Preprints:

 

Hilbert ZA, Chung KY, Bednarek JM, Schwiesow MW, Brown JCS, Elde NC Distinct pathways of adaptive evolution in Cryptococcus neoformans reveal a point mutation in adenylate cyclase with drastic tradeoffs for pathogenicity. bioRxiv. https://doi.org/10.1101/2022.09.27.509772

 

Hilbert ZA, Young HJ, Schwiesow MW, Elde NC Rapid evolution of glycan recognition receptors reveals an axis of host-microbe conflicts at carbohydrate-protein interfaces. bioRxiv. https://doi.org/10.1101/2022.09.07.507018

 

Jacquet S, Culbertson M,  Zang C, El Filali A, De La Myre Mory C, Pons J-B, Filippi-Codaccioni O, Lauterbur ME, Ngoubangoye B, Duhayer J, Verez C, Park C, Dahoui C, Carey CM, Brennan G, Enard D, Cimarelli A, Rothenburg S, Elde NC,Pontier D, Etienne L. Adaptive duplication and functional diversification of Protein kinase R contribute to the uniqueness of bat-virus interactions. bioRxiv. https://doi.org/10.1101/2022.06.28.497829

 

Goldstein S.A., Brown J., Pedersen B.S., Quinlan A.R., Elde N.C. Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. bioRxiv. https://doi.org/10.1101/2021.02.03.429646

 

Peer Reviewed Publications:

 

Fixsen S.M., Cone K.R., Goldstein S.A., Sasani T.A., Quinlan A.R., Rothenburg S., Elde N.C. (2022) Poxviruses capture host genes by LINE-1 retrotransposition. eLife, 11:e63332

 

Fay EJ, Balla KM, Roach SN, Shepherd FK, Putri DS, Wiggen TD, Goldstein SA, Pierson MJ, Ferris MT, Thefaine CE, Tucker A, Salnikov M, Cortez V, Compton SR, Kotenko SV, Hunter RC, Masopust D, Elde NC, Langlois RA. (2022) Natural rodent model of viral transmission reveals biological features of virus population dynamics. J Exp Med. 219:e20211220

 

Rheinemann L., Downhour D.M., Davenport K.A., McKeown A.N., Sundquist W.I., Elde N.C. (2022) Recurrent evolution of an inhibitor of ESCRT-dependent virus budding and LINE-1 retrotransposition in primates. Current Biology, 32: 1511-1522.e6

 

Rheinemann L., Downhour D.M., Bredbenner K., Mercenne G., Davenport K.A., Schmitt P.T., Necessary C.R., McCullough J., Schmitt A.P., Simon S.M., Sundquist W.I., Elde N.C. (2021) RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis. Cell, 184: 5419-5431.e16.

 

Carey C.M., Apple S.E., Hilbert Z.A., Kay M.S., Elde N.C. (2021) Diarrheal pathogens trigger rapid evolution of the Guanylate Cyclase-C signaling axis in bats. Cell Host and Microbe, 29: 1342-1350.e5

 

Sorouri M., Chang T., Jesudhasan P., Pinkham C., Elde N.C., Hancks D.C. Signatures of host–pathogen evolutionary conflict reveal MISTR—A conserved MItochondrial STress Response network. (2020). Plos Biology, 18: e3001045.

 

Balla K.M., Rice M.C., Gagnon J.A., Elde N.C. (2020) Linking Virus Discovery to Immune Responses Visualized during Zebrafish Infections. Current Biology, 30: 2092-2103.e5

 

Boguslawski K.M., McKeown A.N., Day C.J., Lacey K.A., Tam K., Vozhilla N., Kim S.Y., Jennings M.P., Koralov S.B., Elde N.C., Torres V.J.(2020) Exploiting species specificity to understand the tropism of a human-specific toxin. Science Advances, 6: eaax7515.

 

Rubenstein D.R., Agren J.A., Carbone L., Elde N.C., Hoekstra H.E., Kapheim K.M., Keller L., Moreau C.S., Toth A.L., Yeaman S., Hofmann H.A. (2019) Coevolution of Genome Architecture and Social Behavior. Trends in Ecology and Evolution, 34: 844-855.

 

Carey C.M., Govande A.A., Cooper J.M., Hartley M.K., Kranzusch P.J., Elde N.C. (2019) Recurrent Loss-of-Function Mutations Reveal Costs to OAS1 Antiviral Activity in Primates. Cell Host and Microbe, 25: 336-343.e4.

 

Sasani T.A., Cone K.R., Quinlan A.R., Elde N.C. (2018) Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays. eLife, 7: e35453.

 

Barber M.F., Lee E.M., Griffin H., Elde N.C. (2017) Rapid evolution of primate type 2 immune response factors linked to asthma susceptibility. Genome Biology and Evolution, 9: 1757-1765.

 

Cone K.R., Kronenberg Z.N., Yandell M., Elde N.C. (2017) Emergence of a viral RNA polymerase variant during gene copy number amplification promotes rapid evolution of vaccinia virus. Journal of Virology, 91: e01428-16.

 

Chuong E.B., Elde N.C., Feschotte C. (2017) Regulatory evolution of transposable elements: from conflicts to benefits. Nature Reviews Genetics, 18: 71-86.

 

Yaxin Y., Yarrington R.M., Choung E.B., Elde N.C., Stillman D.J. (2016) Disruption of promoter memory by a long noncoding RNA. Proc Natl Acad Sci U S A., 113: 9575-80.

 

Barber M.F., Kronenberg Z., Yandell M., Elde N.C. (2016) Antimicrobial functions of lactoferrin promote genetic conflicts in ancient primates and modern humans. PLOS Genetics, 12: e1006063.

 

Chuong E.B., Elde N.C.,* Feschotte, C.* (2016) Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science, 351: 1083-7.

*equal contributions

 

Kronenberg Z.N., Osborne E.J., Cone K.R., Kennedy B.J., Domyan E.T., Shapiro M.D., Elde N.C., Yandell M. (2015) Wham: Identifying structural variants of biological consequence. PLOS Computational Biology, 11: e1004572.

 

Barber M.F., Elde N.C. (2015) Buried treasure: Evolutionary perspectives on microbial iron piracy. Trends in Genetics, 31: 627-36.

 

Li J., Cao C., Fixsen S.M., Young J.M., Ono C., Bando H., Elde N.C., Katsuma S., Dever T.E., Sicheri F. (2015) Baculovirus protein PK2 subverts eIF2alpha kinase function by mimicry of its kinase domain C-lobe. Proc Natl Acad Sci U S A., 112: e4364-73.

 

Hancks D.C., Hartley M.K., Hagan C., Clark N.L., Elde N.C. (2015) Overlapping patterns of rapid evolution in the nucleic acid sensors cGAS and OAS suggest a common mechanism of pathogen antagonism and escape. PLOS Genetics, 11: e1005203.

 

Orzalli M.H., Broekema N.M., Diner B.A., Hancks D.C., Elde N.C., Cristea I.M., Knipe D.M. (2015) cGAS and IFI16 cooperate by a novel mechanism to sense nuclear herpesviral DNA. Proc Natl Acad Sci U S A., 112: 1773-81.

 

DePaula-Silva A.B., Cassiday P.A., Chumley J., Bosque A., Monteiro-Filho C.M., Mohan C.S., Cone K.R., Krogan N., Elde N.C., Planelles V. (2015) Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr. Virology, 477: 10-17.

 

Galati D.F., Bonney S., Kronenberg Z., Clarissa C., Yandell M., Elde N.C., Jerka-Dziadosz M., Giddings T.H., Frankel J., Pearson C.G. (2014) DisAp-dependent striated fiber elongation is required to organize ciliary arrays. Journal of Cell Biology, 207: 705-15.

 

Barber M.F., Elde N.C. (2014) Escape from bacterial iron piracy through rapid evolution of transferrin. Science, 346: 1362-6.     ABSTRACT      FULL-TEXT        REPRINT

 

Barber M.F., Elde N.C. (2013) Mimicry all the way down. Nature, 501: 38-9.

 

Elde N.C. (2012) Poliovirus evolution: the strong, silent type. Cell Host & Microbe, 12: 605-6.

 

Elde N.C., Child S.J., Eickbush M.T., Kitzman J.O., Rogers, K.S., Shendure J., Geballe A.P., Malik H.S. (2012) Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell, 150: 831-841.

 

Sawyer, S.L., Elde N.C. (2012) A cross-species view on viruses. Current Opinion in Virology, 2: 561-8.

 

Elde N.C., Roach, K., Yao M.C., Malik H.S. (2011) Absence of positive selection on centromeric histones in Tetrahymena suggests unsuppressed centromere-drive in lineages lacking male meiosis. Journal of Molecular Evolution, 72: 510-520.

 

Elde N.C., Malik H.S. (2009) The evolutionary conundrum of pathogen mimicry. Nature Reviews Microbiology, 7: 787-797.

 

Elde N.C., Child S.J., Geballe A.P., Malik H.S. (2009) Protein kinase R reveals an evolutionary model for defeating viral mimicry. Nature, 457: 485-489.

 

Rahaman A., Elde N.C., Turkewitz A.P. (2008) A dynamin-related protein required for nuclear remodeling in Tetrahymena. Current Biology, 18: 1227-1233.

 

Elde N.C., Long M., Turkewitz A.P. (2007) A role for convergent evolution in the secretory life of cells.  Trends in Cell Biology, 17: 157-164.

 

Eisen J.A., Wu M., Wu D., Thiagarajan M., Wortman J.R., Badger J.H., Ren Q., Delcher A.L., Salzberg S.L., Silva J.C., Haas B.J., Majoros W.H., Farzad M., Carlton J.M., Garg J., Pearlman R.E., Karrer K.M., Sun L., Smith R.K., Elde N.C., Turkewitz A.P., Asai D.J., Wilkes D.E., Wang Y., Cai H., Collins K., Wilamowska K., Ruzzo W.L., Weinberg Z., Stewart B.W., Lee S.R., Wloga D., Rogowski K., Frankel J., Gaertig J., Gorovsky M.A., Cherry J.M., Stover N.A., Krieger C.J., Hamilton E.P., Orias E., Coyne R.S. (2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology, 4: e286.

 

Elde N.C., Morgan G., Winey M., Sperling L., Turkewitz A.P. (2005) Elucidation of clathrin-mediated endocytosis in Tetrahymena reveals an evolutionarily convergent recruitment of dynamin. PLoS Genetics, 1: e52.

 

Bowman G.R., Elde N.C., Morgan G., Winey M., Turkewitz A.P. (2005) Core formation and the acquisition of fusion competence are linked during secretory granule maturation in Tetrahymena. Traffic, 6: 303-323.

 

Doherty K.R., Zweifel E.W., Elde N.C., McKone M.J., Zweifel S.G. (2003) Random amplified polymorphic DNA markers reveal genetic variation in the symbiotic fungus of leaf-cutting ants. Mycologia, 95: 19-23.

 

Chilcoat N.D., Elde N.C., Turkewitz A.P. (2001) An antisense approach to phenotype-based gene cloning in Tetrahymena. Proc Natl Acad Sci U S A, 98: 8709-13.