- 2025
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Song, D., Sun, H., Ngumbi, E., & Kamruzzaman, M. (2025). Multispectral image reconstruction from RGB image for maize growth status monitoring based on window-adaptive spatial-spectral attention transformer. Computers and Electronics in Agriculture, 239, Article 111062. https://doi.org/10.1016/j.compag.2025.111062
Rayamajhi, N., Rivera-Colón, A. G., Minhas, B. F., Christina Cheng, C. H., & Catchen, J. M. (2025). The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki. G3: Genes, Genomes, Genetics, 15(1), Article jkae257. https://doi.org/10.1093/g3journal/jkae267
Paris, J. R., King, R. A., Ferrer Obiol, J., Shaw, S., Lange, A., Bourret, V., Hamilton, P. B., Rowe, D., Laing, L. V., Farbos, A., Moore, K., Urbina, M. A., van Aerle, R., Catchen, J. M., Wilson, R. W., Bury, N. R., Santos, E. M., & Stevens, J. R. (2025). The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers. Molecular ecology, 34(1), Article e17591. https://doi.org/10.1111/mec.17591
Ngumbi, E. N. (2025). Could flooding undermine progress in building climate-resilient crops? Trends in Plant Science, 30(1), 85-94. https://doi.org/10.1016/j.tplants.2024.07.017
Ngumbi, E., Dady, E., Raglin, S., & Kent, A. (2025). Interactions between soil source, flooding, and herbivory shape tomato plant volatile emissions and rhizosphere bacterial and fungal communities. Plant and Soil, 516(1), 835-854. https://doi.org/10.1007/s11104-025-07762-3
Ngumbi, E. N. (2025). Beneficial soil microbes as drivers of plant–insect interactions: a perspective. Current Opinion in Insect Science, 72, Article 101432. https://doi.org/10.1016/j.cois.2025.101432
Madrigal, G., Minhas, B. F., & Catchen, J. (2025). Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs. Molecular ecology resources, 25(1), Article e13982. https://doi.org/10.1111/1755-0998.13982
Krupa, K. L., & Davis, J. L. (2025). Repatriation and Generative Return. In Fwd Museums: Guide To {...} 2025
Dudaniec, R. Y., Yadav, S., Catchen, J., & Kleindorfer, S. (2025). Genomic Introgression Between Critically Endangered and Stable Species of Darwin's Tree Finches on the Galapagos Islands. Evolutionary Applications, 18(1), Article e70066. https://doi.org/10.1111/eva.70066
Dong, Y., & Malhi, R. S. (2025). Ancient DNA offers clues about mysterious prehistoric settlement in China. Nature, 648(8094), 548-549. https://doi.org/10.1038/d41586-025-03593-5
Davis, J. L. (2025). How the Oak Tree Came to Be. Meridians, 24(1), 12-13. https://doi.org/10.1215/15366936-11530834
Davis, J. L. (2025). Welcome to the Indigenous Languages Slipstream. American Indian Culture and Research Journal, 48(1). https://doi.org/10.17953/A3.41969
Davis, J. L. (2025, Jan 9). Home-Carrying: A Repatriation Trip to Vanuatu 100 Years in the Making. SAPIENS. https://www.sapiens.org/culture/international-repatriation-ancestor-van…
Bishop, K. J. (2025). Integrating cross-collections research and archival study: new insights on macaws and parrots from Chaco Canyon, NM. Journal of Anthropological Archaeology, 78, Article 101690. https://doi.org/10.1016/j.jaa.2025.101690
Bishop, K. J. (2025). Reconstructing Context for the Macaws and Parrots of Chaco Canyon, New Mexico. KIVA. Advance online publication. https://doi.org/10.1080/00231940.2025.2505360
The above report is produced using the following setup
- 2024
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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
- 2023
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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
- 2022
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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