Giulia Palermo

Also affiliated with École Polytechnique Fédérale de Lausanne

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 46 papers. Top paper: “An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a”.

An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a

Nature Communications(2024)10.1038/s41467-024-45762-6

N/A

1.4DataRank · unranked

60 citations

Mohd Ahsan, Pablo Arantes, Michael Schmitz, Christelle Chanez, Martin Jínek +2 more

Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a

Nucleic Acids Research(2023)10.1093/nar/gkad1127

N/A

0.868DataRank · unranked

37 citations

Adrian M. Molina Vargas, Pablo Arantes, Amun C. Patel, Mitchell R. O’Connell, Giulia Palermo +1 more

Structural basis for Cas9 off-target activity

Cell(2022)10.1016/j.cell.2022.09.026

N/A

0.799DataRank · unranked

205 citations

Chun‐Han Lin, Antoine Cléry, Aakash Saha, Pablo Arantes, Katja Bargsten +7 more

Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9

Nature Catalysis(2022)10.1038/s41929-022-00848-6

N/A

0.659DataRank · unranked

80 citations

Kyle W. East, Jonas M. Binz, Rohaine V. Hsu, Mohd Ahsan, Pablo R. Arantes +6 more

Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9

eLife(2021)10.7554/elife.73601

N/A

0.639DataRank · unranked

70 citations

Kyle W East, Uriel N Morzan, Pablo R Arantes, Victor S Batista, George P. Lisi +2 more

Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9

Frontiers in Molecular Biosciences(2020)10.3389/fmolb.2020.00039

N/A

0.553DataRank · unranked

39 citations

Rohaine V. Hsu, Marco A. Medrano, Nehemiah T. Zewde, Yogesh B. Narkhede, Giulia Palermo +1 more

Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage

The Journal of Chemical Physics(2022)10.1063/5.0128815

N/A

0.434DataRank · unranked

17 citations

Carmelissa Norbrun, Jinping Luo, Chinmai Pindi, Souvik Sinha, Alexandra M. D’Ordine +4 more

New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.26.550755

N/A

0.345DataRank · unranked

9 citations

Raven M. Osborn, Souvik Sinha, Pablo R. Arantes, Amun C. Patel, Stephen Dewhurst +3 more

Structural and dynamic impacts of single-atom disruptions to guide RNA interactions within the recognition lobe of Geobacillus stearothermophilus Cas9

eLife(2024)10.7554/elife.99275

N/A

0.269DataRank · unranked

5 citations

Alexa L Knight, Alexandra M. D’Ordine, Chinmai Pindi, Zhi-Qiang Fan, Jinping Luo +4 more

Type III CRISPR-Cas effectors act as protein-assisted ribozymes during RNA cleavage

Research Square(2023)10.21203/rs.3.rs-2837968/v1

N/A

0.241DataRank · unranked

4 citations

Evan A. Schwartz, Jack P. K. Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L McCafferty +7 more

Factor H-Inspired Design of Peptide Biomarkers of the Complement C3d Protein

ACS Medicinal Chemistry Letters(2020)10.1021/acsmedchemlett.9b00663

N/A

0.208DataRank · unranked

3 citations

Nehemiah T. Zewde, Yogesh B. Narkhede, Rohaine V. Hsu, Dimitrios Morikis, Valentine I. Vullev +2 more

High-Fidelity, Hyper-Accurate, and Evolved Mutants Rewire Atomic Level Communication in CRISPR-Cas9

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.25.554853

N/A

0.208DataRank · unranked

3 citations

Souvik Sinha, Mohd Ahsan, Alexandra M. D’Ordine, G. Jogl, Giulia Palermo +2 more

Flexibility in PAM recognition expands DNA targeting in xCas9

eLife(2025)10.7554/elife.102538.3

N/A

0.208DataRank · unranked

3 citations

Łukasz Nierzwicki, Modesto Orozco, Jacek Czub, Giulia Palermo, Kazi Amirul Hossain

Flexibility in PAM recognition expands DNA targeting in xCas9

eLife(2024)10.7554/elife.102538

N/A

0.200DataRank · unranked

2 citations

Łukasz Nierzwicki, Modesto Orozco, Jacek Czub, Giulia Palermo, Kazi Amirul Hossain

A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.25.672025

N/A

0.199DataRank · unranked

2 citations

Aakash Saha, Delisa Ramos, Isabel Strohkendl, Alexa L. Knight, Erin Skeens +4 more

Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.618068

N/A

0.104DataRank · unranked

1 citations

Avneesh Gautam, Rohaine V. Hsu, Wilson Rodriguez, Nehemiah T. Zewde, R Harrison +8 more

Structural and dynamic impacts of single-atom disruptions to guide RNA interactions within the recognition lobe of Geobacillus stearothermophilus Cas9

eLife(2025)10.7554/elife.99275.4

N/A

0.104DataRank · unranked

1 citations

Alexa L Knight, Alexandra M D'Ordine, Chinmai Pindi, Zhi-Qiang Fan, Jinping Luo +4 more

RNA targeting and cleavage by the type III-Dv CRISPR effector complex

Nature Communications(2024)10.1038/s41467-024-47506-y

N/A

0DataRank · unranked

28 citations

Jack P. K. Bravo, Mohd Ahsan, Luis A. Macias, Caitlyn L McCafferty, Tyler L. Dangerfield +7 more

Structural and Dynamic Impacts of Single-atom Disruptions to Guide RNA Interactions within the Recognition Lobe of Geobacillus stearothermophilus Cas9

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.26.591382

N/A

0DataRank · unranked

0 citations

Alexa L Knight, Alexandra M D'Ordine, Chinmai Pindi, Zhi-Qiang Fan, Jinping Luo +4 more

Fine-tuning pH sensor H98 by remote essential residues in the hydrogen-bond network of mTASK-3

International Journal of Biological Macromolecules(2024)10.1016/j.ijbiomac.2024.132892

N/A

0DataRank · unranked

0 citations

Yifei Ye, Aakash Saha, Peng Li, Chinmai Pindi, Qi Wang +9 more

The Future of Chemistry is through Computations

QRB Discovery(2024)10.1017/qrd.2024.16

N/A

0DataRank · unranked

0 citations

Bengt Nordén, Giulia Palermo

Flexibility in PAM Recognition Expands DNA Targeting in xCas9

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.26.609653

N/A

0DataRank · unranked

0 citations

Łukasz Nierzwicki, Modesto Orozco, Jacek Czub, Giulia Palermo, Kazi Amirul Hossain

Mechanism of expanded DNA recognition in xCas9

eLife(2024)10.7554/elife.102538.1

N/A

0DataRank · unranked

0 citations

Łukasz Nierzwicki, Modesto Orozco, Jacek Czub, Giulia Palermo, Kazi Amirul Hossain

CRISPR-Cas12a REC2–Nuc interactions drive target-strand cleavage and constrain trans cleavage

Nucleic Acids Research(2025)10.1093/nar/gkaf988

N/A

0DataRank · unranked

9 citations

Aakash Saha, Lora Starrs, Pablo R. Arantes, Giulia Palermo, Gaétan Burgio +1 more

Unveiling Cas8 dynamics and regulation within a transposon-encoded Cascade–TniQ complex

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2422895122

N/A

0DataRank · unranked

7 citations

Souvik Sinha, Pablo R. Arantes, Giulia Palermo, Amun C. Patel

Flexibility in PAM Recognition Expands DNA Targeting in xCas9

eLife(2025)10.7554/elife.102538.2

N/A

0DataRank · unranked

2 citations

Łukasz Nierzwicki, Modesto Orozco, Jacek Czub, Giulia Palermo, Kazi Amirul Hossain

Structural and Dynamic Impacts of Single-atom Disruptions to Guide RNA Interactions within the Recognition Lobe of Geobacillus stearothermophilus Cas9

eLife(2025)10.7554/elife.99275.2

N/A

0DataRank · unranked

0 citations

Alexa L Knight, Alexandra M. D’Ordine, Chinmai Pindi, Zhi-Qiang Fan, Jinping Luo +4 more

ParametrizANI: Fast, Accurate, and Free Parametrization for Small Molecules

ChemRxiv(2025)10.26434/chemrxiv-2025-m26n9

N/A

0DataRank · unranked

0 citations

Souvik Sinha, Giulia Palermo, Pablo Arantes

Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a

Journal of Chemical Information and Modeling(2020)10.1021/acs.jcim.0c00929

N/A

0DataRank · unranked

64 citations

Pablo R. Arantes, Rohaine V. Hsu, Yogesh B. Narkhede, Martin Jínek, Giulia Palermo +1 more

Design Rules for Expanding PAM Compatibility in CRISPR-Cas9 from the VQR, VRER and EQR variants

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.03.673821

N/A

0DataRank · unranked

0 citations

Chinmai Pindi, George P. Lisi, Uriel N. Morzan, Giulia Palermo, Francisco H. Vieya

Gaussian accelerated molecular dynamics: Principles and applications

Wiley Interdisciplinary Reviews Computational Molecular Science(2021)10.1002/wcms.1521

N/A

0DataRank · unranked

308 citations

Pablo Arantes, Apurba Bhattarai, Rohaine V. Hsu, Shristi Pawnikar, Yu‐ming M. Huang +3 more

Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.641208

N/A

0DataRank · unranked

28 citations

Giulia Palermo, Łukasz Nierzwicki

Systems Biology Modeling of the Complement System Under Immune Susceptible Pathogens

Frontiers in Physics(2021)10.3389/fphy.2021.603704

N/A

0DataRank · unranked

9 citations

Rohaine V. Hsu, Dimitrios Morikis, Giulia Palermo, Nehemiah T. Zewde

Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters

Nucleic Acids Research(2022)10.1093/nar/gkac578

N/A

0DataRank · unranked

162 citations

Rosa Merlo, Neda Bagheri, Danila Moscone, Anna Valenti, Aakash Saha +10 more

Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167518

N/A

0DataRank · unranked

41 citations

Amun C. Patel, Giulia Palermo, Pablo R. Arantes

Celebrating Women of Color in Computational Chemistry

Journal of Chemical Information and Modeling(2022)10.1021/acs.jcim.2c00663

N/A

0DataRank · unranked

0 citations

Giulia Palermo

New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity

Nucleic Acids Research(2023)10.1093/nar/gkad1132

N/A

0DataRank · unranked

84 citations

Souvik Sinha, Raven M. Osborn, Pablo Arantes, Amun C. Patel, Stephen Dewhurst +5 more

Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes

Frontiers in Molecular Biosciences(2023)10.3389/fmolb.2022.1072733

N/A

0DataRank · unranked

22 citations

Pablo R. Arantes, Mohd Ahsan, Souvik Sinha, Gregory W. Kyro, Federica Maschietto +6 more

GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems

Molecules(2023)10.3390/molecules28031277

N/A

0DataRank · unranked

18 citations

Pablo R. Arantes, Aakash Saha, Giulia Palermo, Bryan M. Wong, Anshuman Kumar

Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease

Biophysical Journal(2023)10.1016/j.bpj.2023.11.005

N/A

0DataRank · unranked

6 citations

Federica Maschietto, Tianyin Qiu, Pablo R. Arantes, Erin Skeens, Giulia Palermo +3 more

GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems

ChemRxiv(2023)10.26434/chemrxiv-2023-vbdgm

N/A

0DataRank · unranked

2 citations

Pablo R. Arantes, Aakash Saha, Giulia Palermo, Bryan M. Wong, Anshuman Kumar

Editorial: Editing DNA and RNA through Computations

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c01824

N/A

0DataRank · unranked

1 citations

Thereza A. Soares, Giulia Palermo

RNA-mediated Allosteric Activation in CRISPR-Cas13a

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.27.550797

N/A

0DataRank · unranked

0 citations

Adrian M. Molina Vargas, Pablo Arantes, Amun C. Patel, Mitchell R. O’Connell, Giulia Palermo +1 more

Cas12a domain flexibility guides R-loop formation and forces RuvC resetting

Molecular Cell(2024)10.1016/j.molcel.2024.06.007

N/A

0DataRank · unranked

60 citations

Aakash Saha, Catherine Moy, Alexander-Hoi Nguyen, Mohd Ahsan, Rick Russell +3 more

Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e

Nucleic Acids Research(2024)10.1093/nar/gkae1066

N/A

0DataRank · unranked

24 citations

Xiaoyu Chen, Souvik Sinha, Aakash Saha, Amun C. Patel, Matthew Sample +4 more

Graph theory approaches for molecular dynamics simulations

Quarterly Reviews of Biophysics(2024)10.1017/s0033583524000143

N/A

0DataRank · unranked

24 citations

Souvik Sinha, Giulia Palermo, Amun C. Patel