Honglue Shi

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 29

Top Venues

Nature communications

Nucleic acids research

bioRxiv : the preprint server for biology

Science (New York, N.Y.)

Duke University (PHD)

This page only lists publications with an associated author ORCID identifier.

Education History

Duke University Sep 01 2015

United States

PHD :: Chemistry

Publications

Peter H Yoon, Zeyuan Zhang, Kenneth J Loi, Benja-Min A Adler, Arushi Lahiri, Kamakshi Vohra, Honglue Shi, Daniel Bellieny Rabelo, Marena Trinidad, Ron S Boger, Muntathar J Al-Shimary, Jennifer A Doudna
Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases. Science (New York, N.Y.) 385 (6708) (2024)
Yekaterina Shulgina, Marena I Trinidad, Conner J Langeberg, Hunter M Nisonoff, Seyone Chithrananda, Petr Skopintsev, Amos J Nissley, Jaymin R Patel, Ron S Boger, Honglue Shi, Peter H Yoon, Erin E Doherty, Tara Pande, Aditya M Iyer, Jennifer A Doudna, Jamie H D Cate
RNA language models predict mutations that improve RNA function. bioRxiv : the preprint server for biology (2024)
Peter H Yoon, Zeyuan Zhang, Kenneth J Loi, Benja-Min A Adler, Arushi Lahiri, Kamakshi Vohra, Honglue Shi, Daniel Bellieny Rabelo, Marena Trinidad, Ron S Boger, Muntathar J Al-Shimary, Jennifer A Doudna
Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases. Science (New York, N.Y.) 385 (6708) (2024)
Yekaterina Shulgina, Marena I Trinidad, Conner J Langeberg, Hunter M Nisonoff, Seyone Chithrananda, Petr Skopintsev, Amos J Nissley, Jaymin R Patel, Ron S Boger, Honglue Shi, Peter H Yoon, Erin E Doherty, Tara Pande, Aditya M Iyer, Jennifer A Doudna, Jamie H D Cate
RNA language models predict mutations that improve RNA function. bioRxiv : the preprint server for biology (2024)
Peter H Yoon, Zeyuan Zhang, Kenneth J Loi, Benja-Min A Adler, Arushi Lahiri, Kamakshi Vohra, Honglue Shi, Daniel Bellieny Rabelo, Marena Trinidad, Ron S Boger, Muntathar J Al-Shimary, Jennifer A Doudna
Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases. Science (New York, N.Y.) (2024)
Yekaterina Shulgina, Marena I Trinidad, Conner J Langeberg, Hunter M Nisonoff, Seyone Chithrananda, Petr Skopintsev, Amos J Nissley, Jaymin R Patel, Ron S Boger, Honglue Shi, Peter H Yoon, Erin E Doherty, Tara Pande, Aditya M Iyer, Jennifer A Doudna, Jamie H D Cate
RNA language models predict mutations that improve RNA function. bioRxiv : the preprint server for biology (2024)
Yekaterina Shulgina, Marena I Trinidad, Conner J Langeberg, Hunter M Nisonoff, Seyone Chithrananda, Petr Skopintsev, Amos J Nissley, Jaymin R Patel, Ron S Boger, Honglue Shi, Peter H Yoon, Erin E Doherty, Tara Pande, Aditya M Iyer, Jennifer A Doudna, Jamie H D Cate
RNA language models predict mutations that improve RNA function. bioRxiv : the preprint server for biology (2024)
Ainan Geng, Laura Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A Case, Hashim M Al-Hashimi
An RNA excited conformational state at atomic resolution. Nature communications 14 (1) (2023)
Enbo Ma, Kai Chen, Honglue Shi, Elizabeth C Stahl, Benja-Min A Adler, Marena Trinidad, Junjie Liu, Kaihong Zhou, Jinjuan Ye, Jennifer A Doudna
Improved genome editing by an engineered CRISPR-Cas12a. Nucleic acids research 50 (22) (2023)
Peter H Yoon, Petr Skopintsev, Honglue Shi, LinXing Chen, Benja-Min A Adler, Muntathar Al-Shimary, Rory J Craig, Kenneth J Loi, Evan C DeTurk, Zheng Li, Jasmine Amerasekera, Marena Trinidad, Hunter Nisonoff, Kai Chen, Arushi Lahiri, Ron Boger, Steven E Jacobsen, Jillian F Banfield, Jennifer A Doudna
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes. Nucleic acids research (2023)
Ainan Geng, Laura Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A Case, Hashim M Al-Hashimi
An RNA excited conformational state at atomic resolution. Nature communications 14 (1) (2023)
Ainan Geng, Laura Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A Case, Hashim M Al-Hashimi
An RNA excited conformational state at atomic resolution. Nature communications 14 (1) (2023)
Enbo Ma, Kai Chen, Honglue Shi, Elizabeth C Stahl, Benja-Min A Adler, Marena Trinidad, Junjie Liu, Kaihong Zhou, Jinjuan Ye, Jennifer A Doudna
Improved genome editing by an engineered CRISPR-Cas12a. Nucleic acids research 50 (22) (2023)
Ainan Geng, Laura Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A Case, Hashim M Al-Hashimi
An RNA excited conformational state at atomic resolution. Nature communications 14 (1) (2023)
Benja-Min A Adler, Marena I Trinidad, Daniel Bellieny Rabelo, Elaine Zhang, Hannah M Karp, Petr Skopintsev, Brittney W Thornton, Rachel F Weissman, Peter H Yoon, Lin-Xing Chen, Tomas Hessler, Amy R Eggers, David Colognori, Ron S Boger, Erin E Doherty, Connor A Tsuchida, Ryan V Tran, Laura Hofman, Honglue Shi, Kevin M Wasko, Zehan Zhou, Chenglong Xia, Muntathar J Al-Shimary, Jaymin R Patel, Vienna C J X Thomas, Rithu Pattali, Matthew J Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Michaela F Maxwell, Andrew G Murdock, Glenn C Ramit, Hope R Henderson, Roland W Calvert, Rebecca S Bamert, Gavin J Knott, Audrone Lapinaite, Patrick Pausch, Joshua C Cofsky, Erik J Sontheimer, Blake Wiedenheft, Peter C Fineran, Stan J J Brouns, Dipali G Sashital, Brian C Thomas, Christopher T Brown, Daniela S A Goltsman, Rodolphe Barrangou, Virginijus Siksnys, Jillian F Banfield, David F Savage, Jennifer A Doudna
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic acids research (2023)
Enbo Ma, Kai Chen, Honglue Shi, Elizabeth C Stahl, Benja-Min A Adler, Marena Trinidad, Junjie Liu, Kaihong Zhou, Jinjuan Ye, Jennifer A Doudna
Improved genome editing by an engineered CRISPR-Cas12a. Nucleic acids research 50 (22) (2023)
Ainan Geng, Laura Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A Case, Hashim M Al-Hashimi
An RNA excited conformational state at atomic resolution. Nature communications 14 (1) (2023)
Ainan Geng, Laura Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A Case, Hashim M Al-Hashimi
An RNA excited conformational state at atomic resolution. Nature communications 14 (1) (2023)
Enbo Ma, Kai Chen, Honglue Shi, Elizabeth C Stahl, Benja-Min A Adler, Marena Trinidad, Junjie Liu, Kaihong Zhou, Jinjuan Ye, Jennifer A Doudna
Improved genome editing by an engineered CRISPR-Cas12a. Nucleic acids research (2022)
Daniel W Conroy, Yu Xu, Honglue Shi, Nicole Gonzalez Salguero, Rudra N Purusottam, Matthew D Shannon, Hashim M Al-Hashimi, Christopher P Jaroniec
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 119 (30) (2022)
Honglue Shi, Isaac J Kimsey, Stephanie Gu, Hsuan-Fu Liu, Uyen Pham, Maria A Schumacher, Hashim M Al-Hashimi
Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. Nucleic acids research 49 (21) (2022)
Robert J Fick, Amy Y Liu, Felix Nussbaumer, Christoph Kreutz, Atul Rangadurai, Yu Xu, Roger D Sommer, Honglue Shi, Steve Scheiner, Allison L Stelling
Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy. The journal of physical chemistry. B 125 (28) (2021)
Bei Liu, Honglue Shi, Atul Rangadurai, Felix Nussbaumer, Chia-Chieh Chu, Kevin Andreas Erharter, David A Case, Christoph Kreutz, Hashim M Al-Hashimi
A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. Nature communications 12 (1) (2021)
Megan L Kelly, Chia-Chieh Chu, Honglue Shi, Laura R Ganser, Hal P Bogerd, Kelly Huynh, Yuze Hou, Bryan R Cullen, Hashim M Al-Hashimi
Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA (New York, N.Y.) 27 (1) (2020)
Atul Kaushik Rangadurai, Honglue Shi, Hashim M Al-Hashimi
Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields. Angewandte Chemie (International ed. in English) 59 (28) (2020)
Honglue Shi, Atul Rangadurai, Hala Abou Assi, Rohit Roy, David A Case, Daniel Herschlag, Joseph D Yesselman, Hashim M Al-Hashimi
Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nature communications 11 (1) (2020)
Ariel Afek, Honglue Shi, Atul Rangadurai, Harshit Sahay, Alon Senitzki, Suela Xhani, Mimi Fang, Raul Salinas, Zachery Mielko, Miles A Pufall, Gregory M K Poon, Tali E Haran, Maria A Schumacher, Hashim M Al-Hashimi, Raluca Gordân
DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature 587 (7833) (2020)
Honglue Shi, Bei Liu, Felix Nussbaumer, Atul Rangadurai, Christoph Kreutz, Hashim M Al-Hashimi
NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing. Journal of the American Chemical Society 141 (51) (2019)
Dawn K Merriman, Jiayi Yuan, Honglue Shi, Ananya Majumdar, Daniel Herschlag, Hashim M Al-Hashimi
Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. RNA (New York, N.Y.) 24 (10) (2018)

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Publication Activity (10 Years)

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Honglue Shi