Ved Topkar

Three-dimensional structure-guided evolution of a ribosome with tethered subunits
Do Soon Kim, Andrew Watkins, Erik Bidstrup, Joongoo Lee, Ved V. Topkar, Camila Kofman, Kevin J. Schwarz, Yan Liu, Grigore Pintilie, Emily Roney, Rhiju Das, Michael C. Jewett
Nature Chemical Biology
DOI: https://doi.org/10.1038/s41589-022-01064-w. Published on July 14, 2022.
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Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Kathrin Leppek, Gun Woo Byeon, Wipapat Kladwang, Hannah K. Wayment-Steele, Craig H. Kerr, Adele F. Xu, Do Soon Kim, Ved V. Topkar, Christian Choe, Daphna Rothschild, Gerald C. Tiu, Roger Wellington-Oguri, Kotaro Fujii, Eesha Sharma, Andrew M. Watkins, John J. Nicol, Jonathan Romano, Bojan Tunguz, Eterna Participants, Maria Barna, Rhiju Das
Nature Communications
DOI: https://doi.org/10.1038/s41467-022-28776-w. Published on March 22, 2022.
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Defining genome-wide CRISPR–Cas genome-editing nuclease activity with GUIDE-seq
Nikolay L. Malinin, GaHyun Lee, Cicera R. Lazzarotto, Yichao Li, Zongli Zheng, Nhu T. Nguyen, Matthew Liebers, Ved V. Topkar, A. John Iafrate, Long P. Le, Martin J. Aryee, J. Keith Joung & Shengdar Q. Tsai
Nature Protocols
DOI: https://doi.org/10.1038/s41596-021-00626-x. Published on November 12, 2021.
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mRNA Transport and Local Translation in Glia
Lindsey Madsen Meservey, Ved V.Topkar, Meng-meng Fu
Trends in Cell Biology
DOI: 10.1016/j.tcb.2021.03.006. Published on April 8, 2021.
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Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures
Kalli Kappel, Kaiming Zhang, Zhaoming Su, Wipapat Kladwang, Shanshan Li, Grigore Pintilie, Ved V Topkar, Ramya Rangan, Ivan N Zheludev, Andrew M Watkins, Joseph D Yesselman, Wah Chiu, Rhiju Das
Nature Methods
DOI: 10.1038/s41592-020-0878-9. Published on July 2, 2020.
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Anomalous reverse transcription through chemical modifications in polyadenosine stretches
Wipapat Kladwang, Ved V Topkar, Bei Liu, Tracy L Hodges, Sarah C Keane, Hashim Al-Hashimi, Rhiju Das
Journal of the American Chemical Society
DOI: 10.1021/acs.biochem.0c00020. Published on May 14, 2020.
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Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant
Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils
PLoS ONE
DOI: 10.1371/journal.pone.0186324. Published on December 7, 2017.
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CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets
Shengdar Q Tsai, Nhu T Nguyen, Jose Malagon-Lopez, Ved V Topkar, Martin J Aryee, J Keith Joung
Nature Methods
DOI: 10.1038/nmeth.4278. Published on May 1, 2017.
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Open-source guideseq software for analysis of GUIDE-seq data
Shengdar Q Tsai*, Ved V Topkar*, J Keith Joung, Martin J Aryee
Nature Biotechnology
DOI: 10.1038/nbt.3534. Published on May 1, 2016.
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Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition
Benjamin P Kleinstiver, Michelle S Prew, Shengdar Q Tsai, Nhu T Nguyen, Ved V Topkar, Zongli Zheng, J Keith Joung
Nature Biotechnology
DOI: 10.1038/nbt.3404. Published on November 2, 2015.
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Engineered CRISPR-Cas9 nucleases with altered and improved PAM specificities
Benjamin P Kleinstiver, Michelle S Prew, Shengdar Q Tsai, Ved V Topkar, Nhu T Nguyen, Zongli Zheng, Andrew P W Gonzales, Zhuyun Li, Randall T Peterson, Ring-Ruey Joanna Yeh, Martin J Aryee, J Keith Joung
Nature
DOI: 10.1038/nature14592. Published on June 22, 2015.
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Dimeric CRISPR RNA-guided FolkI-dCas9 nucleases (RFNs) directed by truncated gRNAs for highly specific genome editing
Nicolas Wyvekens, Ved V Topkar, Cyd Khayter, J Keith Joung, Shengdar Q Tsai
Human Gene Therapy
DOI: 10.1089/hum.2015.084. Published on June 12, 2015.
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Replacing Uridine with 2-Thiouridine Enhances the Rate and Fidelity of Nonenzymatic RNA Primer Extension
Benjamin D Heuberger, Ayan Pal, Francesca Del Frate, Ved V Topkar, Jack W Szostak
Journal of the American Chemical Society
DOI: 10.1021/jacs.5b00445. Published on February 5, 2015.
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GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
Shengdar Q Tsai, Zongli Zheng, Nhu T Nguyen, Matthew Liebers, Ved V Topkar, Vishal Thapar, Nicolas Wyvekens, Cyd Khayter, A John Iafrate, Long P Le, Martin J Aryee, J Keith Joung
Nature Biotechnology
DOI: 10.1038/nbt.3117. Published on December 16, 2014.
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