Thomas, A. E., Hill, M. E., Stricker, L., Lavin, M., Givens, D., de Flamingh, A., Witt, K. E., Malhi, R. S., & Kitchen, A. (2024). The Dogs of Tsenacomoco: Ancient DNA Reveals the Presence of Local Dogs at Jamestown Colony in the Early Seventeenth Century. American Antiquity, 89(3), 341-359. https://doi.org/10.1017/aaq.2024.25

Rider, D. F., Wolf, A. C. E., Murray, J., De Flamingh, A., Dos Santos, A. L. C., Lanoë, F., Zedeño, M. N., DeGiorgio, M., Lindo, J., & Malhi, R. S. (2024). Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times. Science Advances, 10(14), Article eadl6595. https://doi.org/10.1126/sciadv.adl6595

Rai, R., Vittore, K. M., Pasion, J., Malvino, M. L., Mason, J. D., Liu, Q., Sulley, S., Babadoost, M., Catchen, J. M., & Hind, S. R. (2024). Comparative genomics of Xanthomonas cucurbitae isolates collected from Midwestern United States pumpkin fields. Plant Pathology, 73(8), 2211-2223. https://doi.org/10.1111/ppa.13965

Ngumbi, E. N. (in press). Could flooding undermine progress in building climate-resilient crops? Trends in Plant Science. https://doi.org/10.1016/j.tplants.2024.07.017

Mleziva, A. D., & Ngumbi, E. N. (2024). Comparative analysis of defensive secondary metabolites in wild teosinte and cultivated maize under flooding and herbivory stress. Physiologia Plantarum, 176(1), Article e14216. https://doi.org/10.1111/ppl.14216

Hanson, K. E., Fladd, S. G., Oas, S. E., & Bishop, K. J. (2024). The Social Construction of Backdirt in Chaco Archaeology. Journal of Field Archaeology, 49(2), 129-139. https://doi.org/10.1080/00934690.2024.2307122

de Flamingh, A., Gnoske, T. P., Rivera-Colón, A. G., Simeonovski, V. A., Kerbis Peterhans, J. C., Yamaguchi, N., Witt, K. E., Catchen, J., Roca, A. L., & Malhi, R. S. (2024). Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction. Journal of Heredity, 115(2), 155-165. Article esad081. https://doi.org/10.1093/jhered/esad081

de Flamingh, A., Gnoske, T. P., Kerbis Peterhans, J. C., Simeonovski, V. A., Gitahi, N., Mwebi, O., Agwanda, B. R., Catchen, J. M., Roca, A. L., & Malhi, R. S. (2024). Compacted hair in broken teeth reveals dietary prey of historic lions. Current Biology, 34(21), 5104-5111.e4. https://doi.org/10.1016/j.cub.2024.09.029

Davis, J. L. (2024). Attending to settler colonialism in Black/Native American histories in Alaina Roberts' I've been Here All the While. Settler Colonial Studies. https://doi.org/10.1080/2201473X.2024.2302717

David, L. K. T. (2024). Supporting the use of genetic genealogy in restoring family narratives following the transatlantic slave trade. American Anthropologist, 126(1), 153-157. https://doi.org/10.1111/aman.13939

Burton, A. M., Davis, J. L., & Brennan, M. L. (2024). Reciprocity and Redistribution: Methodologies for Rethinking Public and Community-based Humanities Research . In D. Fisher-Livne, & M. May-Curry (Eds.), The Routledge Companion to Public Humanities Scholarship (Routledge Literature Companions). Routledge.

Bosch, N., Chan, A. S., Davis, J. L., Gutiérrez, R., He, J., Karahalios, K., Koyejo, S., Loui, M. C., Mendenhall, R., Sanfilippo, M. R., Tong, H., Varshney, L. R., & Wang, Y. (2024). Artificial Intelligence, Social Responsibility, and the Roles of the University. Communications of the ACM, 67(8), 22-25. https://doi.org/10.1145/3640541

Rogers-Lavanne, M. P., Bader, A. C., de Flamingh, A., Saboowala, S., Smythe, C., Atchison, B., Moulton, N., Wilson, A., Wildman, D. E., Boraas, A., Uddin, M., Worl, R., & Malhi, R. S. (2023). Association between gene methylation and experiences of historical trauma in Alaska Native peoples. International Journal for Equity in Health, 22(1), Article 182. https://doi.org/10.1186/s12939-023-01967-7

Minhas, B. F., Beck, E. A., Cheng, C. H. C., & Catchen, J. (2023). Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes. Scientific reports, 13(1), Article 6939. https://doi.org/10.1038/s41598-023-34237-1

Wroblewski, T. H., Witt, K. E., Lee, S., Malhi, R. S., Peede, D., Huerta-Sánchez, E., Villanea, F. A., & Claw, K. G. (2023). Pharmacogenetic variation in Neanderthals and Denisovans and implications for human health and response to medications. Genome biology and evolution, 15(12), Article evad222. https://doi.org/10.1093/gbe/evad222

Bader, A. C., Carbaugh, A. E., Davis, J. L., Krupa, K., & Malhi, R. S. (2023). Biological samples taken from Native American Ancestors are human remains under NAGPRA. American Journal of Biological Anthropology, 181(4), 527-534. https://doi.org/10.1002/ajpa.24726

Schablitsky, J. M., Witt, K. E., Madrigal, J. R., Ellegaard, M. R., Malhi, R. S., & Schroeder, H. (2023). Corrigendum to “Ancient DNA analysis of a nineteenth century tobacco pipe from a Maryland slave quarter” [J. Archaeol. Sci. 105 (2019) 11–18, (S0305440318305661), (10.1016/j.jas.2019.02.006)]. Journal of Archaeological Science, 156, Article 105801. https://doi.org/10.1016/j.jas.2023.105801

Rochette, N. C., Rivera-Colón, A. G., Walsh, J., Sanger, T. J., Campbell-Staton, S. C., & Catchen, J. M. (2023). On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity. Molecular ecology resources, 23(6), 1299-1318. https://doi.org/10.1111/1755-0998.13800

Traniello, I. M., Bukhari, S. A., Dibaeinia, P., Serrano, G., Avalos, A., Ahmed, A. C., Sankey, A. L., Hernaez, M., Sinha, S., Zhao, S. D., Catchen, J., & Robinson, G. E. (2023). Single-cell dissection of aggression in honeybee colonies. Nature Ecology and Evolution, 7(8), 1232-1244. https://doi.org/10.1038/s41559-023-02090-0

David, L. T. (2023). Addressing the feasibility of people of African descent finding living African relatives using direct-to-consumer genetic testing. American Journal of Biological Anthropology, 181(2), 163-165. https://doi.org/10.1002/ajpa.24705

Cheng, C-H. C., Rivera-Colón, A. G., Minhas, B. F., Wilson, L., Rayamajhi, N., Vargas-Chacoff, L., & Catchen, J. M. (2023). Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus—The Closest Ancestral Proxy of Antarctic Cryonotothenioids. Genes, 14(6), Article 1196. https://doi.org/10.3390/genes14061196

Thomas, G., Rusman, Q., Morrison, W. R., Magalhães, D. M., Dowell, J. A., Ngumbi, E., Osei-Owusu, J., Kansman, J., Gaffke, A., Pagadala Damodaram, K. J., Kim, S. J., & Tabanca, N. (2023). Deciphering Plant-Insect-Microorganism Signals for Sustainable Crop Production. Biomolecules, 13(6), Article 997. https://doi.org/10.3390/biom13060997

Aqil, A., Gill, S., Gokcumen, O., Malhi, R. S., Reese, E. A., Smith, J. L., Heaton, T. T., & Lindqvist, C. (2023). A paleogenome from a Holocene individual supports genetic continuity in Southeast Alaska. iScience, 26(5), Article 106581. https://doi.org/10.1016/j.isci.2023.106581

Kowal, E., Weyrich, L. S., Argüelles, J. M., Bader, A. C., Colwell, C., Cortez, A. D., Davis, J. L., Figueiro, G., Fox, K., Malhi, R. S., Matisoo-Smith, E., Nayak, A., Nelson, E. A., Nicholas, G., Nieves-Colón, M. A., Russell, L., Ulm, S., Vergara-Silva, F., Villanea, F. A., ... Tsosie, K. S. (2023). Community partnerships are fundamental to ethical ancient DNA research. Human Genetics and Genomics Advances, 4(2), Article 100161. https://doi.org/10.1016/j.xhgg.2022.100161

de Flamingh, A., Rivera-Colón, A. G., Gnoske, T. P., Kerbis Peterhans, J. C., Catchen, J., Malhi, R. S., & Roca, A. L. (2023). Numt Parser: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera. Journal of Heredity, 114(2), 120-130. Article esac065. https://doi.org/10.1093/jhered/esac065

Smalls, K. A., & Davis, J. L. (2023). Language and Racism. In A. Duranti, R. George, & R. C. Riner (Eds.), A New Companion to Linguistic Anthropology (pp. 560-576). (Wiley Blackwell Companions to Anthropology). Wiley-Blackwell. https://doi.org/10.1002/9781119780830.ch31

Rivera-Colón, A. G., Rayamajhi, N., Fazal Minhas, B., Madrigal, G., Bilyk, K. T., Yoon, V., Hüne, M., Gregory, S., Cheng, C-H. C., & Catchen, J. M. (2023). Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish. Molecular biology and evolution, 40(3), Article msad029. https://doi.org/10.1093/molbev/msad029

de Flamingh, A., Ishida, Y., Pečnerová, P., Vilchis, S., Siegismund, H. R., Van aarde, R. J., Malhi, R. S., & Roca, A. L. (2023). Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology. Frontiers in Genetics, 13, Article 1021004. https://doi.org/10.3389/fgene.2022.1021004

Cortez, A. D., Lippert, D., Davis, J. L., Nicholas, G., Malhi, R. S., Weyrich, L. S., Claw, K. G., Bader, A. C., & Colwell, C. (in press). Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples. American Journal of Biological Anthropology. https://doi.org/10.1002/ajpa.24714

Dady, E. R., Kleczewski, N. M., Ugarte, C. M., & Ngumbi, E. (in press). Plant Variety, Mycorrhization, and Herbivory Influence Induced Volatile Emissions and Plant Growth Characteristics in Tomato. Journal of Chemical Ecology. https://doi.org/10.1007/s10886-023-01455-w

Ngumbi, E., Dady, E., & Calla, B. (2022). Flooding and herbivory: the effect of concurrent stress factors on plant volatile emissions and gene expression in two heirloom tomato varieties. BMC Plant Biology, 22(1), [536]. https://doi.org/10.1186/s12870-022-03911-3

Cerca, J., Petersen, B., Lazaro-Guevara, J. M., Rivera-Colón, A., Birkeland, S., Vizueta, J., Li, S., Li, Q., Loureiro, J., Kosawang, C., Díaz, P. J., Rivas-Torres, G., Fernández-Mazuecos, M., Vargas, P., McCauley, R. A., Petersen, G., Santos-Bay, L., Wales, N., Catchen, J. M., ... Martin, M. D. (2022). The genomic basis of the plant island syndrome in Darwin’s giant daisies. Nature communications, 13(1), [3729]. https://doi.org/10.1038/s41467-022-31280-w

Rayamajhi, N., Cheng, C-H. C., & Catchen, J. M. (2022). Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki. G3 Genes|Genomes|Genetics, 12(11), [jkac192]. https://doi.org/10.1093/g3journal/jkac192

Cramb, J., Ritchison, B. T., Hadden, C. S., Zhang, Q., Alarcón-Tinajero, E., Chen, X., Jones, K. C., Jones, T., Napora, K., Veres, M., & Thompson, V. D. (2022). The Changing Profile of Tenure-Track Faculty in Archaeology. Advances in Archaeological Practice, 10(4), 371-381. https://doi.org/10.1017/aap.2022.8

Small, C. M., Healey, H. M., Currey, M. C., Beck, E. A., Catchen, J., Lin, A. S. P., Cresko, W. A., & Bassham, S. (2022). Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes. Proceedings of the National Academy of Sciences of the United States of America, 119(26), [e2119602119]. https://doi.org/10.1073/pnas.2119602119

Raglin, S. S., Kent, A. D., & Ngumbi, E. N. (2022). Herbivory Protection via Volatile Organic Compounds Is Influenced by Maize Genotype, Not Bacillus altitudinis-Enriched Bacterial Communities. Frontiers in Microbiology, 13, [826635]. https://doi.org/10.3389/fmicb.2022.826635

Severson, A. L., Byrd, B. F., Mallott, E. K., Owings, A. C., DeGiorgio, M., de Flamingh, A., Nijmeh, C., Arellano, M. V., Leventhal, A., Rosenberg, N. A., & Malhi, R. S. (2022). Ancient and modern genomics of the Ohlone Indigenous population of California. Proceedings of the National Academy of Sciences, 119(13), e2111533119. [e2111533119]. https://doi.org/10.1073/pnas.2111533119

Davis, J. L., & Krupa, K. (2022). Toward a Language of Possibility in Curation and Consultation Practices. Collections: A Journal for Museum and Archives Professionals, 18(1), 18-27. https://doi.org/10.1177/15501906211073074

Capel, S. L. R., Bouzat, J. L., Catchen, J. M., Johnson, J. A., Dunn, P. O., & Paige, K. N. (2022). Evaluating the genome-wide impacts of species translocations: the greater prairie-chicken as a case study. Conservation Genetics, 23(1), 179-191. https://doi.org/10.1007/s10592-021-01412-8

Davis, J. L. (2022). Trickster Academy. (Sun Tracks). University of Arizona Press.

Ritchison, B. T., & Anderson, D. G. (2022). “Vacant Quarters” and Population Movements: Legacy Data and the Investigation of a Large-Scale Emigration Event from the Savannah River Valley to the Georgia Coast. In Following the Mississippian Spread: Climate Change and Migration in the Eastern US (ca. AD 1000-1600) (pp. 257-299). Springer. https://doi.org/10.1007/978-3-030-89082-7_9

Davis, J. L. (2022). "Anadromous". Humana Obscura, (4), 39. https://www.humanaobscura.com/issue-4

Potter, B. A., Chatters, J. C., Prentiss, A. M., Fiedel, S. J., Haynes, G., Kelly, R. L., Kilby, J. D., Lanoë, F., Holland-Lulewicz, J., Miller, D. S., Morrow, J. E., Perri, A. R., Rademaker, K. M., Reuther, J. D., Ritchison, B. T., Sanchez, G., Sánchez-Morales, I., Spivey-Faulkner, S. M., Tune, J. W., & Haynes, C. V. (2022). Current Understanding of the Earliest Human Occupations in the Americas: Evaluation of Becerra-Valdivia and Higham (2020). PaleoAmerica, 8(1), 62-76. https://doi.org/10.1080/20555563.2021.1978721

Chatters, J. C., Potter, B. A., Prentiss, A. M., Fiedel, S. J., Haynes, G., Kelly, R. L., Kilby, J. D., Lanoë, F., Holland-Lulewicz, J., Miller, D. S., Morrow, J. E., Perri, A. R., Rademaker, K. M., Reuther, J. D., Ritchison, B. T., Sanchez, G., Sánchez-Morales, I., Spivey-Faulkner, S. M., Tune, J. W., & Haynes, C. V. (2022). Evaluating Claims of Early Human Occupation at Chiquihuite Cave, Mexico. PaleoAmerica, 8(1), 1-16. https://doi.org/10.1080/20555563.2021.1940441

Yarlagadda, K., Zachwieja, A. J., de Flamingh, A., Phungviwatnikul, T., Rivera-Colón, A. G., Roseman, C., Shackelford, L., Swanson, K. S., & Malhi, R. S. (2022). Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes. Proceedings of the Royal Society B: Biological Sciences, 289(1974), [20220052]. https://doi.org/10.1098/rspb.2022.0052

Rivera-Colón, A. G., & Catchen, J. (2022). Population Genomics Analysis with RAD, Reprised: Stacks 2. In Methods in Molecular Biology (pp. 99-149). (Methods in Molecular Biology; Vol. 2498). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-2313-8_7