For the most up-to-date publication list, please visit Ellie’s Google Scholar!

2025

Akopyan, M.‡, Genchev, M., Armstrong, E. E., & Mooney, J. A. (2025). Reference genome choice compromises population genetic analyses. Cell, 188(24), 6939-6952.

Salih, D., Armstrong, E. E., Robbins, C. T., Waits, L. P., & Kelley, J. L. (2025). Bridging the Gap Between Legacy PCR-based Microsatellite Data with High-Throughput Sequencing Data in Conservation Genomics. The Journal of heredity, esaf090-esaf090.

Solari, K. A., Morgan, S., Poyarkov, A. D., Weckworth, B., Samelius, G., Sharma, K., ... Armstrong, E.E.*, & Petrov, D. A.* (2025). Exceedingly low genetic diversity in snow leopards due to persistently small population size. Proceedings of the National Academy of Sciences, 122(41), e2502584122.

Solari, K. A., Ahmad, S., Armstrong, E. E., Campana, M. G., Ali, H., Hameed, S., ... & Petrov, D. A. (2025). Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces. Molecular Ecology Resources, 25(4), e14074.

Armstrong, E. E.*, Li, C.,* Campana, M. G., Ferrari, T., Kelley, J. L., Petrov, D. A., ... & Mooney, J. A. (2025). A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non‐Model Species. Molecular Ecology Resources, 25(3), e14048.

Armstrong, E. E., Carey, S. B., Harkess, A., Zenato Lazzari, G., Solari, K. A., Maldonado, J. E., ... & Campana, M. G. (2025). Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees. Genome Biology and Evolution, 17(4), evaf060.

2024

Armstrong, E. E.*, Mooney, J. A.*, Solari, K. A., Kim, B. Y., Barsh, G. S., Grant, V. B., ... & Hadly, E. A. (2024). Unraveling the genomic diversity and admixture history of captive tigers in the United States. Proceedings of the National Academy of Sciences, 121(39), e2402924121.

Armstrong, E. E., Bissell, K. L., Fatima, H. S., Heikkinen, M. A., Jessup, A., Junaid, M. O., ... & Mychajliw, A. M. (2024). Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3: Genes, Genomes, Genetics, 14(4), jkae034.

Schiebelhut, L. M., Guillaume, A. S., Kuhn, A., Schweizer, R. M., Armstrong, E. E., Beaumont, M. A., ... & Luikart, G. (2024). Genomics and conservation: Guidance from training to analyses and applications. Molecular Ecology Resources, 24(2), e13893.

2023

Pelaez, J. N., Gloss, A. D., Goldman-Huertas, B., Kim, B., Lapoint, R. T., Pimentel-Solorio, G., Verster, K. I., Aguilar, J. M., Nelson Dittrich, A.C., Singhal, M., Suzuki, H.C., Matsunaga, T., Armstrong, E.E., Charboneau, J. L. M., Groen, S. C., Hembry, D. H., Ochoa, C. J., O’Connor, K.T., Prost, S., Zaaijer, S., Nabity, P. D., Wang, J., Rodas, E., Liang, I., & Whiteman, N. K. (2023). Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. bioRxiv, https://doi.org/10.1101/2023.03.16.532987

Prado, N.A., Armstrong, E.E., Brown, J.L., Godenberg, S.Z., Leimgruber, P., Pearson, V.R., Maldonado, J.E., Campana, M.G. (2023). Genomic Resources for Asian (Elephas maximus)and African Savannah Elephant (Loxodonta africana) Conservation and Health Research. bioRxiv, https://doi.org/10.1101/2023.02.10.528067

Armstrong, E. E., & Campana, M. G. (2023). RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data.  Bioinformatics, 39(1), btac784.

2022

Armstrong, E.E., Perry, B.W., Huang, Y., Garimella, K.V., Jansen, H.T., Robbins, C.T., Tucker, N.R. and Kelley, J.L., 2022. A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos). Genome biology and evolution, 14(9), p.evac125.

Armstrong, E.E., Campana, M.G., Solari, K.A., Morgan, S.R., Ryder, O.A., Naude, V.N., Samelius, G., Sharma, K., Hadly, E.A. and Petrov, D.A., 2022. Genome Report: Chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 Genes| Genomes| Genetics. In press.

Perry, B.W., Armstrong, E.E., Robbins, C.T., Jansen, H.T. and Kelley, J.L., 2022. Temporal analysis of gene expression and isoform switching in brown bears (Ursus arctos). Integrative and Comparative Biology. In press.

Cerca, J., Armstrong, E.E., Vizueta, J., Fernández, R., Dimitrov, D., Petersen, B., Prost, S., Rozas, J., Petrov, D. and Gillespie, R.G., 2021. The Tetragnatha kauaiensis genome sheds light on the origins of genomic novelty in spiders. Genome biology and evolution, 13(12), p.evab262.

Bergeron, L.A., Besenbacher, S., Turner, T., Versoza, C.J., Wang, R.J., Price, A.L., Armstrong, E.E., Riera, M., Carlson, J., Chen, H.Y. and Hahn, M.W., 2022. The Mutationathon highlights the importance of reaching standardization in estimates of pedigree-based germline mutation rates. eLife, 11, pe73577.

Armstrong, E.E., Perez‐Lamarque, B., Bi, K., Chen, C., Becking, L.E., Lim, J.Y., Linderoth, T., Krehenwinkel, H. and Gillespie, R.G., 2022. A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates. Molecular Ecology, 31(4):1299-1316.

Suvorov, A., Kim, B.Y., Wang, J., Armstrong, E.E., Peede, D., D’agostino, E.R., Price, D.K., Waddell, P.J., Lang, M., Courtier-Orgogozo, V. David, J.R., …Comeault, A.A. 2022. Widespread introgression across a phylogeny of 155 Drosophila genomes. Current Biology, 32(1):111-123.

2021 and prior

Bentley, B. P.* & Armstrong, E.E*. (2021). Good from far, but far from good: The impact of a reference genome on evolutionary inference. Molecular Ecology Resources. 22(1):12-14.

Kardos, M., Armstrong, E.E., Fitzpatrick, S.W., Hauser, S., Hedrick, P.W., Miller, J.M., Tallmon, D.A. and Funk, W.C., 2021. The crucial role of genome-wide genetic variation in conservation. Proceedings of the National Academy of Sciences, 118(48), p.e2104642118.

Kim, B. Y., Wang, J. R., Miller, D. E., Barmina, O., Delaney, E., Thompson, A.,...Armstrong, E.E.,... & Petrov, D. A. (2020). Highly contiguous assemblies of 101 drosophilid genomes. eLife, 10, e66045.

Armstrong, E. E.*, Khan, A.*, Taylor, R. W., Gouy, A., Greenbaum, G., Thiery, Kang, J.T., Redondo, S.A., Prost, S., Barsh, G., A., Kaelin, C., Phalke, S., Chugani, A., Gilbert, M., Miquelle, D., Zachariah, A., Borthakur, U., Reddy, A., Louis, E., Ryder, O.A., Jhala, Y.V., Petrov, D., Excoffier, L., Hadly, E.A., Ramakrishnan, U. (2019). Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection. Molecular Biology and Evolution. 38(6):2366-2379.

Armstrong, E. E., Taylor, R. W., Miller, D. E., Kaelin, C., Barsh, G., Hadly, E. A., & Petrov, D. (2020). Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data. BMC Biology,18.1: 1-14.

Sakai-Kawada, F. E., Ip, C. Gai-Ming, Hagiwara, K. A., Nguyen, H.Y.X., Yakym, C.J., Helmkampf, M., Armstrong, E.E., Awaya, J.D. (2020). Characterization of Prodiginine Pathway in Marine Sponge-Associated Pseudoalteromonas sp. PPB1 in Hilo, Hawai'i. (2020).‍ ‍Frontiers in Sustainable Food Systems. 4:275.

Verster, K.I., Wisecaver, J.H., Duncan, R.P., Karageorgi, M., Gloss, A.D., Armstrong, E.E., Price, D.K., Menon, A.R., Ali, Z.M., Whiteman, N.K. (2019). Horizontal transfer of bacterial cytolethal distending toxin B genes to insects. Molecular Biology and Evolution, 36(10):2105-2110.

Armstrong, E. E., Taylor, R. W., Prost, S., Blinston, P., van der Meer, E., Madzikanda, H., Mufute, O., Mandisodza-Chikerema, R., Stuelpnagel, J., Silleero-Zubiri, C., Petrov, D. (2019). Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads. GigaScience, 8(2), giy124.

Prost, S., Armstrong, E. E., Nylander, J., Thomas, G.W.C., Suh, A., Petersen, B., Dalen, L., Benz, B.W., Blom, M.P.K., Palkopoulou, E., Ericson, P. G., Irestedt, M. (2018). Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise. GigaScience, 8(5), giz003.

Armstrong, E. E., Prost, S., Ertz, D., Westberg, M., Frisch, A., Bendiksby, M. (2018). Draft Genome Sequence and Annotation of the Lichen-Forming Fungus Arthonia radiata. Genome Announcements, 6(14), e00281-18.

Maas, D. L., Prost, S., Bi, K., Smith, L. L., Armstrong, E. E., Aji, L. P., Aji, L.P., Toha, A.H.A., Gillespie, R.G., & Becking, L. E. (2018). Rapid divergence of mussel populations despite incomplete barriers to dispersal. Molecular Ecology, 27(7), 1556-1571.

Sakai-Kawada, F.E., Yakym, C.J., Helmkampf, M., Hagiwara, K., Ip, C.G., Antonio, B.J., Armstrong, E.E., Ulloa, W.J. and Awaya, J.D. (2016). Draft genome sequence of marine sponge symbiont Pseudoalteromonas luteoviolacea IPB1, isolated from Hilo, Hawai’i. Genome Announcements, 4(5), pp.e01002-16.

Rominger, A. J., Goodman, K. R., Lim, J. Y., Armstrong, E. E., Becking, L. E., Bennett, G. M., ... & Gillespie, R. G. (2016). Community assembly on isolated islands: macroecology meets evolution. Global ecology and biogeography, 25(7), 769-780.