Dmitry Lyumkis

Also affiliated with University of California San Diego

Immunology and MicrobiologyBiochemistry, Genetics and Molecular BiologyMedicine

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 44 papers. Top paper: “Overcoming resolution attenuation during tilted cryo-EM data collection”.

Overcoming resolution attenuation during tilted cryo-EM data collection

Nature Communications(2024)10.1038/s41467-023-44555-7

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0.905DataRank · unranked

24 citations

Philip R. Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani +17 more

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants

Science Advances(2023)10.1126/sciadv.adg5953

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0.843DataRank · unranked

38 citations

Dario Oliveira Passos, Zelin Shan, Steven J. Smith, Qinfang Sun, Avik Biswas +14 more

Tools for visualizing and analyzing Fourier space sampling in Cryo-EM

Progress in Biophysics and Molecular Biology(2020)10.1016/j.pbiomolbio.2020.06.003

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0DataRank · unranked

39 citations

Dmitry Lyumkis, Philip R. Baldwin

Evaluating Local and Directional Resolution of Cryo-EM Density Maps

Methods in molecular biology(2020)10.1007/978-1-0716-0966-8_8

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0DataRank · unranked

38 citations

Cheng Zhang, Philp R. Baldwin, Dmitry Lyumkis, Sriram Aiyer

HIV-1 Integrase Inhibitors That Are Active against Drug-Resistant Integrase Mutants

Antimicrobial Agents and Chemotherapy(2020)10.1128/aac.00611-20

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0DataRank · unranked

32 citations

Xue Zhi Zhao, Dario Oliveira Passos, Dmitry Lyumkis, Terrence R. Burke, Stephen H. Hughes +1 more

Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd

Nature Communications(2020)10.1038/s41467-020-17457-1

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0DataRank · unranked

24 citations

Cheng Zhang, Margaret M. Suhanovsky, David D. Kim, Amy N. Sinclair, Dmitry Lyumkis +2 more

Tools for Visualizing and Analyzing Fourier Space Sampling in Cryo-EM

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.08.140863

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0DataRank · unranked

0 citations

Dmitry Lyumkis, Philip R. Baldwin

Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs

Viruses(2021)10.3390/v13020205

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0DataRank · unranked

104 citations

Xue Zhi Zhao, Dario Oliveira Passos, Dmitry Lyumkis, Terrence R. Burke, Stephen H. Hughes +1 more

Retroviral integrase: Structure, mechanism, and inhibition

The Enzymes(2021)10.1016/bs.enz.2021.06.007

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0DataRank · unranked

15 citations

Min Li, Robert Craigie, Dmitry Lyumkis, Dario Oliveira Passos

Quantitative Mining of Compositional Heterogeneity in Cryo-EM Datasets of Ribosome Assembly Intermediates

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.23.449614

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0DataRank · unranked

2 citations

Dmitry Lyumkis, James R. Williamson, Jessica N. Rabuck-Gibbons

Cryo-EM Structure of the Pol Polyprotein Provides Insights into HIV Maturation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.03.462959

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0DataRank · unranked

2 citations

Dario Oliveira Passos, Jessica F. Bruhn, Joseph D. Bauman, Lynda Tuberty, Jeffrey J. DeStefano +4 more

Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates

Structure(2022)10.1016/j.str.2021.12.005

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0DataRank · unranked

31 citations

Dmitry Lyumkis, James R. Williamson, Jessica N. Rabuck-Gibbons

Multivalent interactions essential for lentiviral integrase function

Nature Communications(2022)10.1038/s41467-022-29928-8

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0DataRank · unranked

24 citations

Vidya Chivukula, Dominika T. Gruszka, Zelin Shan, Parmit K. Singh, Valerie E. Pye +15 more

B-to-A transition in target DNA during retroviral integration

Nucleic Acids Research(2022)10.1093/nar/gkac644

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0DataRank · unranked

21 citations

Wen Li, Dawei Zhang, Doris Wong, Julia Grawenhoff, Allison Ballandras-Colas +5 more

The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI

Biochemical Society Transactions(2022)10.1042/bst20220547

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0DataRank · unranked

4 citations

Nancy C. Horton, Dmitry Lyumkis

Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.04.519057

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0DataRank · unranked

3 citations

Dario Oliveira Passos, Zelin Shan, Steven J. Smith, Qinfang Sun, Avik Biswas +12 more

Near-Physiological in vitro Assembly of 50S Ribosomes Involves Parallel Pathways

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.09.515862

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0DataRank · unranked

2 citations

Lili K. Doerfel, Kai Sheng, Jessica N. Rabuck-Gibbons, A.M. Popova, Dmitry Lyumkis +2 more

Multivalent interactions essential for lentiviral integrase function

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.26.477893

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0DataRank · unranked

1 citations

Vidya Chivukula, Dominika T. Gruszka, Zelin Shan, Parmit K. Singh, Valerie E. Pye +15 more

Kinetic co-evolutionary models predict the temporal emergence of HIV resistance mutations under drug selection pressure

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.30.518575

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0DataRank · unranked

1 citations

Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M. Levy +1 more

Unsupervised Voxel-based Segmentation reveals a Landscape of Bacterial Ribosome Large Subunit Early Assembly

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.09.515851

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0DataRank · unranked

0 citations

Ning Li, Jessica N. Rabuck-Gibbons, Xiyu Dong, Dmitry Lyumkis, James R. Williamson +1 more

Assembly landscape for the bacterial large ribosomal subunit

Nature Communications(2023)10.1038/s41467-023-40859-w

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0DataRank · unranked

32 citations

Ning Li, Jessica N. Rabuck-Gibbons, Xiyu Dong, Dmitry Lyumkis, James R. Williamson +1 more

Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways

Nucleic Acids Research(2023)10.1093/nar/gkad082

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0DataRank · unranked

27 citations

Lili K. Doerfel, Kai Sheng, Jessica N. Rabuck-Gibbons, A.M. Popova, Dmitry Lyumkis +2 more

Structural basis of branching during RNA splicing

Nature Structural & Molecular Biology(2023)10.1038/s41594-023-01150-0

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0DataRank · unranked

16 citations

Boris Rudolfs, Cheng Zhang, Dmitry Lyumkis, Navtej Toor, Daniel B. Haack

A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase

Nature Communications(2023)10.1038/s41467-023-43735-9

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0DataRank · unranked

4 citations

Zelin Shan, Shuichi Hoshika, Jun Xu, Jenny Chong, Steven A. Benner +3 more

Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.14.548955

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0DataRank · unranked

4 citations

Philip R. Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani +17 more

Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.29.569269

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0DataRank · unranked

0 citations

Avik Biswas, Dmitry Lyumkis, Ronald Levy, Nanjie Deng, Qinfang Sun

Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure

Proceedings of the National Academy of Sciences(2024)10.1073/pnas.2316662121

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0DataRank · unranked

18 citations

Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M. Levy +1 more

Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization

Viruses(2024)10.3390/v16010076

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0DataRank · unranked

6 citations

Avik Biswas, Dmitry Lyumkis, Ronald Levy, Nanjie Deng, Qinfang Sun

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks

International Journal of Molecular Sciences(2024)10.3390/ijms25105473

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0DataRank · unranked

7 citations

Jesús G. Galaz-Montoya, Liyue Shen, Philip R. Baldwin, Akshay Chaudhari, Dmitry Lyumkis +4 more

Assembly of the bacterial ribosome with circularly permuted rRNA

Nucleic Acids Research(2024)10.1093/nar/gkae636

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0DataRank · unranked

4 citations

Kai Sheng, Luca F. R. Gebert, Sriram Aiyer, Ian J. MacRae, Dmitry Lyumkis +2 more

Two-metal ion mechanism of DNA cleavage by activated, filamentous SgrAI

Journal of Biological Chemistry(2024)10.1016/j.jbc.2024.107576

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0DataRank · unranked

1 citations

Andres Rivero-Gamez, Dmitry Lyumkis, Nancy C. Horton, Zelin Shan

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.26.577436

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0DataRank · unranked

4 citations

Zelin Shan, Tung Dinh, Avik Biswas, Sooin Jang, Juliet Greenwood +16 more

Assembly of the Bacterial Ribosome with Circularly Permuted rRNA

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.10.588894

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0DataRank · unranked

1 citations

Kai Sheng, Luca F. R. Gebert, Sriram Aiyer, Ian J. MacRae, Dmitry Lyumkis +2 more

Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.08.593220

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0DataRank · unranked

1 citations

Xiyu Dong, Sriram Aiyer, Joan Lee, Selena Djordjevic Marquardt, Dmitry Lyumkis +2 more

Using phage display for rational engineering of a higher affinity humanized 3’phosphohistidine-specific antibody

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.04.621849

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0DataRank · unranked

1 citations

Rajasree Kalagiri, Gianluca Veggiani, Robyn L. Stanfield, Indrani Choudhuri, Margaux Sala +9 more

Anti-sense oligonucleotide probing as a structural platform for studying ribonucleoprotein complex assembly

Nature Communications(2025)10.1038/s41467-025-61640-1

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0DataRank · unranked

5 citations

Xiyu Dong, Sriram Aiyer, Joan Lee, Selena Đorđević-Marquardt, Dmitry Lyumkis +2 more

Time-Resolved Fluorescence Imaging and Correlative Cryo-Electron Tomography to Study Structural Changes of the HIV-1 Capsid

ACS Nano(2025)10.1021/acsnano.5c06724

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4 citations

Jonathan R. Andino-Moncada, S.A. Buth, Atousa Mehrani, Ahinsa Ranaweera, Jincheng Shi +12 more

Oligomeric HIV-1 integrase structures reveal functional plasticity for intasome assembly and RNA binding

Nature Communications(2025)10.1038/s41467-025-64479-8

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0DataRank · unranked

4 citations

Zelin Shan, Tung Dinh, Avik Biswas, Sooin Jang, Juliet Greenwood +16 more

Pi–pi stacking interactions with viral DNA contribute to the potency of naphthyridine-based HIV-1 integrase inhibitors

NAR Molecular Medicine(2025)10.1093/narmme/ugaf039

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0DataRank · unranked

2 citations

Min Li, Steven J. Smith, Arvin Karbasi, Indrani Choudhuri, Tao Jing +4 more

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.30.651576

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0DataRank · unranked

2 citations

Indrani Choudhuri, Kenneth Huang, Qinfang Sun, Andrej Săli, Ignacia Echeverria +4 more

De Novo Hydration of Cryo-EM Reconstructions through Molecular Dynamics Simulations of the Excess Chemical Potential

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.23.655847

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0DataRank · unranked

0 citations

Sriram Aiyer, Avik Biswas, Allan Haldane, Sompriya Chatterjee, Nobuyuki Matubayasi +3 more

Structural basis for strand-transfer inhibitor binding to HIV intasomes

Science(2020)10.1126/science.aay8015

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0DataRank · unranked

111 citations

Min Li, I.K. Jozwik, Xue Zhi Zhao, Diogo Santos‐Martins, Renbin Yang +8 more

Using phage display for rational engineering of a higher-affinity humanized 3’ phosphohistidine-specific antibody

Communications Chemistry(2025)10.1038/s42004-025-01768-9

N/A

0DataRank · unranked

0 citations

Rajasree Kalagiri, Gianluca Veggiani, Robyn L. Stanfield, Indrani Choudhuri, Margaux Sala +9 more

Structural Biology of HIV Integrase Strand Transfer Inhibitors

Trends in Pharmacological Sciences(2020)10.1016/j.tips.2020.06.003

N/A

0DataRank · unranked

55 citations

Dario Oliveira Passos, Dmitry Lyumkis, I.K. Jozwik