Publications

Profeta, L.; Doherty, E.E.; Ebner, J.; Ünal, G.D.; Arasa, E.; Poehlman, L.; Shukla. A.; Kikugawa, M.S.; Barnett, A.L.; Jordan, T.; Malik, W.; Nomburg, J. Conserved folds enable immune antagonism across the tree of life. bioRxiv. 2026. [Preprint]

 

Zhou, Z.*; Saffarian-Deemyad,I.*; Shi, H.*; Weiss, T.*; Moez ur-Rehman, M.; Vohra, K.; Skopinstev, P.; Yoon, P.H.; Trinidad, M.I.; Langeberg, C. J.; Kamalu, M.; Amerasekera, J.; Doherty, E.E.; …; Savage, D.F.; Jacobsen, S.E.; Bryant,; Z. Doudna, J.A. Stepwise DNA unwinding gates TnpB genome-editing activity. bioRxiv. 2026. [Preprint]

 

Doherty, E.E.*; Nomburg, J.*; Adler, B.A.; Lopez, S.; Hsieh, K.; Price, N.; Blount, N.; Doudna, J.A. Divergent viral phosphodiesterases for immune signaling evasion. Cell Host & Microbe. 2025, 33:12, 2043-2051.  

         [Press] Press Release: New Method Uncovers How Viruses Evade Immune Responses — and How We Might Fight Back. Innovative Genomics Institute. 

         [Press] Preview: Viral Enzymes Degrade to Evade. Fernando, C.M. & Marino, N. Cell Host & Microbe. 

 

Tuck, O. T.*; Hu, J.J.*; Adler, B.A.; O’Brien, C.E.; Lopez, S.C.; Hsieh, K.; Meredith, C.; Lahiri, A.; Doherty, E.E.; Doudna, J.A. Recurrent acquisition of nuclease-protease pairs in antiviral immunity. Science, 2025, Online ahead of print. 

 

Doherty, E.E.*; Adler, B.A.*; Yoon, P.H.; Hsieh, K.; Loi, K.; Armbruster, E.G.; Bolling, C.S.; Wilcox, X.E.; Akkati, A.; Iavarone, A.T.; Pogliano, J.; Doudna, J.A. A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway. Nature. 2025, 647, 997-1004. 

            [Press] News & Views: Bacteria use a decoy defence molecule to set a trap for viruses. White, M.A. Nature. 

            [Press] Press Release: How Microbes – and humans – defend against viruses. Innovative Genomics Institute. 

            Selected for Stanford Synchrotron Radiation Lightsource (SSRL) Science Highlight, In Press.

            [Media] Press: Nucleotides to the Defense: This Week in Microbiology, American Society for Microbiology.

 

Shi, H.*; Al-Sayyad, N.*; Wasko, K.*; Trinidad, M.I.; Doherty, E.E.; Vohra, K.; Boger, R.S.; Colognori, D.; Cofsky, J.C.; Skopinstev, P.; Bryant, Z.; Doudna, J.A. Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing. Mol. Cell. 2025, 85:9, 1730-1742.

 

Shulgina, Y.; Trinidad, M. I.; Langeberg, C.J.; Nisonoff, H.; Chithrananda, S.; Skopinstev, P.; Nissley, A.J.; Patel, J.; Boger, R.S.; Shi, H.; Yoon, P. H.; Doherty, E.E.; Pande, T.; Iyer, A.M.; Doudna, J.A.; Cate, J.H.D. RNA language models predict mutations that improve RNA function. Nat. Commun. 2024, 15:1, 10627.

 

Manjunath, A.; Cheng, J.; Campbell, K.B.; Jacobsen, C.S.; Mendoza, H.G.; Bierbaum, L.; Jauregui-Matos, V.; Doherty, E.E.; Fisher, A.J.; Beal, P.A. Purine Analogs in ADAR Guide Strands Enable Editing at 5’-GA Sites. Biomolecules. 2024, 14:10, 1229.  

 

Nomburg, J.; Doherty, E.E.; Price, N.; Belliney-Rabelo, D.; Zhu, Y.; Doudna, J.A. Birth of protein folds and functions in the virome. Nature. 2024, 633, 710-717.  

            [Press] Press Release: 3D shapes of viral proteins point to previously unknown roles. AAAS.

 

Eggers, A.*; Chen, K.*; Soczek, K.; Tuck, O.; Doherty, E.E.; Thornton, B.; Xu, B.; Trinidad, M.; Doudna, J.A. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. Cell. 2024, 187:13, 3249-3261. 

 

Adler, B.A.*; Trinidad, M. I.*; Bellieny-Rabelo, D.; Zhang, E.; …Doherty, E.E.;… Doudna, J.A. CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes. Nucleic Acids. Res. 2023, 52:D1, 590-596. 

 

Brinkman, H.F.; Jauregui Matos, V.; Mendoza, H.L.; Doherty, E.E.; Beal, P.A. Nucleoside Analogs in ADAR Guide Strands Targeting 5’-UA sites. RSC Chem Biol. 2024, 4, 74-83. 

 

Doherty, E.E.; Karki, A.; Wilcox, X.E.; Mendoza, H.G.; Manjunath, A.; Jauregui Matos, V.; Fisher, A.J.; Beal, P.A. ADAR Activation by Inducing a Syn Conformation at Guanosine Adjacent to an Editing Site. Nucleic Acids Res. 2022, 50:19, 10857-10868.

 

Doherty, E.E.; Beal, P.A.; Karki, A.; Wilcox, X.; Fisher, A.; de Visser, P.C.; Oligonucleotides for ADAR-Mediated Editing and Use Thereof. U.S. Patent Application No. 18/994,572. Filed August 5, 2025. [Patent]

Also published as WO2024013360A1 (International Patent Application).

 

Doherty, E.E.; Beal, P.A. Oligonucleotide-directed RNA editing in Primates (Invited Commentary). Mol. Ther. 2022, 30:6, 2117-2119.

 

Doherty, E.E.; Wilcox, X.; van Sint Fiet, L.; Kemmel, C.; Turunen, J.J.; Klein, B.; Tantillo, D.J.; Fisher, A.J.; Beal, P.A. Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position. J. Am. Chem. Soc. 2021, 143:18, 6685-6876.

[Press] Press Release: Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position. ProQR Therapeutics.

[Press] Presentation: Development of RNA Base Editing Technologies for Precision Medicines. ProQR Therapeutics.  

 

Malik, T. N.; Doherty, E.E.; Gaded, V.M.; Beal, P.A.; Emeson, R.B. Regulation of RNA editing by intracellular acidification. Nucleic Acids Res. 2021, 49:7, 4020-4036.  

 

Park, S.; Doherty, E.E.; Xie, Y.; Padyana, A. K.; Fang, F.; Zhang, Y.; Karki, A.; Lebrilla, C.B.; Siegel, J.B.; Beal, P.A. High-throughput Mutagenesis Reveals Unique Structural Features of Human ADAR1. Nat. Commun. 2020, 11:1, 5130-5143. 

 

Rowe, R.K.; Matasci, K. R.; Rickelmann, A.R.; Muli, C.S.; Doherty, E.E.; Smith, T.B.; Pistel II, W.L.; McIntyre, S.; Palandoken, H.; Hagen, J.P. The Physio-Chemical Properties of Sugar-Oxime-Ether Surfactants. Tenside Surface Detergents. 2020, 57:1, 6-12. 

 

Turunen, J. J.; van Sint Fiet, L.; Kemmel, C.P.; Beal, P.A.; Doherty, E.E. Antisense RNA Editing Oligonucleotides Comprising Cytidine Analogs. U.S. Patent Application No. US 17/618,313. Filed June 12, 2020. [Patent]

            Also published as WO2020252376A1 (International Patent Application). 

 

Bellinghiere, A.T.; Doherty, E.E.; Pistel II, W.L.; Browne, J.E.; Palandoken, H. A Facile Synthesis Of O-[(3-Methyloxetan-3-yl)Methyl]Hydroxylamine. Org. Prep. Proced. Int. 2015, 47:3, 232-235.