9

2020-11-01

OAAI

Xu, Yu; Manghrani, Akanksha; Liu, Bei; Shi, Honglue; Pham, Uyen; Liu, Amy; Al-Hashimi, Hashim M.

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Research Directions