• 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 7 December 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 Online 1 May 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
  34(5):483 DOI: 10.1038/nbt.3534. Published 1 May 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
  33(12):1293-1298 DOI: 10.1038/nbt.3404. Published 2 November 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
  523(7561): 481-485. DOI: 10.1038/nature14592. Published 22 June 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
  26(7): 425-431 (2015). DOI: 10.1089/hum.2015.084. Published 12 June 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
  137(7): 2769−2775 (2015). DOI: 10.1021/jacs.5b00445. Published 5 February 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
  33(2): 187–197 (2015). DOI: 10.1038/nbt.3117. Published 16 December 2014.
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(* Indicates shared authorship)