Dmitry Lyumkis

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 46

Top Topics

Structural Basis

Convolutional Neural Network

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

Nucleic acids research

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

Publications

Sriram Aiyer, Philip R Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani, Marianne E Bowman, Gordon Louie, Dario Oliveira Passos, Selena Đorđević-Marquardt, Mario Mietzsch, Joshua A Hull, Shuichi Hoshika, Benjamin A Barad, Danielle A Grotjahn, Robert McKenna, Mavis Agbandje-McKenna, Steven A Benner, Joseph A P Noel, Dong Wang, Yong Zi Tan, Dmitry Lyumkis
Overcoming resolution attenuation during tilted cryo-EM data collection. Nature communications 15 (1) (2024)
Sriram Aiyer, Philip R Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani, Marianne E Bowman, Gordon Louie, Dario Oliveira Passos, Selena Đorđević-Marquardt, Mario Mietzsch, Joshua A Hull, Shuichi Hoshika, Benjamin A Barad, Danielle A Grotjahn, Robert McKenna, Mavis Agbandje-McKenna, Steven A Benner, Joseph A P Noel, Dong Wang, Yong Zi Tan, Dmitry Lyumkis
Overcoming resolution attenuation during tilted cryo-EM data collection. Nature communications 15 (1) (2024)
Sriram Aiyer, Philip R Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani, Marianne E Bowman, Gordon Louie, Dario Oliveira Passos, Selena Đorđević-Marquardt, Mario Mietzsch, Joshua A Hull, Shuichi Hoshika, Benjamin A Barad, Danielle A Grotjahn, Robert McKenna, Mavis Agbandje-McKenna, Steven A Benner, Joseph A P Noel, Dong Wang, Yong Zi Tan, Dmitry Lyumkis
Overcoming resolution attenuation during tilted cryo-EM data collection. Nature communications 15 (1) (2024)
Sriram Aiyer, Philip R Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani, Marianne E Bowman, Gordon Louie, Dario Oliveira Passos, Selena Đorđević-Marquardt, Mario Mietzsch, Joshua A Hull, Shuichi Hoshika, Benjamin A Barad, Danielle A Grotjahn, Robert McKenna, Mavis Agbandje-McKenna, Steven A Benner, Joseph A P Noel, Dong Wang, Yong Zi Tan, Dmitry Lyumkis
Overcoming resolution attenuation during tilted cryo-EM data collection. Nature communications 15 (1) (2024)
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae, Dmitry Lyumkis, James R Williamson
Assembly of the Bacterial Ribosome with Circularly Permuted rRNA. bioRxiv : the preprint server for biology (2024)
Avik Biswas, Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M Levy
Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Avik Biswas, Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M Levy
Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae, Dmitry Lyumkis, James R Williamson
Assembly of the bacterial ribosome with circularly permuted rRNA. Nucleic acids research (2024)
Avik Biswas, Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M Levy
Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Dave Van Veen, Jesus G Galaz-Montoya, Liyue Shen, Philip R Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John M Pauly
Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. bioRxiv : the preprint server for biology (2024)
Avik Biswas, Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M Levy
Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Tao Jing, Zelin Shan, Tung Dinh, Avik Biswas, Sooin Jang, Juliet Greenwood, Min Li, Zeyuan Zhang, Gennavieve Gray, Hye Jeong Shin, Bo Zhou, Dario Oliveira Passos, Sriram Aiyer, Zhen Li, Robert Craigie, Alan N Engelman, Mamuka Kvaratskhelia, Dmitry Lyumkis
Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. bioRxiv : the preprint server for biology (2024)
Dave Van Veen, Jesus G Galaz-Montoya, Liyue Shen, Philip R Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John M Pauly
Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. bioRxiv : the preprint server for biology (2024)
Tao Jing, Zelin Shan, Tung Dinh, Avik Biswas, Sooin Jang, Juliet Greenwood, Min Li, Zeyuan Zhang, Gennavieve Gray, Hye Jeong Shin, Bo Zhou, Dario Oliveira Passos, Sriram Aiyer, Zhen Li, Robert Craigie, Alan N Engelman, Mamuka Kvaratskhelia, Dmitry Lyumkis
Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. bioRxiv : the preprint server for biology (2024)
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae, Dmitry Lyumkis, James R Williamson
Assembly of the Bacterial Ribosome with Circularly Permuted rRNA. bioRxiv : the preprint server for biology (2024)
Sriram Aiyer, Philip R Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani, Marianne E Bowman, Gordon Louie, Dario Oliveira Passos, Selena Đorđević-Marquardt, Mario Mietzsch, Joshua A Hull, Shuichi Hoshika, Benjamin A Barad, Danielle A Grotjahn, Robert McKenna, Mavis Agbandje-McKenna, Steven A Benner, Joseph A P Noel, Dong Wang, Yong Zi Tan, Dmitry Lyumkis
Overcoming resolution attenuation during tilted cryo-EM data collection. Nature communications 15 (1) (2024)
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae, Dmitry Lyumkis, James R Williamson
Assembly of the Bacterial Ribosome with Circularly Permuted rRNA. bioRxiv : the preprint server for biology (2024)
Dave Van Veen, Jesus G Galaz-Montoya, Liyue Shen, Philip R Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John M Pauly
Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. bioRxiv : the preprint server for biology (2024)
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae, Dmitry Lyumkis, James R Williamson
Assembly of the Bacterial Ribosome with Circularly Permuted rRNA. bioRxiv : the preprint server for biology (2024)
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae, Dmitry Lyumkis, James R Williamson
Assembly of the Bacterial Ribosome with Circularly Permuted rRNA. bioRxiv : the preprint server for biology (2024)
Dave Van Veen, Jesus G Galaz-Montoya, Liyue Shen, Philip R Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John M Pauly
Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. bioRxiv : the preprint server for biology (2024)
Kai Sheng, Xiyu Dong, Sriram Aiyer, Joan Lee, Selena Djordjevic Marquardt, Dmitry Lyumkis, James R Williamson
Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing. bioRxiv : the preprint server for biology (2024)
Tao Jing, Zelin Shan, Tung Dinh, Avik Biswas, Sooin Jang, Juliet Greenwood, Min Li, Zeyuan Zhang, Gennavieve Gray, Hye Jeong Shin, Bo Zhou, Dario Oliveira Passos, Sriram Aiyer, Zhen Li, Robert Craigie, Alan N Engelman, Mamuka Kvaratskhelia, Dmitry Lyumkis
Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. bioRxiv : the preprint server for biology (2024)
Xiyu Dong, Kai Sheng, Luca F R Gebert, Sriram Aiyer, Ian J MacRae, Dmitry Lyumkis, James R Williamson
Assembly of the bacterial ribosome with circularly permuted rRNA. Nucleic acids research (2024)
Kai Sheng, Xiyu Dong, Sriram Aiyer, Joan Lee, Selena Djordjevic Marquardt, Dmitry Lyumkis, James R Williamson
Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing. bioRxiv : the preprint server for biology (2024)
Avik Biswas, Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M Levy
Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Sriram Aiyer, Philip R Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani, Marianne E Bowman, Gordon Louie, Dario Oliveira Passos, Selena Đorđević-Marquardt, Mario Mietzsch, Joshua A Hull, Shuichi Hoshika, Benjamin A Barad, Danielle A Grotjahn, Robert McKenna, Mavis Agbandje-McKenna, Steven A Benner, Joseph A P Noel, Dong Wang, Yong Zi Tan, Dmitry Lyumkis
Overcoming resolution attenuation during tilted cryo-EM data collection. Nature communications 15 (1) (2024)
Kai Sheng, Xiyu Dong, Sriram Aiyer, Joan Lee, Selena Djordjevic Marquardt, Dmitry Lyumkis, James R Williamson
Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing. bioRxiv : the preprint server for biology (2024)
Dave Van Veen, Jesus G Galaz-Montoya, Liyue Shen, Philip R Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John M Pauly
Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. bioRxiv : the preprint server for biology (2024)
Sriram Aiyer, Philip R Baldwin, Shi Min Tan, Zelin Shan, Juntaek Oh, Atousa Mehrani, Marianne E Bowman, Gordon Louie, Dario Oliveira Passos, Selena Đorđević-Marquardt, Mario Mietzsch, Joshua A Hull, Shuichi Hoshika, Benjamin A Barad, Danielle A Grotjahn, Robert McKenna, Mavis Agbandje-McKenna, Steven A Benner, Joseph A P Noel, Dong Wang, Yong Zi Tan, Dmitry Lyumkis
Overcoming resolution attenuation during tilted cryo-EM data collection. Nature communications 15 (1) (2024)
Avik Biswas, Indrani Choudhuri, Eddy Arnold, Dmitry Lyumkis, Allan Haldane, Ronald M Levy
Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proceedings of the National Academy of Sciences of the United States of America 121 (15) (2024)
Dave Van Veen, Jesus G Galaz-Montoya, Liyue Shen, Philip R Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John M Pauly
Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. bioRxiv : the preprint server for biology (2024)
Daniel B Haack, Boris Rudolfs, Cheng Zhang, Dmitry Lyumkis, Navtej Toor
Structural basis of branching during RNA splicing. Nature structural & molecular biology (2023)
Xiyu Dong, Lili K Doerfel, Kai Sheng, Jessica N Rabuck-Gibbons, Anna M Popova, Dmitry Lyumkis, James R Williamson
Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways. Nucleic acids research (2023)
Kai Sheng, Ning Li, Jessica N Rabuck-Gibbons, Xiyu Dong, Dmitry Lyumkis, James R Williamson
Assembly landscape for the bacterial large ribosomal subunit. Nature communications 14 (1) (2023)
Xiyu Dong, Lili K Doerfel, Kai Sheng, Jessica N Rabuck-Gibbons, Anna M Popova, Dmitry Lyumkis, James R Williamson
Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways. Nucleic acids research (2023)
Juntaek Oh, Zelin Shan, Shuichi Hoshika, Jun Xu, Jenny Chong, Steven A Benner, Dmitry Lyumkis, Dong Wang
A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nature communications 14 (1) (2023)
Min Li, Dario Oliveira Passos, Zelin Shan, Steven J Smith, Qinfang Sun, Avik Biswas, Indrani Choudhuri, Timothy S Strutzenberg, Allan Haldane, Nanjie Deng, Zhaoyang Li, Xue Zhi Zhao, Lorenzo Briganti, Mamuka Kvaratskhelia, Terrence R Burke, Ronald M Levy, Stephen H Hughes, Robert Craigie, Dmitry Lyumkis
Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. Science advances 9 (29) (2023)
Jerry Joe E K Harrison, Dario Oliveira Passos, Jessica F Bruhn, Joseph D Bauman, Lynda Tuberty, Jeffrey J DeStefano, Francesc Xavier Ruiz, Dmitry Lyumkis, Eddy Arnold
Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation. Science advances 8 (27) (2022)
Allison Ballandras-Colas, Vidya Chivukula, Dominika T Gruszka, Zelin Shan, Parmit Kumar Singh, Valerie E Pye, Rebecca K McLean, Gregory J Bedwell, Wen Li, Andrea Nans, Nicola J Cook, Hind J Fadel, Eric M Poeschla, David J Griffiths, Javier Vargas, Ian A Taylor, Dmitry Lyumkis, Hasan Yardimci, Alan N Engelman, Peter Cherepanov
Multivalent interactions essential for lentiviral integrase function. Nature communications 13 (1) (2022)
Ilona K Jóźwik, Wen Li, Da-Wei Zhang, Doris Wong, Julia Grawenhoff, Allison Ballandras-Colas, Sriram Aiyer, Peter Cherepanov, Alan N Engelman, Dmitry Lyumkis
B-to-A transition in target DNA during retroviral integration. Nucleic acids research 50 (15) (2022)
Christiane Brugger, Cheng Zhang, Margaret M Suhanovsky, David D Kim, Amy N Sinclair, Dmitry Lyumkis, Alexandra M Deaconescu
Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. Nature communications 11 (1) (2020)
Dario Oliveira Passos, Min Li, Ilona K Jóźwik, Xue Zhi Zhao, Diogo Santos-Martins, Renbin Yang, Steven J Smith, Youngmin Jeon, Stefano Forli, Stephen H Hughes, Terrence R Burke, Robert Craigie, Dmitry Lyumkis
Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science (New York, N.Y.) 367 (6479) (2020)
Pratibha C Koneru, Ashwanth C Francis, Nanjie Deng, Stephanie V Rebensburg, Ashley C Hoyte, Jared Lindenberger, Daniel Adu-Ampratwum, Ross C Larue, Michael F Wempe, Alan N Engelman, Dmitry Lyumkis, James R Fuchs, Ronald M Levy, Gregory B Melikyan, Mamuka Kvaratskhelia
HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. eLife 8 (2019)
Yong Zi Tan, Sriram Aiyer, Mario Mietzsch, Joshua A Hull, Robert McKenna, Joshua Grieger, R Jude Samulski, Timothy S Baker, Mavis Agbandje-McKenna, Dmitry Lyumkis
Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant. Nature communications 9 (1) (2018)
Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher, Dmitry Lyumkis
Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nature methods 14 (8) (2017)