Honglue Shi

Also affiliated with Howard Hughes Medical Institute, Innovative Genomics Institute, University of California, Berkeley

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 29 papers. Top paper: “DNA mismatches reveal conformational penalties in protein–DNA recognition”.

DNA mismatches reveal conformational penalties in protein–DNA recognition

Nature(2020)10.1038/s41586-020-2843-2

N/A

0.753DataRank · unranked

150 citations

Honglue Shi, Atul Rangadurai, Harshit Sahay, Alon Senitzki, Suela Xhani +10 more

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

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2112496119

N/A

0.661DataRank · unranked

20 citations

Honglue Shi, Yu Xu, Bei Liu, Hala Abou Assi, John D. Boom +4 more

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

Nucleic Acids Research(2021)10.1093/nar/gkab936

N/A

0.500DataRank · unranked

27 citations

Isaac J. Kimsey, Stephanie Gu, Hsuan-Fu Liu, Uyen Pham, Maria A. Schumacher +2 more

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

Nucleic Acids Research(2024)10.1093/nar/gkae1192

N/A

0.484DataRank · unranked

11 citations

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

Directed evolution expands CRISPR–Cas12a genome-editing capacity

Nucleic Acids Research(2025)10.1093/nar/gkaf649

N/A

0.425DataRank · unranked

16 citations

Kai Chen, Honglue Shi, Kevin Wasko, Isabel Esain-Garcia, Marena Trinidad +4 more

Rapid measurement of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1 H CEST

(2021)10.5194/mr-2021-58

N/A

0.165DataRank · unranked

2 citations

Atul Rangadurai, Honglue Shi, Hashim M. Al‐Hashimi, Bei Liu

Improved Genome Editing by an Engineered CRISPR-Cas12a

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.02.506401

N/A

0.165DataRank · unranked

2 citations

Kai Chen, Honglue Shi, Elizabeth C. Stahl, Benjamin A. Adler, Junjie Liu +4 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.07.31.606079

N/A

0.104DataRank · unranked

1 citations

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

Rapid assessment of Watson–Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1 H CEST

Magnetic Resonance(2021)10.5194/mr-2-715-2021

N/A

0DataRank · unranked

15 citations

Atul Rangadurai, Honglue Shi, Hashim M. Al‐Hashimi, Bei Liu

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.05.447203

N/A

0DataRank · unranked

9 citations

Issac J. Kimsey, Hsuan-Fu Liu, Uyen Pham, Maria A. Schumacher, Hashim M. Al‐Hashimi +1 more

delta-Melt: Nucleic acid conformational penalties from melting experiments

Research Square(2021)10.21203/rs.3.rs-136535/v1

N/A

0DataRank · unranked

0 citations

Atul Rangadurai, Honglue Shi, Yu Xu, Bei Liu, Hala Abou Assi +3 more

Comment on mr-2021-58

(2021)10.5194/mr-2021-58-rc2

N/A

0DataRank · unranked

0 citations

Atul Rangadurai, Honglue Shi, Hashim M. Al‐Hashimi, Bei Liu

Improved genome editing by an engineered CRISPR-Cas12a

Nucleic Acids Research(2022)10.1093/nar/gkac1192

N/A

0DataRank · unranked

109 citations

Kai Chen, Honglue Shi, Elizabeth C. Stahl, Benjamin A. Adler, Marena Trinidad +5 more

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

Nucleic Acids Research(2023)10.1093/nar/gkad890

N/A

0DataRank · unranked

38 citations

Marena Trinidad, Daniel Bellieny‐Rabelo, Elaine Zhang, Hannah Karp, Petr Skopintsev +48 more

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

Nucleic Acids Research(2023)10.1093/nar/gkad1053

N/A

0DataRank · unranked

37 citations

Petr Skopintsev, Honglue Shi, Lin-Xing Chen, Benjamin A. Adler, Muntathar Al-Shimary +14 more

An RNA excited conformational state at atomic resolution

Nature Communications(2023)10.1038/s41467-023-43673-6

N/A

0DataRank · unranked

19 citations

Laura R. Ganser, Rohit Roy, Honglue Shi, Supriya Pratihar, David A. Case +2 more

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(2023)10.1021/jacs.3c04614

N/A

0DataRank · unranked

13 citations

Ainan Geng, Honglue Shi, Dawn K. Merriman, Elizabeth A. Dethoff, Loïc Salmon +2 more

CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes

(2023)10.32942/x2c31f

N/A

0DataRank · unranked

6 citations

Marena Trinidad, Daniel Bellieny‐Rabelo, Elaine Zhang, Hannah Karp, Petr Skopintsev +47 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.09.552727

N/A

0DataRank · unranked

2 citations

Petr Skopintsev, Honglue Shi, Lin-Xing Chen, Benjamin A. Adler, Muntathar Al-Shimary +12 more

RNA language models predict mutations that improve RNA function

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.05.588317

N/A

0DataRank · unranked

11 citations

Marena Trinidad, Conner J. Langeberg, Hunter Nisonoff, Seyone Chithrananda, Petr Skopintsev +11 more

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

Molecular Cell(2025)10.1016/j.molcel.2025.03.024

N/A

0DataRank · unranked

21 citations

Noor Al-Sayyad, Kevin Wasko, Marena Trinidad, Erin Doherty, Kamakshi Vohra +7 more

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

Nature Communications(2025)10.1038/s41467-025-57703-y

N/A

0DataRank · unranked

10 citations

Joshua C. Cofsky, Honglue Shi, Noor Al-Sayyad, Ivan E. Ivanov, Ashwin Balaji +3 more

2′-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states

Nucleic Acids Research(2020)10.1093/nar/gkaa928

N/A

0DataRank · unranked

113 citations

Atul Rangadurai, Honglue Shi, Bei Liu, Mary C. Clay, Kevin Erharter +4 more

Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem–loop RNAs and their implications for functional cellular assays

RNA(2020)10.1261/rna.076257.120

N/A

0DataRank · unranked

35 citations

Chia-Chieh Chu, Honglue Shi, Laura R. Ganser, Hal P. Bogerd, Kelly Huynh +4 more

Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion

Journal of Biomolecular NMR(2020)10.1007/s10858-020-00337-7

N/A

0DataRank · unranked

25 citations

Eric S. Szymanski, Isaac J. Kimsey, Honglue Shi, Hashim M. Al‐Hashimi, Atul Rangadurai

2’- O -methylation alters the RNA secondary structural ensemble

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.28.121996

N/A

0DataRank · unranked

2 citations

Honglue Shi, Bei Liu, Mary C. Clay, Kevin Erharter, Christopher Kreutz +3 more

Measuring thermodynamic preferences to form non-native conformations in nucleic acids using melting experiments reveals a rich sequence-specific DNA conformational landscape

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.26.424438

N/A

0DataRank · unranked

2 citations

Honglue Shi, Yu Xu, Bei Liu, Hala Abou Assi, John D. Boom +4 more

Revealing the high propensity of RNAs to non-specifically bind drug-like small molecules

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.02.074336

N/A

0DataRank · unranked

0 citations

Chia-Chieh Chu, Honglue Shi, Laura R. Ganser, Hal P. Bogerd, Kelly Huynh +4 more

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

Current Opinion in Structural Biology(2021)10.1016/j.sbi.2021.02.007

N/A

0DataRank · unranked

58 citations

Honglue Shi, Hashim M. Al‐Hashimi, Bei Liu