65. Nhan Huynh, Sin Kwon, Thomas A McMurrough, Kurt W Loedige, Marjan Tavassoli, Weijuan Shao, Heyuan Qin, Khanh Luu, Balpreet Dharni, Olha Haydaychuk, Brent E Stead, David R Edgell. Harnessing RNA-based DNA repair pathways for targeted gene editing. bioRxiv (2024) https://www.biorxiv.org/content/10.1101/2024.04.09.588775v2.abstract

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64. Gary W Foo, Christopher D Leichthammer, Ibrahim M Saita, Nicholas D Lukas, Izabela Z Batko, David E Heinrichs, David R Edgell. Intein-based thermoregulated meganucleases for containment of genetic material. Nucleic Acids Research (2023) 52: 2066-2077.

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63. Thomas A Hamilton, Benjamin R Joris, Arina Shrestha, Tyler S Browne, Sébastien Rodrigue, Bogumil J Karas, Gregory B Gloor, David R Edgell. De novo synthesis of a conjugative system from human gut metagenomic data for targeted delivery of Cas9 antimicrobials. ACS Synthetic Biology (2023) 12: 3578-3590

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62. Ham, Dalton T, Tyler S. Browne, Pooja N Banglorewala, Tyler L. Wilson, Richard K. Michael, Gregory B Gloor, David R Edgell. A generalizable Cas9/sgRNA prediction model using machine learning with small high-quality datasets. Nature Communications (2023) 14, 5514

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61. Kelly, Rachel D, Gursimran Parmar, Laila Bayat, Matthew ER Maitland, Gilles A Lajoie, David R Edgell, Caroline Schild-Poulter. Noncanonical functions of Ku may underlie essentiality in human cells. Scientific Reports (2023) 13:12162.

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60. Pellegrino, Gregory P, Tyler S. Browne, Keerthana Sharath, Khaleda A Bari, Sarah J Vancuren, Emma Allen-Vercoe, Gregory G. Gloor, David R. Edgell. Metabolically-targeted dCas9 expression in bacteria. Nucleic Acids Research (2023) 51:982-996.

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59. Ryan R Cochrane, Arina Shrestha, Mariana M Severo de Almeida, Michelle Agyare-Tabbi, Stephanie L Brumwell, Samir Hamadache, Jordyn S Meaney, Daniel P Nucifora, Henry Heng Say, Jehoshua Sharma, Maximillian PM Soltysiak, Cheryl Tong, Katherine Van Belois, Emma JL Walker, Marc-André Lachance, Gregory B Gloor, David R Edgell, Rebecca S Shapiro, Bogumil J Karas. Superior Conjugative Plasmids Delivered by Bacteria to Diverse Fungi. BioDesign Research (2022) Sep 1, 2022.

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58. Brumwell, Stephanie L, Katherine D Van Belois, Daniel J Giguere, David R Edgell, and Bogumil J Karas. Conjugation-based genome engineering in Deinococcus radiodurans. ACS Synthetic Biology 11.3 (2022), pp. 1068–1076.

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57. Slattery, Samuel S, Daniel J Giguere, Stuckless, Emily E, Arina Shrestha, Lee-Ann K Briere, Alexa Galbraith, Stephen Reaume, Boyko, Xenia, Henry H Say, Tyler S Browne, et al. Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics. Scientific Reports 12.1 (2022), pp. 1–15.

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56. Cochrane, Ryan R, Brumwell, Stephanie L, Arina Shrestha, Daniel J Giguere, Samir Hamadache, Gregory B Gloor, Edgell, David R, and Bogumil J Karas. (2020) Cloning of Thalassiosira pseudonana’s

Mitochondrial Genome in Saccharomyces cerevisiae and Escherichia coli. Biology 9.11 (2020), p. 358.

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55. Cochrane, Ryan R, Brumwell, Stephanie L, Maximillian PM Soltysiak, Samir Hamadache, Jennifer G Davis, Jiayi Wang, Samuel Q Tholl, Preetam Janakirama, Edgell, David R, and Bogumil J Karas. (2020) Rapid method for generating designer algal mitochondrial genomes. Algal Research (2020), p. 102014.

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54. Slattery, Samuel S, Wang, Helen, Daniel J Giguere, Kocsis, Csanad, Bradley L Urquhart, Bogumil J

Karas, and Edgell, David R. (2020) Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing. Scientific Reports 10.1 (2020), pp. 1–12.

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53. Maximillian PM Soltysiak, Meaney, Rebecca S, Samir Hamadache, Preetam Janakirama,
Edgell, David R, and Bogumil J Karas. (2019) Trans-Kingdom Conjugation within Solid Media from Escherichia coli to Saccharomyces cerevisiae. International Journal of Molecular Sciences 20.20 (2019), p. 5212.

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52. Brumwell, Stephanie L, Michael R MacLeod, Tony Huang, Cochrane, Ryan, Rebecca S Meaney, Maryam Zamani, Ola Matysiakiewicz, Preetam Janakirama, Edgell, David, Trevor C Charles, et al. (2019)

Designer Sinorhizobium meliloti strains and multi-functional vectors for direct inter-kingdom transfer of high G+ C content DNA. PloS ONE (2019), e0219562.

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51. Laforet, M., McMurrough, T.A., Vu, M., Brown, C.M., Zhang, K., Junop, M.S., Gloor, G.B., and Edgell, D.R. (2019) Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease. Nucleic Acids Research, https://doi.org/10.1093/nar/gkz866.

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50. Hamilton, T.A., Pellegrino, G.M., Therrien, J.A., Ham, D.T., Bartlett, P.C., Karas, B.J., Gloor, G.B. and Edgell, D.R. (2019) Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing. Nature Communications 10: 4544.

 

49.  McMurrough T.A., Brown, C.M., Zhang, Z., Hausner, G., Junop, M.S., Gloor, G.B. and D. R. Edgell (2018) Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases. Nucleic Acids Research, 2018 Dec 14;46(22):11990-12007. doi: 10.1093/nar/gky976.

 

48.  Wang, H., Slattery, S.S., Karas, B.J. and D. R. Edgell (2018) Delivery of the Cas9 or TevCas9 system into Phaeodactylum tricornutum via conjugation of plasmids from a bacterial donor. Bio-protocol, 8(16):e2974. DOI: 10.21769/BioProtoc.2974.

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47.  Pereira, C.V., Arguello, T., Bacmam, S.R., Zekonyte, U., Williams, S.L, Edgell, D.R. and C.T. Moraes (2018) MitoTev-TALE: a monomeric DNA editing enzyme to reduce mutant mitochondrial DNA levels in patient-derived cells. EMBO Molecular Medicine, e8084.

 

46.   Kaiser, J.C., King, A.N., Grigg, J.C., Sheldon, J.R., Edgell, D.R., Murphy, M.E., Brinsmade, S.R., and D.E. Heinrichs (2018) Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide. PLoS Genetics, Jan 22;14(1):e1007159. doi: 10.1371/journal.pgen.1007159.

 

45.  Slattery, S.S., Diamond, A., Therrien, J., Jazey, T., Lee, K., Klassen, Z., Desgagne-Penix, I., Karas, B.J., and D.R Edgell (2018) An expanded plasmid-based genetic toolbox enables Cas9 genome editing and stable maintenance of synthetic pathways in Phaeodactylum tricornutum. ACS Synthetic Biology, 7 (2), 328-338.

 

44.  Guha, T. and D.R. Edgell (2017) Applications of alternative nucleases in the age of CRISPR/Cas9. International Journal of Molecular Sciences, 18 (12): 2565

 

43. Celis, J.S, Edgell, D.R., Stelbrink, B., Wibberg, D., Haufee, T., Blom, J., Kalinowski, J. and T. Wilke (2017) Evolutionary and Biogeographical Implications of Degraded LAGLIDADG Endonuclease Functionality and Group I Intron Occurrence in Stony Corals (Scleractinia) and Mushroom Corals (Corallimorpharia). PLoS ONE, doi: 10.1371/journal.pone.0173734.

 

42.  Wolfs, J.M., Hamilton, T.A., Lant, J.T., Laforet, M., Zhang, J., Salemi, J., Gloor, G.B., Schild-Poulter, C., and D.R. Edgell (2016) Biasing genome-editing events towards precise length deletions with an RNA-guided TevCas9 dual nuclease. Proceedings of the National Academy of Sciences USA, Dec 27;113(52):14988-14993. doi: 10.1073/pnas.1616343114.

 

41.  Roy, A.C., Wilson, G.G., and D.R. Edgell (2016) Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference. Nucleic Acids Research, 44 (15): 7350-7359.doi: 10.1093/nar/gkw614.

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40.  Wolfs, J.M., DaSilva, M., Meister, S.E., Wang, X., Schild-Poulter, C. and D.R. Edgell (2014) MegaTevs: Single chain dual nucleases for efficient gene disruption. Nucleic Acids Research, 42(13): 8816-8829.doi: 10.1093/nar/gku573.

 

39. McMurrough, T.A, Dickson, R.J., Thibert, S.M.F., Gloor, G.B. and D.R. Edgell (2014) Control of catalytic efficiency by a co-evolving network of catalytic and non-catalytic residues. Proceedings of the National Academy of Sciences USA, 111(23):E2376-83. doi: 10.1073/pnas.1322352111.

  

38. Fernandes, A.D., Reid, J.N., Macklaim, J.M., McMurrough, T.A., Edgell, D.R., and G.B. Gloor (2104) Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome. 2: 15. doi: 10.1186/2049-2618-2-15.

 

37. Kleinstiver, B.P., Wang, L., Wolfs, J.A., Kolaczyk, T., McDowell, B., Wang, X., Schild-Poulter, C., Bodganove, A.J. and D. R. Edgell (2014) The I-TevI nuclease and linker domains contribute to the specificity of monomeric TALENs. G3: Genes, Genomes, Genetics. 4: 1155-1165. doi 10.1534/g3.114.011445.

 

36. Hausner, G, Hafnez, M. and D.R. Edgell (2013) Group I introns: mobile DNA catalysts (invited review, Mobile DNA). Mobile DNA 5: 8.doi: 10.1186/1759-8753-5-8.

 

35. Wolfs, J.M., Kleinstiver, B.P. and D.R Edgell (2014) Rapid screening of endonuclease target site preference using a modified bacterial two-plasmid selection. Methods in Molecular Biology. 1123.

 

34. Kleinstiver, B.P., Wolfs, J.M, and D.R. Edgell (2013) The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA. Nucleic Acids Research (2013) 41: 5413-5427. doi: 10.1093/nar/gkt186.

 

33. Kleinstiver, B.P, Wolfs, J.M., Kolaczyk, T., Roberts, A.K., Hu, S.X., and D.R. Edgell (2012) Monomeric site-specific nucleases for genome editing. Proceedings of the National Academy of Sciences USA 109: 8061-8066.

 

32. Kleinstiver, B.P., Bérubé-Janzen, W., Fernandes, A.D., and D.R. Edgell (2011) Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI. PLoS ONE 6(8): e23804. doi:10.1371/journal.pone.0023804.

 

31. Takeuchi, R., Lambert, A.R., Mak, A., Jacoby, K., Dickson, R.J., Gloor, G.B., Scharenberg, A.M., Edgell, D.R., and B.L. Stoddard (2011) Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proceedings of the National Academy of Sciences USA, 10.1073/pnas.1107719108.

 

30. Edgell, D.R., Chalamcharla, V.R. and M. Belfort (2011) Learning to live together: mutualism between self-splicing introns and their hosts. BMC Biol. 2011 Apr 11;9:22.

 

29. Crona, M., Moffatt, C., Friedrich, N.C., Hofer, A., Sjoberg, B-M, and D.R. Edgell (2010) Assembly of a fragmented ribonucleotide reductase by protein interaction domains derived from a mobile genetic element. Nucleic Acids Research, doi: 10.1093/nar/gkq924.

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28. Edgell, D.R., Gibb, E.A. and M. Belfort (2010) Mobile DNA elements in T4 and related phage. Virology Journal, 7:290. (Highly accessed)

 

27. Gibb, E.A. and D.R. Edgell (2010) Better late than never: Delayed translation of intron-encoded endonuclease I-TevI is necessary for efficient splicing of its host group I intron. Molecular Microbiology, 78: 35-46.

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26. Crona, M., Furrer, E., Torrents, E., Edgell, D.R. and B-M. Sjoberg (2010) Subunit and small-molecule interaction of ribonucleotide reductase via surface plasmon resonance biosensor analyses. Protein Engineering, Design and Selection, 23:633-641.

 

25. Fernandes, A., Kleinstiver, B., Edgell, D.R., Wahl, L. M. and G. Gloor (2010) Estimating the evidence of selection and the reliability of inference in unigenic evolution. Algorithms for Molecular Biology, 5:35.

 

24. Kleinstiver, B., Fernandes, A., Gloor, G., and D.R. Edgell (2010) A unified genetic, computational, and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI. Nucleic Acids Research, 38:2411-2427.

 

23. Wilson, G. W. and D.R. Edgell (2009) Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII. Nucleic Acids Research, 37:7110-7123.

 

22. Sethuraman, J., Majer, A., Friedrich, N.C., Edgell, D.R., and G. Hausner (2009) Genes-within-genes: Multiple LAGLIDADG homing endonucleases target the ribosomal protein S3 gene encoded within a rnl group I intron of Ophiostoma and related taxa. Molecular Biology and Evolution, 26:2299-2315.

  Citations: 57

 

21. Gibb, E.A., and D.R. Edgell (2009) An RNA Hairpin Sequesters the Ribosome Binding Site of the Homing Endonuclease mobE Gene. Journal of Bacteriology 191:2409-2413.

 

20. Edgell, D.R. (2009) Selfish DNA: Homing Endonucleases Find a Home. Current Biology 19:R115-117.

 

19. Carter, J.M., Friedrich, N.C., Kleinstiver, B., and D.R. Edgell (2007) Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI. Journal of Molecular Biology 374(2):306-321.

 

18. Gibb, E.A., and D.R. Edgell (2007) Multiple controls regulate the expression of mobE, an HNH homing endonuclease gene embedded within a ribonucleotide reductase gene of phage Aeh1. Journal of Bacteriology  189(13):4648-4661.

 

17. Friedrich, N.C., Torrents, E., Gibb, E. A., Sahlin, M., Sjoberg, B-M, and D.R. Edgell (2007) Insertion of a homing endonuclease creates a genes-in-pieces ribonucleotide reductase that retains function. Proceedings of the National Academy of Sciences USA, 104:6176-6181.

 

16. Liu, Q., Derbyshire, V., Shub, D. A., Belfort, M. and D.R. Edgell (2006) Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions. Nucleic Acids Research 34:1755-64.

 

15. Edgell, D.R. (2005) Free-Standing Homing Endonucleases of T-even Phage: Freeloaders of Functionaries? In Homing endonucleases and Inteins. eds Marlene Belfort, David Wood, Vicky Derbyshire, Barry Stoddard. Springer-Verlag, Heidelberg.

 

14. Edgell, D.R., Stanger, M. J., and M. Belfort. (2004) Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene. Journal of Molecular Biology 343, 1231-1241.

 

13. Selbulsky, M .T., Speziali, C. D., Shilton, B. H., Edgell, D.R., and D. E. Heinrichs (2004) FhuD1, a ferric hydroxamate binding lipoprotein in Staphylococcus aureus: a case of gene duplication and lateral transfer? Journal of Biological Chemistry 279, 53152-53159.

 

12. Edgell, D.R., Derbyshire, V., Van Roey, P., LaBonne, S., Stanger, M.J., Li, Z., Boyd, T.M., Shub, D.A., and M. Belfort (2004) Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor. Nature Structural and Molecular Biology 11, 936-944.

** see also News and Views article "Double duty" by Windbichler and Schroeder. highlighted in Faculty of 1000

 

11. Liu, Q., Belle, A., Shub, D.A., Belfort, M and D.R. Edgell (2003) SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site. Journal of Molecular Biology 334, 13-23.

 

10. Edgell, D.R., Stanger, M.J., and M. Belfort. (2003) Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI. Current Biology 13, 973-978.

 

9. Edgell, D.R. (2002) Selfish DNA: New abode for homing endonucleases. Current Biology 12, R276-278.

 

8. Edgell, D.R. and D.A. Shub. (2001) Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites. Proceedings of the National Academy of Sciences USA 98, 7898-7903.

 

7. Edgell, D.R., Landthaler, M. and D.A. Shub. (2001) Intron Homing. Encyclopedia of Life Sciences.

 

6. Edgell, D.R., Belfort, M. and D.A. Shub. (2000) Barriers to intron promiscuity in bacteria. Journal of Bacteriology 182, 5281-5289.

 

5. Edgell, D.R., Malik, S-B. and W.F. Doolittle. (1998) Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Molecular Biology and Evolution 15, 1207-1217.

 

4. Edgell, D.R. and W.F. Doolittle. (1997) Archaea and the origin(s) of DNA replication proteins. Cell, 89, 995-998.

 

3. Edgell, D.R., Klenk, H-P. and W.F. Doolittle. (1997) Gene duplications in the evolution of archaeal family B DNA polymerases. Journal of Bacteriology 179, 2632-2640.

 

2. Edgell, D.R., Fast, N.M. and W.F. Doolittle. (1996) Selfish DNA: the best defense is a good offense. Current Biology 6, 385-388.

 

1. Edgell, D.R. and W.F. Doolittle. (1996) Archaebacterial genomics: the complete genome sequence of Methanococcus jannaschii. BioEssays, 19, 1-4.