SELECTED PUBLICATIONS
UCSD
Castro, L.K. and M.D. Daugherty. (2023). Tripping the wire: sensing of viral protease activity by CARD8 and NLRP1 inflammasomes. Current Opinion in Immunology. 83, 122354. [Article link].
Tsu, B.V., Agarwal, R., Gokhale, N.S., Kulsuptrakul, J., Ryan, A.P., Fay, E.J., Castro, L.K., Beierschmitt, C., Yap, C., Turcotte, E.A., Delgado-Rodriguez, S.E., Vance, R.E., Hyde, J.L., Savan, R., Mitchell, P.S.‡, and M.D. Daugherty‡. (2023). Host specific sensing of coronaviruses and picornaviruses by the CARD8 inflammasome. PLoS Biology. 21, e3002144. [Article link]. [Original bioRxiv link].
‡ co-corresponding author
Delgado-Rodriguez, S.E., Ryan, A.P., and M.D. Daugherty. (2023). Recurrent loss of macrodomain activity in host immunity and viral proteins. Pathogens. 12, 674. [Article link].
Kalluraya, C.A., Weitzel, A.J., Tsu, B.V., and M.D. Daugherty. (2023). Bacterial origin of a key innovation in the evolution of the vertebrate eye. PNAS. 120, e2214815120. [Article link]. [Writeup in Science about this paper].
Schindewolf, C., Lokugamage, K., Vu, M.N., Johnson, B.A., Scharton, D., Plante, J.A., Kalveram, B., Crocquet-Valdes, P.A., Sotcheff, S., Jaworski, E., Alvarado, R.E., Debbink. K., Daugherty, M.D., Weaver, S.C., Routh, A.L., Walker, D.H., Plante, K.S., and V.D. Menachery. (2023). SARS-CoV-2 Uses Nonstructural Protein 16 To Evade Restriction by IFIT1 and IFIT3. J. Virology. 97, e0153222. [Article link].
Stevens, D.A.*, Beierschmitt, C.*, Mahesula, S., Corley, M.R., Salogiannis, J., Tsu, B.V., Cao, B., Ryan, A.P., Hakozaki, H., Reck-Peterson, S.L.‡, and M.D. Daugherty‡. (2022). Antiviral function and viral antagonism of the rapidly evolving dynein activating adapter NINL. eLife. 11, e81606. [Article link] [Original bioRxiv link]
* equal contribution
‡ co-corresponding author
Wang, B., Pandey, T., Long, Y., Delgado-Rodriguez, S., Daugherty, M.D.‡, and D.K. Ma‡. (2022). Co-opted genes of algal origin protect C. elegans against cyanogenic toxins. Current Biology. 32, 4941-4948. [Pubmed link] [Original bioRxiv link]
‡ co-corresponding author
Tsu, B.V.*, Fay, E.J.*, Nguyen, K.T., Corley, M.R., Hosuru, B., Dominguez, V.A., and M.D. Daugherty. (2021). Running with scissors: evolutionary conflicts between viral proteases and the host immune system. Frontiers in Immunology. 12, 769543. [Article link]
* equal contribution
Lüscher, B., Ahel, I., Altmeyer, M., Ashworth, A., Bai, P., Chang, P., Cohen, M., Corda, D., Dantzer, F., Daugherty, M.D., Dawson, T.M., Dawson, V.L., Deindl, S., Fehr, A.R., Feijs, K.L.H., Filippov, D.V., Gagné, J-P., Grimaldi, G., Guettler, S., Hoch, N.C., Hottiger, M.O., Korn, P., Kraus, W.L., Ladurner, A., Lehtiö, L., Leung, A.K.L., Lord, C.J., Mangerich, A., Matic, I., Matthews, J., Moldovan, G-L., Moss, J., Natoli, G., Nielsen, M.L., Niepel, M., Nolte, F., Pascal, J., Paschal, B.M., Pawłowski, K., Poirier, G.G., Smith, S., Timinszky, G., Wang, Z-Q., Yélamos, J., Yu, X., Zaja, R., and M. Ziegler. (2021). ADP-ribosyltransferases, an update on function and nomenclature. FEBS J. 10.1111/febs.16142. [Article link].
Sundaramoorthy, E., Ryan, A.P., Fulzele, A., Leonard, M., Daugherty, M.D.‡ and E.J. Bennett‡. (2021) Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection. J. Cell Science. Apr 15;134(8):jcs257188. [J. Cell Science link] [bioRxiv post from 11/2020]
‡ co-corresponding author
Tsu, B.V.*, Beierschmitt, C.*, Ryan, A.P., Agarwal, R., Mitchell, P.S., and M.D. Daugherty. (2021). Diverse viral proteases activate the NLRP1 inflammasome. eLife. 10, e60609. [eLife link] [bioRxiv post from 10/2020]
* equal contribution
Mudla, A., Jiang, Y., Arimoto, K.I., Xu, B., Rajesh, A., Ryan, A.P., Wang, W., Daugherty, M.D., Zhang, D.E., and N. Hao. (2020). Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. eLife. 9, e58825. [Article link]
Garrigues, J.M., Tsu, B.V., Daugherty, M.D., and A.E. Pasquinelli. (2019). Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. eLife. 8, e51139. [Article link]
Schwerk, J., Soveg, F.W., Ryan, A.P., Thomas, K.R., Aarreberg, A.D., Ozarkar, S., Forero, A., Kell, A.M., Roby, J.A., So, L. Hyde, J.L., Gale Jr, M., Daugherty, M.D.‡ and R. Savan‡. (2019). RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions. Nature Immunology. 20, 1610-1620. [Pubmed link]
‡ co-corresponding author
Highlighted as “Editors’ Choice” in Science Signaling [Science Signaling link]
Daugherty, M.D.‡ and S.E. Zanders‡. (2019). Gene conversion generates evolutionary novelty that fuels genetic conflicts. Current Opinion in Genetics & Development. 58-59, 49-54. [Pubmed link]
‡ co-corresponding author
Moens, U., Calvignac-Spencer, S., Lauber, C., Ramqvist, T., Feltkamp, M.C., Daugherty, M.D., Verschoor, E.J., and B. Ehlers. (2017). ICTV Virus Taxonomy Profile: Polyomaviridae. J General Virology. 98, 1159-1160. [Pubmed link]
Chavarria-Smith, J., Mitchell, P.S., Ho, A.M., Daugherty, M.D.‡ and R.E. Vance‡. (2016). Functional and evolutionary analyses identify proteolysis as a general mechanism for NLRP1 inflammasome activation. PLoS Pathogens. 12, e1006052. [PLoS Pathogens link]
‡ co-corresponding author
Calvignac-Spencer, S., Feltkamp, M.C., Daugherty, M.D., Moens, U., Ramqvist, T., Johne, R., and B. Ehlers. (2016). A taxonomy update for the family Polyomaviridae. Archives of Virology. 161, 1739-50. [Pubmed link]
FRED HUTCHINSON CANCER RESEARCH CENTER
Daugherty, M.D.‡, Schaller, A.M., Geballe, A.P. and H.S. Malik‡. (2016). Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. eLife. 5, e14228. [Pubmed link]
‡ co-corresponding author
Insight in eLife by Henzy and Johnson. (2016). 5, e17224. [Pubmed link]
Chou, S.*, Daugherty, M.D.*, Peterson, S.B., Biboy, J., Yang, Y., Jutras, B.L., Fritz-Laylin, L.K., Ferrin, M.A., Harding, B.N., Jacobs-Wagner, C., Yang, X.F., Vollmer, W., Malik, H.S. and J.D. Mougous. (2015). Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature. 518, 98-101. [Pubmed link]
* equal contribution
Highlighted by Ed Yong - National Geographic - November 25, 2014
Covered by the Washington Post - November 26, 2014
Highlighted in Cell Host & Microbe - December 8, 2014
Highlighted in Nature Reviews Microbiology - January 14, 2015
Discussed on This Week in Microbiology (TWiM), episode 98 - February 18, 2015
Daugherty, M.D. and H.S. Malik. (2014). How a Virus Blocks a Cellular Emergency Access Lane to the Nucleus, STAT! Cell Host & Microbe. 16, 150-2. [Pubmed link]
Preview for: Xu, W., et al., (2014). Cell Host & Microbe. 16, 187-200.
Daugherty, M.D., Young, J.M., Kerns, J.A., and H.S. Malik. (2014). Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts. PLoS Genetics. 10, e1004403. [Pubmed link]
Tenthorey, J.L., Kofoed, E.M., Daugherty, M.D., Malik, H.S., and R.E. Vance. (2014). Molecular basis for specific recognition of bacterial ligands by NAIP/NLRC4 inflammasomes. Molecular Cell. 54, 17-29. [Pubmed link]
Carter, J.J.*, Daugherty, M.D.*, Qi, X., Bheda-Malge, A., Wipf, G.C., Robinson, K., Roman, A., Malik, H.S. and D.A. Galloway. (2013). Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes. PNAS 110, 12744-9. [Pubmed link]
* equal contribution
Daugherty, M.D. and H.S. Malik. (2012). Rules of engagement: molecular insights from host-virus arms races. Annual Reviews in Genetics. 46, 677-700. [Pubmed link]
Faculty of 1000 recommended
UCSF
Daugherty, M.D., Liu, B, and A.D. Frankel. (2010). Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol 17, 1337-42. [Pubmed link]
Faculty of 1000 recommended
Daugherty, M.D., Booth, D.S., Jayaraman, B, Cheng, Y., and A.D. Frankel. (2010). HIV RRE directs assembly of the Rev homo-oligomer into discrete, asymmetric complexes. PNAS 107, 12481-6. [Pubmed link]
Daugherty, M.D., D’Orso, I., and A.D. Frankel (2008). A solution to limited genomic capacity: Using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Molecular Cell 31, 824-834. [Pubmed link]
