Sodagari, H. R., Agrawal, I., Yudhanto, S., & Varga, C. (2023). Longitudinal analysis of differences and similarities in antimicrobial resistance among commensal Escherichia coli isolated from market swine and sows at slaughter in the United States of America, 2013–2019. International Journal of Food Microbiology, 407, Article 110388. https://doi.org/10.1016/j.ijfoodmicro.2023.110388
Shen, C., Liu, B., Williams, K. P., & Warnow, T. (2023). EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment. Algorithms for Molecular Biology, 18(1). https://doi.org/10.1186/s13015-023-00247-x
Bush, D. S., Demkovich, M., Aldunate, M., Siegel, J., & Berenbaum, M. R. (2023). Kaolin as a management alternative for insecticide-resistant navel orangeworm (Lepidoptera: Pyralidae). Journal of economic entomology, 116(6), 2095-2103. Article toad194. https://doi.org/10.1093/jee/toad194
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
Krist, C., & Kubsch, M. (2023). Bias, bias everywhere: A response to Li et al. and Zhai and Nehm. Journal of Research in Science Teaching, 60(10), 2395-2399. https://doi.org/10.1002/tea.21913
Palma-Salgado, S., Ku, K. M., Juvik, J. A., Nguyen, T. H., & Feng, H. (2023). Corrigendum to “Artificial phylloplanes resembling physicochemical characteristics of selected fresh produce and their potential use in bacterial attachment/removal studies” [Food Control 149 (2023) 109730] (Food Control (2023) 149, (S0956713523001305), (10.1016/j.foodcont.2023.109730)). Food Control, 154, Article 109998. https://doi.org/10.1016/j.foodcont.2023.109998
Karlikow, M., Amalfitano, E., Yang, X., Doucet, J., Chapman, A., Mousavi, P. S., Homme, P., Sutyrina, P., Chan, W., Lemak, S., Yakunin, A. F., Dolezal, A. G., Kelley, S., Foster, L. J., Harpur, B. A., & Pardee, K. (2023). CRISPR-induced DNA reorganization for multiplexed nucleic acid detection. Nature communications, 14(1), Article 1505. https://doi.org/10.1038/s41467-023-36874-6
Wu, W. Y., Liao, L. H., Lin, C. H., Johnson, R. M., & Berenbaum, M. R. (2023). Effects of pesticide-adjuvant combinations used in almond orchards on olfactory responses to social signals in honey bees (Apis mellifera). Scientific reports, 13(1), Article 15577. https://doi.org/10.1038/s41598-023-41818-7
Tan, T. J. C., Mou, Z., Lei, R., Ouyang, W. O., Yuan, M., Song, G., Andrabi, R., Wilson, I. A., Kieffer, C., Dai, X., Matreyek, K. A., & Wu, N. C. (2023). High-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike. Nature communications, 14(1), Article 2003. https://doi.org/10.1038/s41467-023-37786-1
Uelmen, J. A., Lamcyzk, B., Irwin, P., Bartlett, D., Stone, C., Mackay, A., Arsenault-Benoit, A., Ryan, S. J., Mutebi, J. P., Hamer, G. L., Fritz, M., & Smith, R. L. (2023). Human biting mosquitoes and implications for West Nile virus transmission. Parasites and Vectors, 16(1), Article 2. https://doi.org/10.1186/s13071-022-05603-1
Uelmen, J. A., Kopsco, H., Mori, J., Brown, W. M., & Smith, R. L. (2023). Modeling community COVID-19 transmission risk associated with U.S. universities. Scientific reports, 13(1), Article 1428. https://doi.org/10.1038/s41598-023-28212-z
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
Liu, B., & Warnow, T. (2023). Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms for Molecular Biology, 18(1), Article 6. https://doi.org/10.1186/s13015-023-00230-6
Lei, R., Kim, W., Lv, H., Mou, Z., Scherm, M. J., Schmitz, A. J., Turner, J. S., Tan, T. J. C., Wang, Y., Ouyang, W. O., Liang, W., Rivera-Cardona, J., Teo, C., Graham, C. S., Brooke, C. B., Presti, R. M., Mok, C. K. P., Krammer, F., Dai, X., ... Wu, N. C. (2023). Leveraging vaccination-induced protective antibodies to define conserved epitopes on influenza N2 neuraminidase. Immunity, 56(11), 2621-2634.e6. https://doi.org/10.1016/j.immuni.2023.10.005
Huang, C., Ginn, T. R., Clark, G. G., Zaki, F. R., Won, J., Boppart, S. A., & Nguyen, T. H. (2023). Phosphate-Based Corrosion Inhibition in Drinking Water Systems and Effects on Disinfectant Decay and Biofilm Growth. Environmental Engineering Science, 40(11), 634-644. https://doi.org/10.1089/ees.2023.0065
Tabatabaee, Y., Roch, S., & Warnow, T. (2023). QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. Journal of Computational Biology, 30(11), 1146-1181. https://doi.org/10.1089/cmb.2023.0185
Mao, Y., Zeineldin, M., Usmani, M., Jutla, A., Shisler, J. L., Whitaker, R. J., & Nguyen, T. H. (2023). Local and Environmental Reservoirs of Salmonella enterica After Hurricane Florence Flooding. GeoHealth, 7(11), Article e2023GH000877. https://doi.org/10.1029/2023GH000877
Resendiz-Moctezuma, C., Fonville, A. P. L., Harsh, B. N., Stasiewicz, M. J., & Miller, M. J. (2023). Use of Doehlert Matrix as a Tool for High-Throughput Screening of Organic Acids and Essential Oils on Miniaturized Pork Loins, Followed by Lab-Scale Validation That Confirmed Tested Compounds Do Not Show Synergistic Effects against Salmonella Typhimurium. Foods, 12(21), Article 4034. https://doi.org/10.3390/foods12214034
Lei, R., Hernandez Garcia, A., Tan, T. J. C., Teo, Q. W., Wang, Y., Zhang, X., Luo, S., Nair, S. K., Peng, J., & Wu, N. C. (2023). Erratum: Mutational fitness landscape of human influenza H3N2 neuraminidase (Cell Reports (2023) 42(1), (S2211124722018526), (10.1016/j.celrep.2022.111951)). Cell Reports, 42(10), Article 113356. https://doi.org/10.1016/j.celrep.2023.113356
Yuan, M., Feng, Z., Lv, H., So, N., Shen, I. R., Tan, T. J. C., Teo, Q. W., Ouyang, W. O., Talmage, L., Wilson, I. A., & Wu, N. C. (2023). Widespread impact of immunoglobulin V-gene allelic polymorphisms on antibody reactivity. Cell Reports, 42(10), Article 113194. https://doi.org/10.1016/j.celrep.2023.113194
Fisher, A., Tadei, R., Berenbaum, M., Nieh, J., Siviter, H., Crall, J., Glass, J. R., Muth, F., Liao, L-H., Traynor, K., Desjardins, N., Nocelli, R., Simon-Delso, N., & Harrison, J. F. (2023). Breaking the cycle: Reforming pesticide regulation to protect pollinators. BioScience, Article biad088. Advance online publication. https://doi.org/10.1093/biosci/biad088
Weber, L. L., Zhang, C., Ochoa, I., & El-Kebir, M. (2023). Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. PLoS computational biology, 19(10), Article e1011544. https://doi.org/10.1371/journal.pcbi.1011544
Park, G. L., Sander, W. E., Martenies, S. E., Rosencranz, H., Rice, L. A., Jayasingh-Ramkumar, J., Michaels, S., & Aldridge, B. (2023). Beyond the Imodium, a One Health Discussion on Diarrhea and the Impact of Climate Change. Medical Science Educator, 33(5), 1049-1053. https://doi.org/10.1007/s40670-023-01865-1
Ghorbani, A., Ngunjiri, J. M., Rendon, G., Brooke, C. B., Kenney, S. P., & Lee, C-W. (2023). Diversity and Complexity of Internally Deleted Viral Genomes in Influenza A Virus Subpopulations with Enhanced Interferon-Inducing Phenotypes. Viruses, 15(10), Article 2107. https://doi.org/10.3390/v15102107
Oh, C., Zhou, A., O'Brien, K., Schmidt, A. R., Geltz, J., Shisler, J. L., Schmidt, A. R., Keefer, L., Brown, W. M., & Nguyen, T. H. (2023). Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. Applied and environmental microbiology, 89(10). https://doi.org/10.1128/aem.00331-23
Ramezanifard, R., Golubeva, Y. A., Palmer, A. D., & Slauch, J. M. (2023). TamAB is regulated by PhoPQ and functions in outer membrane homeostasis during Salmonella pathogenesis. Journal of bacteriology, 205(10). https://doi.org/10.1128/jb.00183-23
Capel, S. L. R., Allan, B. F., Favela, A., Clem, C. S., Ooi, S. K., Virrueta Herrera, S., Wilson, L. J., & Strickland, L. R. (2023). Education in the Anthropocene: assessing planetary health science standards in the USA. Proceedings of the Royal Society B: Biological Sciences, 290(2007), Article 20230975. https://doi.org/10.1098/rspb.2023.0975
Miller, R. C., Lee, J., Kim, Y. J., Han, H. S., & Kong, H. (2023). In-Drop Thermal Cycling of Microcrystal Assembly for Senescence Control with Minimal Variation in Efficacy. Advanced Functional Materials, 33(37), Article 2302232. https://doi.org/10.1002/adfm.202302232
Shrestha, R. D., Agunos, A., Gow, S. P., & Varga, C. (2023). Assessing antimicrobial resistance in Campylobacter jejuni and Campylobacter coli and its association with antimicrobial use in Canadian turkey flocks. Epidemiology and Infection, 151, Article e152. https://doi.org/10.1017/S0950268823001462
Ruhland, E. L., Johnson, L., Moore, J., Pelly, C., Bess, S., & Dariotis, J. K. (2023). Positionality, intersectionality, power dynamics in community participatory research to define public safety in Black communities. Journal of Community Psychology, 51(7), 2845-2860. https://doi.org/10.1002/jcop.23046
Parr, E. D., Dyer, E. B., Machaka, N., & Krist, C. (2023). Understanding Joint Exploration: the Epistemic Positioning Underlying Collaborative Activity in a Secondary Mathematics Classroom. Canadian Journal of Science, Mathematics and Technology Education, 23(3), 479-496. https://doi.org/10.1007/s42330-023-00295-w
Usmani, M., Uprety, S., Bonham, N., Jamal, Y., Mao, Y., Sano, D., Shisler, J., Unnikrishnan, A., Nguyen, T. H., & Jutla, A. (2023). Assessment of pathogens in flood waters in coastal rural regions: Case study after Hurricane Michael and Florence. PloS one, 18(8 August), Article e0273757. https://doi.org/10.1371/journal.pone.0273757
Collins, A. J., & Whitaker, R. J. (2023). CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity. CRISPR Journal, 6(4), 386-400. https://doi.org/10.1089/crispr.2022.0080
Rappazzo, C. G., Fernandez-Quintero, M. L., Mayer, A., Wu, N. C., Greiff, V., & Guthmiller, J. J. (2023). Defining and studying B cell receptor and TCR interactions. Journal of Immunology, 211(3), 311-322. https://doi.org/10.4049/jimmunol.2300136
Gu, X., Qi, Y., & El-Kebir, M. (2023). Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. In D. Belazzougui, & A. Ouangraoua (Eds.), 23rd International Workshop on Algorithms in Bioinformatics, WABI 2023 Article 21 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 273). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.WABI.2023.21
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
Terrill Sondag, E. E., Stewart Merrill, T. E., Drnevich, J., Holmes, J. R., Fischer, E. K., Cáceres, C. E., & Strickland, L. R. (2023). Differential gene expression in response to fungal pathogen exposure in the aquatic invertebrate, Daphnia dentifera. Ecology and Evolution, 13(8), Article e10354. https://doi.org/10.1002/ece3.10354
Trujillo, J., Schwing, C. D., Muturi, E., & Cáceres, C. E. (2023). Heterocypris incongruens maintains an egg bank in stormwater habitats and influences the development of larval mosquito, Culex restuans. Ecology and Evolution, 13(8), Article e10445. https://doi.org/10.1002/ece3.10445
Roddur, M. S., Snir, S., & El-Kebir, M. (2023). Inferring Temporally Consistent Migration Histories. In D. Belazzougui, & A. Ouangraoua (Eds.), 23rd International Workshop on Algorithms in Bioinformatics, WABI 2023 Article 9 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 273). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.WABI.2023.9
Ragunathan, P. T., Lim, E. N. K., Ma, X., Massé, E., & Vanderpool, C. K. (2023). Mechanisms of Regulation of Cryptic Prophage-Encoded Gene Products in Escherichia coli. Journal of bacteriology, 205(8). https://doi.org/10.1128/jb.00129-23
Kim, J., Atkinson, C., Miller, M. J., Kim, K. H., & Jina, Y. S. (2023). Microbiome Engineering Using Probiotic Yeast: Saccharomyces boulardii and the Secreted Human Lysozyme Lead to Changes in the Gut Microbiome and Metabolome of Mice. Microbiology Spectrum, 11(4). https://doi.org/10.1128/spectrum.00780-23
Stroet, M., Caron, B., Engler, M. S., van der Woning, J., Kauffmann, A., van Dijk, M., El-Kebir, M., Visscher, K. M., Holownia, J., Macfarlane, C., Bennion, B. J., Gelpi-Dominguez, S., Lightstone, F. C., van der Storm, T., Geerke, D. P., Mark, A. E., & Klau, G. W. (2023). OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. Journal of Computer-Aided Molecular Design, 37(8), 357-371. https://doi.org/10.1007/s10822-023-00511-7
Berenbaum, M. R. (2023). “Debugging” insect-related conspiracy theories. Annals of the Entomological Society of America, Article saad018. Advance online publication. https://doi.org/10.1093/aesa/saad018
Lopez, L. K., Cortez, M. H., DeBlieux, T. S., Menel, I. A., O'Brien, B., Cáceres, C. E., Hall, S. R., & Duffy, M. A. (2023). A healthy but depleted herd: Predators decrease prey disease and density. Ecology, 104(7), Article e4063. https://doi.org/10.1002/ecy.4063
Palma-Salgado, S., Ku, K. M., Juvik, J. A., Nguyen, T. H., & Feng, H. (2023). Artificial phylloplanes resembling physicochemical characteristics of selected fresh produce and their potential use in bacterial attachment/removal studies. Food Control, 149, Article 109730. https://doi.org/10.1016/j.foodcont.2023.109730
Epstein, B., Burghardt, L. T., Heath, K. D., Grillo, M. A., Kostanecki, A., Hämälä, T., Young, N. D., & Tiffin, P. (2023). Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis. Molecular ecology, 32(14), 3798-3811. https://doi.org/10.1111/mec.16602
Shrestha, R. D., Agunos, A., Gow, S. P., Deckert, A. E., & Varga, C. (2023). Decrease in the prevalence of antimicrobial resistance in Escherichia coli isolates of Canadian turkey flocks driven by the implementation of an antimicrobial stewardship program. PloS one, 18(7), Article e0282897. https://doi.org/10.1371/journal.pone.0282897
Kosmopoulos, J. C., Campbell, D. E., Whitaker, R. J., & Wilbanks, E. G. (2023). Horizontal Gene Transfer and CRISPR Targeting Drive Phage- Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates. Applied and environmental microbiology, 89(7). https://doi.org/10.1128/aem.00177-23
Rivera-Cardona, J., & Brooke, C. B. (2023). How influenza shuts down host transcription. Nature Microbiology, 8(7), 1195-1196. https://doi.org/10.1038/s41564-023-01416-9
Ivanovic, S., & El-Kebir, M. (2023). Modeling and predicting cancer clonal evolution with reinforcement learning. Genome Research, 33(7), 1078-1088. https://doi.org/10.1101/gr.277672.123
Dariotis, J. K., Chen, F. R., Park, Y. R., Nowak, M. K., French, K. M., & Codamon, A. M. (2023). Parentification Vulnerability, Reactivity, Resilience, and Thriving: A Mixed Methods Systematic Literature Review. International journal of environmental research and public health, 20(13), Article 6197. https://doi.org/10.3390/ijerph20136197
Uprety, S., Sherchan, S. P., Narayanan, P., Dangol, B., Maggos, M., Celmer, A., Shisler, J., Amarasiri, M., Sano, D., & Nguyen, T. H. (2023). Microbial assessment of water, sanitation, and hygiene (WaSH) in temporary and permanent settlements two years after Nepal 2015 earthquake. Science of the Total Environment, 877, Article 162867. https://doi.org/10.1016/j.scitotenv.2023.162867
Sodagari, H. R., Shrestha, R. D., Agunos, A., Gow, S. P., & Varga, C. (2023). Comparison of antimicrobial resistance among Salmonella enterica serovars isolated from Canadian turkey flocks, 2013 to 2021. Poultry science, 102(6), Article 102655. https://doi.org/10.1016/j.psj.2023.102655
McCormick, E. C., Cohen, O. R., Dolezal, A. G., & Sadd, B. M. (2023). Consequences of microsporidian prior exposure for virus infection outcomes and bumble bee host health. Oecologia, 202(2), 325-335. https://doi.org/10.1007/s00442-023-05394-x
Valera, E., Kindratenko, V., Jankelow, A. M., Heredia, J., Kim, A. Y., Cowell, T. W., Chen, C. L., White, K., Han, H. S., & Bashir, R. (2023). Electrochemical point-of-care devices for the diagnosis of sepsis. Current Opinion in Electrochemistry, 39, Article 101300. https://doi.org/10.1016/j.coelec.2023.101300
Heiman, S. L., Hirt, E. R., Isch, C., Brinkworth, J. F., Cronk, L., Alcock, J., Aktipis, A., & Todd, P. M. (2023). Identities as predictors of vaccine hesitancy during the COVID-19 pandemic. Journal of Social Issues, 79(2), 556-577. https://doi.org/10.1111/josi.12569
Daulagala, P., Mann, B. R., Leung, K., Lau, E. H. Y., Yung, L., Lei, R., Nizami, S. I. N., Wu, J. T., Chiu, S. S., Daniels, R. S., Wu, N. C., Wentworth, D., Peiris, M., & Yen, H. L. (2023). Imprinted Anti-Hemagglutinin and Anti-Neuraminidase Antibody Responses after Childhood Infections of A(H1N1) and A(H1N1)pdm09 Influenza Viruses. mBio, 14(3). https://doi.org/10.1128/mbio.00084-23
Zhang, G., Murray, C. J., St. Clair, A. L., Cass, R. P., Dolezal, A. G., Schulte, L. A., Toth, A. L., & O'Neal, M. E. (2023). Native vegetation embedded in landscapes dominated by corn and soybean improves honey bee health and productivity. Journal of Applied Ecology, 60(6), 1032-1043. https://doi.org/10.1111/1365-2664.14397
Walsman, J. C., Duffy, M. A., Cáceres, C. E., & Hall, S. R. (2023). “Resistance Is Futile”: Weaker Selection for Resistance by Abundant Parasites Increases Prevalence and Depresses Host Density. American Naturalist, 201(6), 864-879. https://doi.org/10.1086/724426
Mori, J., & Smith, R. L. (2023). Risk of Legionellosis in residential areas around farms irrigating with municipal wastewater. Risk Analysis, 43(6), 1115-1123. https://doi.org/10.1111/risa.13997
Rapti, Z., Cuevas-Maraver, J., Kontou, E., Liu, S., Drossinos, Y., Kevrekidis, P. G., Barmann, M., Chen, Q. Y., & Kevrekidis, G. A. (2023). The Role of Mobility in the Dynamics of the COVID-19 Epidemic in Andalusia. Bulletin of Mathematical Biology, 85(6), Article 54. https://doi.org/10.1007/s11538-023-01152-5
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
Riley, A. B., Grillo, M. A., Epstein, B., Tiffin, P., & Heath, K. D. (2023). Discordant population structure among rhizobium divided genomes and their legume hosts. Molecular ecology, 32(10), 2646-2659. https://doi.org/10.1111/mec.16704
Farjo, M., & Brooke, C. B. (2023). When influenza viruses don’t play well with others. Nature, 616(7958), 668-669. https://doi.org/10.1038/d41586-023-00983-5
Goodrum, F., Lowen, A. C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M. J., Atwood, W., Avgousti, D., Baines, J., Banfield, B., Banks, L., Bhaduri-McIntosh, S., Bhattacharya, D., Blanco-Melo, D., Bloom, D., Boon, A., Boulant, S., Brandt, C., Broadbent, A., ... Yurochko, A. (2023). Virology under the Microscope-a Call for Rational Discourse. mSphere, 8(2), e0003423. https://doi.org/10.1128/msphere.00034-23
Hwang, H. S., Lo, C., Murphy, M., Grudda, T., Gallagher, N., Luo, C. H., Robinson, M. L., Mirza, A., Conte, M., Conte, A., Zhou, R., Vergara, C., Brooke, C. B., Pekosz, A., Mostafa, H. H., Manabe, Y. C., Thio, C. L., & Balagopal, A. (2023). Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction. The Journal of infectious diseases, 227(8), 981-992. Article jiac472. https://doi.org/10.1093/infdis/jiac472
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
Sodagari, H. R., & Varga, C. (2023). Evaluating Antimicrobial Resistance Trends in Commensal Escherichia coli Isolated from Cecal Samples of Swine at Slaughter in the United States, 2013–2019. Microorganisms, 11(4), Article 1033. https://doi.org/10.3390/microorganisms11041033
Rosas, G. (2023). Unsettling: The El Paso Massacre, Resurgent White Nationalism, and the US-Mexico Border. Johns Hopkins University Press. https://doi.org/10.56021/9781421446172
Tsvetkov, N., Bahia, S., Calla, B., Berenbaum, M. R., & Zayed, A. (2023). Genetics of tolerance in honeybees to the neonicotinoid clothianidin. iScience, 26(3), Article 106084. https://doi.org/10.1016/j.isci.2023.106084
Oh, C., Zhou, A., O’Brien, K., Schmidt IV, A. R., Shisler, J. L., Schmidt, A. R., Keefer, L., Brown, W. M., & Nguyen, T. H. (2023). Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. medRxiv. https://doi.org/10.1101/2023.03.13.23286721
Hur, P., Machaka, N., Krist, C., & Bosch, N. (2023). Informing Expert Feature Engineering through Automated Approaches: Implications for Coding Qualitative Classroom Video Data. In LAK 2023 Conference Proceedings - Towards Trustworthy Learning Analytics - 13th International Conference on Learning Analytics and Knowledge (pp. 630-636). (ACM International Conference Proceeding Series). Association for Computing Machinery. https://doi.org/10.1145/3576050.3576090
Storms, S. M., Shisler, J., Nguyen, T. H., Zuckermann, F. A., & Lowe, J. F. (2023). RT-LAMP as Diagnostic Tool for Influenza—A Virus Detection in Swine. Veterinary Sciences, 10(3), Article 220. https://doi.org/10.3390/vetsci10030220
Berenbaum, M. R. (2023). On peer review-then, now, and soon to be? Proceedings of the National Academy of Sciences of the United States of America, 120(11), Article e2302593120. https://doi.org/10.1073/pnas.2302593120
Wedell, E., Cai, Y., & Warnow, T. (2023). SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(2), 1417-1430. https://doi.org/10.1109/TCBB.2022.3170386
Yin, Q., Luo, W., Mallajosyula, V., Bo, Y., Guo, J., Xie, J., Sun, M., Verma, R., Li, C., Constantz, C. M., Wagar, L. E., Li, J., Sola, E., Gupta, N., Wang, C., Kask, O., Chen, X., Yuan, X., Wu, N. C., ... Davis, M. M. (2023). A TLR7-nanoparticle adjuvant promotes a broad immune response against heterologous strains of influenza and SARS-CoV-2. Nature Materials, 22(3), 380-390. https://doi.org/10.1038/s41563-022-01464-2
Sodagari, H. R., Varga, C., Habib, I., & Sahibzada, S. (2023). Comparison of Antimicrobial Resistance among Commensal Escherichia coli Isolated from Retail Table Eggs Produced by Laying Hens from the Cage and Non-Cage Housing Systems in Western Australia. Antibiotics, 12(3), Article 588. https://doi.org/10.3390/antibiotics12030588
Kopsco, H. L., Gronemeyer, P., Mateus-Pinilla, N., & Smith, R. L. (2023). Current and Future Habitat Suitability Models for Four Ticks of Medical Concern in Illinois, USA. Insects, 14(3), Article 213. https://doi.org/10.3390/insects14030213
Yudhanto, S., & Varga, C. (2023). Knowledge and Attitudes of Small Animal Veterinarians on Antimicrobial Use Practices Impacting the Selection of Antimicrobial Resistance in Dogs and Cats in Illinois, United States: A Spatial Epidemiological Approach. Antibiotics, 12(3), Article 542. https://doi.org/10.3390/antibiotics12030542
Luo, Y., Lv, H., Zhao, S., Sun, Y., Liu, C., Chen, C., Liang, W., Kwok, K. O., Teo, Q. W., So, R. TY., Lin, Y., Deng, Y., Li, B., Dai, Z., Zhu, J., Zhang, D., Fernando, J., Wu, N. C., Tun, H. M., ... Mu, X. (2023). Age-related seroprevalence trajectories of seasonal coronaviruses in children including neonates in Guangzhou, China. International Journal of Infectious Diseases, 127, 26-32. https://doi.org/10.1016/j.ijid.2022.11.044
Jobman, E., Hagenmaier, J., Meyer, N., Harper, L. B., Taylor, L., Lukasiewicz, K., Thomson, D., Lowe, J., & Terrell, S. (2023). Cross-Section Observational Study to Assess Antimicrobial Resistance Prevalence among Bovine Respiratory Disease Bacterial Isolates from Commercial US Feedlots. Antibiotics, 12(2), Article 215. https://doi.org/10.3390/antibiotics12020215
Murray, C. E., Varga, C., Ouckama, R., & Guerin, M. T. (2023). Temporal Study of Salmonella enterica Serovars Isolated from Environmental Samples from Ontario Poultry Breeder Flocks between 2009 and 2018. Pathogens, 12(2), Article 278. https://doi.org/10.3390/pathogens12020278
Goodrum, F., Lowen, A. C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M. J., Atwood, W., Avgousti, D., Baines, J., Banfield, B., Banks, L., Bhaduri-McIntosh, S., Bhattacharya, D., Blanco-Melo, D., Bloom, D., Boon, A., Boulant, S., Brandt, C., Broadbent, A., ... Yurochko, A. (2023). Virology under the Microscope—a Call for Rational Discourse. Journal of virology, 97(2). https://doi.org/10.1128/jvi.00089-23
Lei, R., Hernandez Garcia, A., Tan, T. J. C., Teo, Q. W., Wang, Y., Zhang, X., Luo, S., Nair, S. K., Peng, J., & Wu, N. C. (2023). Mutational fitness landscape of human influenza H3N2 neuraminidase. Cell Reports, 42(1), Article 111951. https://doi.org/10.1016/j.celrep.2022.111951
Sanchez-Nieves, R. L., Zhang, C., & Whitaker, R. J. (2023). Integrated conjugative plasmid drives high frequency chromosomal gene transfer in Sulfolobus islandicus. Frontiers in Microbiology, 14, Article 1114574. https://doi.org/10.3389/fmicb.2023.1114574
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
Willson, J., Tabatabaee, Y., Liu, B., & Warnow, T. (2023). DISCO+QR: rooting species trees in the presence of GDL and ILS. Bioinformatics Advances, 3(1), Article vbad015. https://doi.org/10.1093/bioadv/vbad015
Hatcher, K. M., Smith, R. L., Chiang, C., Flaws, J. A., & Mahoney, M. M. (2023). Nocturnal Hot Flashes, but Not Serum Hormone Concentrations, as a Predictor of Insomnia in Menopausal Women: Results from the Midlife Women's Health Study. Journal of Women's Health, 32(1), 94-101. https://doi.org/10.1089/jwh.2021.0502
Iwadate, Y., Golubeva, Y. A., & Slauch, J. M. (2023). Cation Homeostasis: Coordinate Regulation of Polyamine and Magnesium Levels in Salmonella. mBio, 14(1). https://doi.org/10.1128/mbio.02698-22
Farjo, M., & Brooke, C. B. (2023). Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2. mSphere, 8(1). https://doi.org/10.1128/msphere.00544-22
Abdulla, S. Z., Kim, K., Azam, M. S., Golubeva, Y. A., Cakar, F., Slauch, J. M., & Vanderpool, C. K. (2023). Small RNAs Activate Salmonella Pathogenicity Island 1 by Modulating mRNA Stability through the hilD mRNA 39 Untranslated Region. Journal of bacteriology, 205(1). https://doi.org/10.1128/jb.00333-22
Park, M., Ivanovic, S., Chu, G., Shen, C., & Warnow, T. (2023). UPP2: Fast and Accurate Alignment of Datasets with Fragmentary Sequences. Bioinformatics, 39(1), Article btad007. https://doi.org/10.1093/bioinformatics/btad007
Goodrum, F., Lowen, A. C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M. J., Atwood, W., Avgousti, D., Baines, J., Banfield, B., Banks, L., Bhaduri-McIntosh, S., Bhattacharya, D., Blanco-Melo, D., Bloom, D., Boon, A., Boulant, S., Brandt, C., Broadbent, A., ... Yurochko, A. (2023). Virology under the Microscope-a Call for Rational Discourse. mBio, 14(1). https://doi.org/10.1128/mbio.00188-23
Ouellette, E., Lewsirirat, S., Sebastian, R. B., Lundsgaard, M., Krist, C., & Kuo, E. (2023). Alignment between student epistemological views and experiences with course structures in introductory physics: A case study. Physics Education Research Conference Proceedings, 260-265. https://doi.org/10.1119/perc.2023.pr.Ouellette
Agrawal, I., Bromfield, C., & Varga, C. (2023). Assessing and improving on-farm biosecurity knowledge and practices among swine producers and veterinarians through online surveys and an educational website in Illinois, United States. Frontiers in Veterinary Science, 10, Article 1167056. https://doi.org/10.3389/fvets.2023.1167056
Hung, C. C., Varga, C., Reinhart, J. M., Maddox, C. W., Dilger, R. N., Forsythe, L., Stevenson, A. K., Franklin-Guild, R. J., Paul, N. C., & Ramachandran, A. (2023). Assessing the urinary concentration of nitrofurantoin and its antibacterial activity against Escherichia coli, Staphylococcus pseudintermedius, and Enterococcus faecium isolated from dogs with urinary tract infections. Frontiers in Veterinary Science, 10, Article 1189374. https://doi.org/10.3389/fvets.2023.1189374
Berenbaum, M. R. (2023). Box Steps. American Entomologist, 69(2), 14-17. https://doi.org/10.1093/ae/tmad034
Tripati, A., Shepherd, M., Morris, V., Andrade, K., Whyte, K. P., David-Chavez, D. M., Hosbey, J., Trujillo-Falcón, J. E., Hunter, B., Hence, D., Carlis, D. N., Brown, V., Parker, W. L., Geller, A., Reich, A., & Glackin, M. (in press). Centering Equity in the Nation's Weather, Water, and Climate Services. Environmental Justice. https://doi.org/10.1089/env.2022.0048
Berenbaum, M. R. (2023). Editorial Expression of Concern. Proceedings of the National Academy of Sciences of the United States of America, 120(43), Article e2316399120. https://doi.org/10.1073/pnas.2316399120
Metras, B. N., Oba, P. M., Miller, M. J., & Swanson, K. S. (2023). Effects of Commercial and Traditional Kefir Supplementation on Apparent Total Tract Macronutrient Digestibility and the Fecal Characteristics, Metabolites, and Microbiota of Healthy Adult Dogs. Journal of animal science, 101, Article skad316. https://doi.org/10.1093/jas/skad316
Huang, C., Clark, G. G., Zaki, F. R., Won, J., Ning, R., Boppart, S. A., Elbanna, A. E., & Nguyen, T. H. (2023). Effects of phosphate and silicate on stiffness and viscoelasticity of mature biofilms developed with simulated drinking water. Biofouling, 39(1), 36-46. https://doi.org/10.1080/08927014.2023.2177538
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
Chakraborty, S., Steckler, T. L., Gronemeyer, P., Mateus-Pinilla, N., & Smith, R. L. (2023). Farmers’ Knowledge and Practices About Ticks and Tickborne Diseases in Illinois. Journal of Agromedicine, 28(4), 756-768. https://doi.org/10.1080/1059924X.2023.2199003
Kim, H. W., Kim, N. K., Phillips, A. P. R., Parker, D. A., Liu, P., Whitaker, R. J., Rao, C. V., & Mackie, R. I. (2023). Genomic insight and physiological characterization of thermoacidophilic Alicyclobacillus isolated from Yellowstone National Park. Frontiers in Microbiology, 14, Article 1232587. https://doi.org/10.3389/fmicb.2023.1232587
Park, M., & Warnow, T. (2023). HMMerge: An ensemble method for multiple sequence alignment. Bioinformatics Advances, 3(1), Article vbad052. https://doi.org/10.1093/bioadv/vbad052
Berenbaum, M. R. (2023). Pesky Problems in the Sky. American Entomologist, 69(3), 12-14. https://doi.org/10.1093/ae/tmad051
Berdychevsky, L., Cavanaugh, D., & Dariotis, J. K. (2023). Psychological, Socio-Demographic, and Logistical Factors Associated With Changes in Sex Life After Over a Year Into the COVID-19 Pandemic. International Journal of Sexual Health, 35(2), 263-283. https://doi.org/10.1080/19317611.2023.2193568
Chu, G., & Warnow, T. (2023). SCAMPP+FastTree: improving scalability for likelihood-based phylogenetic placement. Bioinformatics Advances, 3(1), Article vbad008. https://doi.org/10.1093/bioadv/vbad008
Farrell, A., Phan, T., Brooke, C. B., Koelle, K., & Ke, R. (2023). Semi-infectious particles contribute substantially to influenza virus within-host dynamics when infection is dominated by spatial structure. Virus Evolution, 9(1), Article vead020. https://doi.org/10.1093/ve/vead020
Tabatabaee, Y., Roch, S., & Warnow, T. (2023). Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model. In H. Tang (Ed.), Research in Computational Molecular Biology - 27th Annual International Conference, RECOMB 2023, Proceedings (pp. 41-57). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13976 LNBI). Springer. https://doi.org/10.1007/978-3-031-29119-7_3
Krist, C., Machaka, N., Voss, D., Mathayas, N., Kelly, S., & Shim, S. Y. (2023). Teacher Noticing for Supporting Students’ Epistemic Agency in Science Sensemaking Discussions. Journal of Science Teacher Education, 34(8), 799-819. https://doi.org/10.1080/1046560X.2022.2155355
John, P., Varga, C., Cooke, M., & Majowicz, S. E. (in press). Temporal, spatial and space–time distribution of infections caused by five major enteric pathogens, Ontario, Canada, 2010–2017. Zoonoses and Public Health. https://doi.org/10.1111/zph.13096
Cáceres, C. E., & Stewart Merrill, T. E. (2023). The role of varying resources on Daphnia dentifera immune responses. Fundamental and Applied Limnology, 196(3-4), 217-228. https://doi.org/10.1127/fal/2022/1458
Krist, C., & Shim, S. Y. (in press). Which ideas, when, and why? An experienced teacher's in-the-moment pedagogical reasoning about facilitating student sense-making discussions. Journal of Research in Science Teaching. https://doi.org/10.1002/tea.21908
Liu, B., & Warnow, T. (2023). WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity. Bioinformatics Advances, 3(1), Article vbad024. https://doi.org/10.1093/bioadv/vbad024
Burke, M. D., Fan, T. M., Hergenrother, P. J., Brooke, C. B., Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., & Wang, L. (2022). Saliva-based Molecular Testing For SARS-CoV-2. (U.S. Patent No. 11530457).
Oh, C., Zhou, A., O'Brien, K., Jamal, Y., Wennerdahl, H., Schmidt, A. R., Shisler, J. L., Jutla, A., Schmidt IV, A. R., Keefer, L., Brown, W. M., & Nguyen, T. H. (2022). Application of neighborhood-scale wastewater-based epidemiology in low COVID-19 incidence situations. Science of the Total Environment, 852, [158448]. https://doi.org/10.1016/j.scitotenv.2022.158448
Dean, C. A. E., Katz, A. D., Wu, W. Y., & Berenbaum, M. R. (2022). Degree of Dietary Specialization on Furanocoumarin-Containing Hostplants in a Newly Invasive Web Building Caterpillar. Journal of Chemical Ecology, 48(11-12), 850-866. https://doi.org/10.1007/s10886-022-01389-9
Lyons, L. A., Mateus-Pinilla, N., & Smith, R. L. (2022). Effects of tick surveillance education on knowledge, attitudes, and practices of local health department employees. BMC public health, 22(1), [215]. https://doi.org/10.1186/s12889-022-12667-2
Batstone, R. T., Lindgren, H., Allsup, C. M., Goralka, L. A., Riley, A. B., Grillo, M. A., Marshall-Colon, A., & Heath, K. D. (2022). Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio, 13(6). https://doi.org/10.1128/mbio.01823-22
Carson, D. A., Kopsco, H., Gronemeyer, P., Mateus-Pinilla, N., Smith, G. S., Sandstrom, E. N., & Smith, R. L. (2022). Knowledge, attitudes, and practices of Illinois medical professionals related to ticks and tick-borne disease. One Health, 15, [100424]. https://doi.org/10.1016/j.onehlt.2022.100424
Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Fredrickson, R. L., Wang, T., Wong, G. N., Uelmen, J., Maslov, S., Weiner, Z. J., Tkachenko, A. V., Zhang, H., Liu, Z., Ibrahim, A., Patel, S. J., Paul, J. M., Vance, N. P., Gulick, J. G., ... Burke, M. D. (2022). Mitigation of SARS-CoV-2 transmission at a large public university. Nature communications, 13(1), [3207]. https://doi.org/10.1038/s41467-022-30833-3
Sashittal, P., Zaccaria, S., & El-Kebir, M. (2022). Parsimonious Clone Tree Integration in cancer. Algorithms for Molecular Biology, 17(1), [3]. https://doi.org/10.1186/s13015-022-00209-9
Lei, R., Tan, T. J. C., Hernandez Garcia, A., Wang, Y., Diefenbacher, M., Teo, C., Gopan, G., Tavakoli Dargani, Z., Teo, Q. W., Graham, C. S., Brooke, C. B., Nair, S. K., & Wu, N. C. (2022). Prevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase. Nature communications, 13(1), [6443]. https://doi.org/10.1038/s41467-022-34060-8
Dorak, S. J., Varga, C., Ruder, M. G., Gronemeyer, P., Rivera, N. A., Dufford, D. R., Skinner, D. J., Roca, A. L., Novakofski, J., & Mateus-Pinilla, N. E. (2022). Spatial epidemiology of hemorrhagic disease in Illinois wild white-tailed deer. Scientific reports, 12(1), [6888]. https://doi.org/10.1038/s41598-022-10694-y
Strickland, L. R., Windsor, D., & Cáceres, C. E. (2022). Variation in contact chemical cues may mediate differential predator response in the colour polymorphic tortoise beetle, Chelymorpha alternans. Ecological Entomology, 47(6), 1032-1043. https://doi.org/10.1111/een.13191
Edwards, J. D., Cook, A. M., Yannarell, A. C., & Yang, W. (2022). Accelerated gross nitrogen cycling following garlic mustard invasion is linked with abiotic and biotic changes to soils. Frontiers in Forests and Global Change, 5, [1050542]. https://doi.org/10.3389/ffgc.2022.1050542
Yuan, M., Wang, Y., Lv, H., Tan, T. J. C., Wilson, I. A., & Wu, N. C. (2022). Molecular analysis of a public cross-neutralizing antibody response to SARS-CoV-2. Cell Reports, 41(7), [111650]. https://doi.org/10.1016/j.celrep.2022.111650
Klunk, J., Vilgalys, T. P., Demeure, C. E., Cheng, X., Shiratori, M., Madej, J., Beau, R., Elli, D., Patino, M. I., Redfern, R., DeWitte, S. N., Gamble, J. A., Boldsen, J. L., Carmichael, A., Varlik, N., Eaton, K., Grenier, J. C., Golding, G. B., Devault, A., ... Barreiro, L. B. (2022). Evolution of immune genes is associated with the Black Death. Nature, 611(7935), 312-319. https://doi.org/10.1038/s41586-022-05349-x
Hubner, A. M., Canisso, I. F., Coelho, W. M., Ribeiro, L., Aldridge, B. M., & Lima, F. S. (2022). A randomized controlled trial examining the effects of treatment with propylene glycol and injectable cyanocobalamin on naturally occurring disease, milk production, and reproductive outcomes of dairy cows diagnosed with concurrent hyperketonemia and hypoglycemia. Journal of Dairy Science, 105(11), 9070-9083. https://doi.org/10.3168/jds.2021-21328
Hubner, A., Canisso, I. F., Peixoto, P. M., Coelho, W. M., Ribeiro, L., Aldridge, B. M., Menta, P., Machado, V. S., & Lima, F. S. (2022). Characterization of metabolic profile, health, milk production, and reproductive outcomes of dairy cows diagnosed with concurrent hyperketonemia and hypoglycemia. Journal of Dairy Science, 105(11), 9054-9069. https://doi.org/10.3168/jds.2021-21327
Wang, F., Nisar, H. J., Li, Y., Araud, E., Nguyen, T. H., & Kesavadas, T. (2022). Low-Cost UVBot Using SLAM to Mitigate the Spread of Noroviruses in Occupational Spaces. Sensors, 22(22), [8926]. https://doi.org/10.3390/s22228926
Audu, C. O., Melvin, W. J., Joshi, A. D., Wolf, S. J., Moon, J. Y., Davis, F. M., Barrett, E. C., Mangum, K. D., Deng, H., Xing, X., Wasikowski, R., Tsoi, L. C., Sharma, S. B., Bauer, T. M., Shadiow, J., Corriere, M. A., Obi, A. T., Kunkel, S. L., Levi, B., ... Gallagher, K. A. (2022). Macrophage-specific inhibition of the histone demethylase JMJD3 decreases STING and pathologic inflammation in diabetic wound repair. Cellular and Molecular Immunology, 19(11), 1251-1262. https://doi.org/10.1038/s41423-022-00919-5
Kim, M., Miller, M. J., & Stasiewicz, M. J. (2022). Perspective: Challenges with product testing in powdered infant formula. Journal of Dairy Science, 105(11), 8591-8593. https://doi.org/10.3168/jds.2022-22374
Ouyang, W. O., Tan, T. J. C., Lei, R., Song, G., Kieffer, C., Andrabi, R., Matreyek, K. A., & Wu, N. C. (2022). Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning. Science Advances, 8(47), [eadd7221]. https://doi.org/10.1126/sciadv.add7221
Brinkworth, J. F., & Rusen, R. M. (2022). SARS-CoV-2 Is Not Special, but the Pandemic Is: The Ecology, Evolution, Policy, and Future of the Deadliest Pandemic in Living Memory. Annual Review of Anthropology, 51, 527-548. https://doi.org/10.1146/annurev-anthro-041420-100047
Berger, B., Tian, D., Li, W. V., El-Kebir, M., Tomescu, A. I., Singh, R., Beerenwinkel, N., Li, Y., Boucher, C., & Bar-Joseph, Z. (2022). What are the keys to succeeding as a computational biologist in today's research climate? Cell Systems, 13(10), 781-785. https://doi.org/10.1016/j.cels.2022.09.005
RNA Virus Discovery Consortium (2022). Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell, 185(21), 4023-4037.e18. https://doi.org/10.1016/j.cell.2022.08.023
Liu, T., Wang, Y., Tan, T. J. C., Wu, N. C., & Brooke, C. B. (2022). The evolutionary potential of influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase. Cell Host and Microbe, 30(10), 1363-1369.e4. https://doi.org/10.1016/j.chom.2022.09.003
Zaharias, P., & Warnow, T. (2022). Recent progress on methods for estimating and updating large phylogenies. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1861), [20210244]. https://doi.org/10.1098/rstb.2021.0244
Chakraborty, S., Andrade, F. C. D., & Smith, R. L. (2022). An Interdisciplinary Approach to One Health: Course Design, Development, and Delivery. Journal of Veterinary Medical Education, 49(5), 568-574. [e20210021]. https://doi.org/10.3138/jvme-2021-0021
Lalani, Z., Chu, G., Hsu, S., Kagawa, S., Xiang, M., Zaccaria, S., & El-Kebir, M. (2022). CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. PLoS computational biology, 18(10), [e1010614]. https://doi.org/10.1371/journal.pcbi.1010614
Lau, J. A., Hammond, M. D., Schmidt, J. E., Weese, D. J., Yang, W. H., & Heath, K. D. (2022). Contemporary evolution rivals the effects of rhizobium presence on community and ecosystem properties in experimental mesocosms. Oecologia, 200(1-2), 133-143. https://doi.org/10.1007/s00442-022-05253-1
Walston, L. J., Barley, T., Bhandari, I., Campbell, B., McCall, J., Hartmann, H. M., & Dolezal, A. G. (2022). Opportunities for agrivoltaic systems to achieve synergistic food-energy-environmental needs and address sustainability goals. Frontiers in Sustainable Food Systems, 6, [932018]. https://doi.org/10.3389/fsufs.2022.932018
Miller, R., Kim, Y., Park, C. G., Torres, C., Kim, B., Lee, J., Flaherty, D., Han, H. S., Kim, Y. J., & Kong, H. J. (2022). Extending the Bioavailability of Hydrophilic Antioxidants for Metal Ion Detoxification via Crystallization with Polysaccharide Dopamine. ACS Applied Materials and Interfaces, 14(35), 39759-39774. https://doi.org/10.1021/acsami.2c08889
Jakatdar, A., Liu, B., Warnow, T., & Chacko, G. (2022). AOC: Assembling overlapping communities. Quantitative Science Studies, 3(4), 1079-1096. https://doi.org/10.1162/qss_a_00227
Liu, B., & Warnow, T. (2022). Fast and Accurate Species Trees from Weighted Internode Distances. In C. Boucher, & S. Rahmann (Eds.), 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022 [8] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 242). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.WABI.2022.8
Li, J., Green-Miller, A. R., Hu, X., Lucic, A., Mahesh Mohan, M. R., Dilger, R. N., Condotta, I. C. F. S., Aldridge, B., Hart, J. M., & Ahuja, N. (2022). Barriers to computer vision applications in pig production facilities. Computers and Electronics in Agriculture, 200, [107227]. https://doi.org/10.1016/j.compag.2022.107227
Liang, W., Tan, T. J. C., Wang, Y., Lv, H., Sun, Y., Bruzzone, R., Mok, C. K. P., & Wu, N. C. (2022). Egg-adaptive mutations of human influenza H3N2 virus are contingent on natural evolution. PLoS pathogens, 18(9), [e1010875]. https://doi.org/10.1371/journal.ppat.1010875
Flenniken, J. M., Tuten, H. C., Rose Vineer, H., Phillips, V. C., Stone, C. M., & Allan, B. F. (2022). Environmental Drivers of Gulf Coast Tick (Acari: Ixodidae) Range Expansion in the United States. Journal of medical entomology, 59(5), 1625-1635. https://doi.org/10.1093/jme/tjac091
Varga, C., McDonald, P., Brown, W. M., Shelton, P., Roca, A. L., Novakofski, J. E., & Mateus-Pinilla, N. E. (2022). Evaluating the ability of a locally focused culling program in removing chronic wasting disease infected free-ranging white-tailed deer in Illinois, USA, 2003–2020. Transboundary and Emerging Diseases, 69(5), 2867-2878. https://doi.org/10.1111/tbed.14441
Dean, C. A. E., Easley, J., Katz, A. D., Berlocher, S. H., & Berenbaum, M. R. (2022). Genetic Structure and Colonization of North America by Depressaria depressana (Fabricius 1775) (Lepidoptera: Depressariidae) over 15 Years; Contrasts with Westward Expansion of Depressaria radiella (Goeze, 1783) over 160 Years. Insects, 13(9), [789]. https://doi.org/10.3390/insects13090789
Jamal, Y., Gangwar, M., Usmani, M., Adams, A., Wu, C-Y., Nguyen, T. H., Colwell, R., & Jutla, A. (2022). Identification of thresholds on population density for understanding transmission of COVID-19. GeoHealth, 6(9), [e2021GH000449]. https://doi.org/10.1029/2021GH000449
Allender, M. C., Adkesson, M. J., Langan, J. N., Delk, K. W., Meehan, T., Aitken-Palmer, C., McEntire, M. M., Killian, M. L., Torchetti, M., Morales, S. A., Austin, C., Fredrickson, R., Olmstead, C., Ke, R., Smith, R., Hostnik, E. T., Terio, K., & Wang, L. (2022). Multi-species outbreak of SARS-CoV-2 Delta variant in a zoological institution, with the detection in two new families of carnivores. Transboundary and Emerging Diseases, 69(5), e3060-e3075. https://doi.org/10.1111/tbed.14662
Migliorisi, A., Hart, K., Vaughn, S., Austin, S., Aldridge, B., & Wilkins, P. (2022). Plasma ascorbic acid, antioxidant capacity, and reactive oxygen species in healthy foals. American journal of veterinary research, 83(9). https://doi.org/10.2460/ajvr.22.02.0025
Usmani, M., Brumfield, K. D., Magers, B. M., Huq, A., Barciela, R., Nguyen, T. H., Colwell, R. R., & Jutla, A. (2022). Predictive Intelligence for Cholera in Ukraine? GeoHealth, 6(9), [e2022GH000681]. https://doi.org/10.1029/2022GH000681
Alomar, A. A., Eastmond, B. H., Rapti, Z., Walker, E. D., & Alto, B. W. (2022). Ingestion of spinosad-containing toxic sugar bait alters Aedes albopictus vector competence and vectorial capacity for dengue virus. Frontiers in Microbiology, 13, [933482]. https://doi.org/10.3389/fmicb.2022.933482
Slauch, J. M. (2022). Interplay between Rho, H-NS, spurious transcription, and Salmonella gene regulation. Proceedings of the National Academy of Sciences of the United States of America, 119(33), [e2211222119]. https://doi.org/10.1073/pnas.2211222119
St. Clair, A. L., Suresh, S., & Dolezal, A. G. (2022). Access to prairie pollen affects honey bee queen fecundity in the field and lab. Frontiers in Sustainable Food Systems, 6, [908667]. https://doi.org/10.3389/fsufs.2022.908667
Stewart Merrill, T. E., Cáceres, C. E., Gray, S., Laird, V. R., Schnitzler, Z. T., & Buck, J. C. (2022). Timescale reverses the relationship between host density and infection risk. Proceedings of the Royal Society B: Biological Sciences, 289(1980), [20221106]. https://doi.org/10.1098/rspb.2022.1106
Shen, C., Park, M., & Warnow, T. (2022). WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. Journal of Computational Biology, 29(8), 782-801. https://doi.org/10.1089/cmb.2021.0585
Heath, K. D., Batstone, R. T., Romero, M. C., & McMullen, J. G. (2022). MGEs as the MVPs of Partner Quality Variation in Legume-Rhizobium Symbiosis. mBio, 13(4). https://doi.org/10.1128/mbio.00888-22
Yan, X., Shang, P., Yim-im, W., Sun, Y., Zhang, J., Firth, A. E., Lowe, J. F., & Fang, Y. (2022). Molecular characterization of emerging variants of PRRSV in the United States: new features of the -2/-1 programmed ribosomal frameshifting signal in the nsp2 region. Virology, 573, 39-49. https://doi.org/10.1016/j.virol.2022.06.004
Brinkworth, J. F., & Shaw, J. G. (2022). On race, human variation, and who gets and dies of sepsis. American Journal of Biological Anthropology, 178(S74), 230-255. https://doi.org/10.1002/ajpa.24527
Shrestha, R. D., Agunos, A., Gow, S. P., Deckert, A. E., & Varga, C. (2022). Associations between antimicrobial resistance in fecal Escherichia coli isolates and antimicrobial use in Canadian turkey flocks. Frontiers in Microbiology, 13, [954123]. https://doi.org/10.3389/fmicb.2022.954123
Zeng, Z., Chen, Y., Pinilla-Redondo, R., Shah, S. A., Zhao, F., Wang, C., Hu, Z., Wu, C., Zhang, C., Whitaker, R. J., She, Q., & Han, W. (2022). A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. Cell Host and Microbe, 30(7), 930-943.e6. https://doi.org/10.1016/j.chom.2022.04.015
Batstone, R. T., Burghardt, L. T., & Heath, K. D. (2022). Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont. Proceedings of the Royal Society B: Biological Sciences, 289(1978), [20220477]. https://doi.org/10.1098/rspb.2022.0477
Harwood, G. P., Prayugo, V., & Dolezal, A. G. (2022). Butenolide Insecticide Flupyradifurone Affects Honey Bee Worker Antiviral Immunity and Survival. Frontiers in Insect Science, 2. https://doi.org/10.3389/finsc.2022.907555
Zhang, C., Sashittal, P., Xiang, M., Zhang, Y., Kazi, A., & El-Kebir, M. (2022). Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. Molecular biology and evolution, 39(7), [msac133]. https://doi.org/10.1093/molbev/msac133
Tabatabaee, Y., Sarker, K., & Warnow, T. (2022). Quintet Rooting: Rooting species trees under the multi-species coalescent model. Bioinformatics, 38, I109-I117. https://doi.org/10.1093/bioinformatics/btac224
Ke, R., Martinez, P. P., Smith, R. L., Gibson, L. L., Achenbach, C. J., McFall, S., Qi, C., Jacob, J., Dembele, E., Bundy, C., Simons, L. M., Ozer, E. A., Hultquist, J. F., Lorenzo-Redondo, R., Opdycke, A. K., Hawkins, C., Murphy, R. L., Mirza, A., Conte, M., ... Brooke, C. B. (2022). Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution. Open Forum Infectious Diseases, 9(7), [ofac192]. https://doi.org/10.1093/ofid/ofac192
Liu, B., & Warnow, T. (2022). Scalable Species Tree Inference with External Constraints. Journal of Computational Biology, 29(7), 664-678. https://doi.org/10.1089/cmb.2021.0543
Thayer, J. D., & Hence, D. A. (2022). Transition of Large-Scale Environmental Conditions and Characteristics of Four Rainfall Types Observed by S-PolKa During the MJO-1 Active Phase of DYNAMO/CINDY/AMIE. Journal of Geophysical Research: Atmospheres, 127(12), [e2021JD036188]. https://doi.org/10.1029/2021JD036188
Global Phage Small Open Reading Frame (GP-SmORF) Consortium (2022). Thousands of small, novel genes predicted in global phage genomes. Cell Reports, 39(12), [110984]. https://doi.org/10.1016/j.celrep.2022.110984
Kopsco, H. L., Smith, R. L., & Halsey, S. J. (2022). A Scoping Review of Species Distribution Modeling Methods for Tick Vectors. Frontiers in Ecology and Evolution, 10, [893016]. https://doi.org/10.3389/fevo.2022.893016
Jing, W., & Han, H. S. (2022). Droplet Microfluidics for High-Resolution Virology. Analytical Chemistry, 94(23), 8085-8100. https://doi.org/10.1021/acs.analchem.2c00615
Smith, L. D., Nalla, S., Kuo, C. W., Kohli, M., & Smith, A. M. (2022). Rapid quantification of microRNA-375 through one-pot primer-generating rolling circle amplification. Analyst, 147(13), 2936-2941. https://doi.org/10.1039/d2an00263a
Slauch, J. M. (2022). Regulation of virulence gene expression in vivo. In Virulence Mechanisms of Bacterial Pathogens (pp. 230-249). Wiley-Blackwell. https://doi.org/10.1128/9781555818111.ch16
Crist, S. D., Kopsco, H., Miller, A., Gronemeyer, P., Mateus-Pinilla, N., & Smith, R. L. (2022). Knowledge, attitudes, and practices of veterinary professionals towards ticks and tick-borne diseases in Illinois. One Health, 14, [100391]. https://doi.org/10.1016/j.onehlt.2022.100391
Orazi, G., Collins, A. J., & Whitaker, R. J. (2022). Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species. mSystems, 7(3). https://doi.org/10.1128/msystems.00083-22
Mei, R., & Liu, W. T. (2022). Meta-Omics-Supervised Characterization of Respiration Activities Associated with Microbial Immigrants in Anaerobic Sludge Digesters. Environmental Science and Technology, 56(10), 6689–6698. https://doi.org/10.1021/acs.est.2c01029
Yudhanto, S., Hung, C. C., Maddox, C. W., & Varga, C. (2022). Antimicrobial Resistance in Bacteria Isolated From Canine Urine Samples Submitted to a Veterinary Diagnostic Laboratory, Illinois, United States. Frontiers in Veterinary Science, 9, [867784]. https://doi.org/10.3389/fvets.2022.867784
Willson, J., Roddur, M. S., Liu, B., Zaharias, P., & Warnow, T. (2022). DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition. Systematic biology, 71(3), 610-629. https://doi.org/10.1093/sysbio/syab070
Ferrer, A., Heath, K. D., Mosquera, S. L., Suaréz, Y., & Dalling, J. W. (2022). Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats. FEMS microbiology ecology, 98(5), [fiac040]. https://doi.org/10.1093/femsec/fiac040
Ke, R., Martinez, P. P., Smith, R. L., Gibson, L. L., Mirza, A., Conte, M., Gallagher, N., Luo, C. H., Jarrett, J., Zhou, R., Conte, A., Liu, T., Farjo, M., Walden, K. K. O., Rendon, G., Fields, C. J., Wang, L., Fredrickson, R., Edmonson, D. C., ... Brooke, C. B. (2022). Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nature Microbiology, 7(5), 640-652. https://doi.org/10.1038/s41564-022-01105-z
Agrawal, R. M., Miller, M. J., Singh, V., Stein, H. H., & Takhar, P. S. (2022). Enzymatic hydrolysis and fermentation of soy flour to produce ethanol and soy protein concentrate with increased polyphenols. JAOCS, Journal of the American Oil Chemists' Society, 99(5), 379-391. https://doi.org/10.1002/aocs.12573
Moodie, E. (2022). Expert Witnessing in the Asylum Economy. Annals of Anthropological Practice, 46(1), 72-75. https://doi.org/10.1111/napa.12178
Oh, C., Chowdhury, R., Samineni, L., Shisler, J. L., Kumar, M., & Nguyen, T. H. (2022). Inactivation Mechanism and Efficacy of Grape Seed Extract for Human Norovirus Surrogate. Applied and environmental microbiology, 88(9), [e02247-21]. https://doi.org/10.1128/aem.02247-21
Diefenbacher, M., Tan, T. J. C., Bauer, D. L. V., Stadtmueller, B. M., Wu, N. C., & Brooke, C. B. (2022). Interactions between Influenza A Virus Nucleoprotein and Gene Segment Untranslated Regions Facilitate Selective Modulation of Viral Gene Expression. Journal of virology, 96(10). https://doi.org/10.1128/jvi.00205-22
Landa, K. J., Mossman, L. M., Whitaker, R. J., Rapti, Z., & Clifton, S. M. (2022). Phage–Antibiotic Synergy Inhibited by Temperate and Chronic Virus Competition. Bulletin of Mathematical Biology, 84(5), [54]. https://doi.org/10.1007/s11538-022-01006-6
Shin, J., Miller, M., & Wang, Y. C. (2022). Recent advances in CRISPR-based systems for the detection of foodborne pathogens. Comprehensive Reviews in Food Science and Food Safety, 21(3), 3010-3029. https://doi.org/10.1111/1541-4337.12956
Blair, B., & Lowe, J. (2022). The Application of an Augmented Gravity Model to Measure the Effects of a Regionalization of Potential Risk Distribution of the US Cull Sow Market. Veterinary Sciences, 9(5), [215]. https://doi.org/10.3390/vetsci9050215
Maino Vieytes, C. A., Rodriguez-Zas, S. L., Madak-Erdogan, Z., Smith, R. L., Zarins, K. R., Wolf, G. T., Rozek, L. S., Mondul, A. M., & Arthur , A. E. (2022). Adherence to a priori-Defined Diet Quality Indices Throughout the Early Disease Course Is Associated With Survival in Head and Neck Cancer Survivors: An Application Involving Marginal Structural Models. Frontiers in Nutrition, 9, [791141]. https://doi.org/10.3389/fnut.2022.791141
Wedell, E., Park, M., Korobskiy, D., Warnow, T., & Chacko, G. (2022). Center–periphery structure in research communities. Quantitative Science Studies, 3(1), 289-314. https://doi.org/10.1162/qss_a_00184
St. Clair, A. L., Zhang, G., Dolezal, A. G., O'Neal, M. E., & Toth, A. L. (2022). Agroecosystem landscape diversity shapes wild bee communities independent of managed honey bee presence. Agriculture, Ecosystems and Environment, 327, [107826]. https://doi.org/10.1016/j.agee.2021.107826
Shi, X., Clark, G. G., Huang, C., Nguyen, T. H., & Yuan, B. (2022). Chlorine decay and disinfection by-products formation during chlorination of biofilms formed with simulated drinking water containing corrosion inhibitors. Science of the Total Environment, 815, [152763]. https://doi.org/10.1016/j.scitotenv.2021.152763
John, P., Varga, C., Cooke, M., & Majowicz, S. E. (2022). Incidence, Demographic, and Seasonal Risk Factors of Infections Caused by Five Major Enteric Pathogens, Ontario, Canada, 2010–2017. Foodborne pathogens and disease, 19(4), 248-258. https://doi.org/10.1089/fpd.2021.0034
Zhao, A., Jeffery, E. H., & Miller, M. J. (2022). Is Bitterness Only a Taste? The Expanding Area of Health Benefits of Brassica Vegetables and Potential for Bitter Taste Receptors to Support Health Benefits. Nutrients, 14(7), [1434]. https://doi.org/10.3390/nu14071434
Halloway, A. H., Heath, K. D., & McNickle, G. G. (2022). When does mutualism offer a competitive advantage? A game-theoretic analysis of host-host competition in mutualism. AoB PLANTS, 14(2), [plac010]. https://doi.org/10.1093/aobpla/plac010
Oh, C., Kim, K., Araud, E., Wang, L., Shisler, J. L., & Nguyen, T. H. (2022). A novel approach to concentrate human and animal viruses from wastewater using receptors-conjugated magnetic beads. Water Research, 212, [118112]. https://doi.org/10.1016/j.watres.2022.118112
Che, S., Wang, C., Iverson, M., Varga, C., Barbut, S., Bienzle, D., & Susta, L. (2022). Characteristics of Broiler Chicken Breast Myopathies (Spaghetti Meat, Woody Breast, White Striping) in Ontario, Canada. Poultry science, 101(4), [101747]. https://doi.org/10.1016/j.psj.2022.101747
Oh, C., Sashittal, P., Zhou, A., Wang, L., El-Kebir, M., & Nguyen, T. H. (2022). Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Applied and environmental microbiology, 88(7), [e0228921]. https://doi.org/10.1128/aem.02289-21
Clair, A. L. S., Beach, N. J., & Dolezal, A. G. (2022). Honey bee hive covers reduce food consumption and colony mortality during overwintering. PloS one, 17(4 April), [e0266219]. https://doi.org/10.1371/journal.pone.0266219
Che, S., Wang, C., Varga, C., Barbut, S., & Susta, L. (2022). Prevalence of breast muscle myopathies (spaghetti meat, woody breast, white striping) and associated risk factors in broiler chickens from Ontario Canada. PloS one, 17(4 April), [e0267019]. https://doi.org/10.1371/journal.pone.0267019
Edwards, J. D., Yang, W. H., & Yannarell, A. C. (2022). Soil microbial communities are not altered by garlic mustard in recently invaded central Illinois forests. Ecosphere, 13(4), [e3967]. https://doi.org/10.1002/ecs2.3967
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
Ibarra-Sánchez, L. A., Miller, M. J., & Holle, M. J. (2022). Recent Advances in Listeria Mitigation for Queso Fresco. ACS Food Science and Technology, 2(3), 425-434. https://doi.org/10.1021/acsfoodscitech.1c00343
Jing, W., & Han, H. S. (2022). Inertial Self-Assembly Dynamics of Interacting Droplet Ensembles in Microfluidic Flows. Analytical Chemistry, 94(9), 3978-3986. https://doi.org/10.1021/acs.analchem.1c05116
Julian Lantry, F., Epsi, N. J., Pollett, S. D., Simons, M. P., Lindholm, D. A., Colombo, R. E., Fries, A. C., Maves, R. C., Ganesan, A., Utz, G. C., Lalani, T., Smith, A. G., Mody, R. M., Colombo, C. J., Chi, S. W., Madar, C., Huprikar, N., Larson, D. T., Bazan, S., ... Peel, S. (2022). Anatomical Site, Viral Ribonucleic Acid Abundance, and Time of Sampling Correlate with Molecular Detection of Severe Acute Respiratory Syndrome Coronavirus 2 during Infection. Open Forum Infectious Diseases, 9(3), [ofab623]. https://doi.org/10.1093/ofid/ofab623
Bacon, E. A., Kopsco, H., Gronemeyer, P., Mateus-Pinilla, N., & Smith, R. L. (2022). Effects of Climate on the Variation in Abundance of Three Tick Species in Illinois. Journal of medical entomology, 59(2), 700-709. https://doi.org/10.1093/jme/tjab189
Clark, G. G., Pan, W., Giammar, D. E., & Nguyen, T. H. (2022). Influence of point-of-use filters and stagnation on water quality at a preschool and under laboratory conditions. Water Research, 211, [118034]. https://doi.org/10.1016/j.watres.2021.118034
Hatcher, K. M., Smith, R. L., Li, Z., Flaws, J. A., Davies, C. R., & Mahoney, M. M. (2022). Preliminary findings reveal that phthalate exposure is associated with both subjective and objective measures of sleep in a small population of midlife women. Maturitas, 157, 62-65. https://doi.org/10.1016/j.maturitas.2021.11.004
Sass, D., Li, B., Clifton, M., Harbison, J., Xamplas, C., & Smith, R. (2022). THE IMPACT OF ADULTICIDE ON CULEX ABUNDANCE AND INFECTION RATE IN NORTH SHORE OF COOK COUNTY, ILLINOIS. Journal of the American Mosquito Control Association, 38(1), 46-58. https://doi.org/10.2987/21-7036
Deng, H., Konopka, C. J., Prabhu, S., Sarkar, S., Medina, N. G., Fayyaz, M., Arogundade, O. H., Vidana Gamage, H. E., Shahoei, S. H., Nall, D., Youn, Y., Dobrucka, I. T., Audu, C. O., Joshi, A., Melvin, W. J., Gallagher, K. A., Selvin, P. R., Nelson, E. R., Dobrucki, L. W., ... Smith, A. M. (2022). Dextran-Mimetic Quantum Dots for Multimodal Macrophage Imaging In Vivo, Ex Vivo, and In Situ. ACS Nano, 16(2), 1999-2012. https://doi.org/10.1021/acsnano.1c07010
Shen, C., Zaharias, P., & Warnow, T. (2022). MAGUS1eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. Bioinformatics, 38(4), 918-924. https://doi.org/10.1093/bioinformatics/btab788
Berenbaum, M. R. (2022). Erratum: Cell engineering with microfluidic squeezing preserves functionality of primary immune cells in vivo (Proc. Natl. Acad. Sci. U.S.A. (2018) 115 (E10907-E10914) DOI: 10.1073/pnas.1809671115). Proceedings of the National Academy of Sciences of the United States of America, 119(6), [e2200126119]. https://doi.org/10.1073/pnas.2200126119
Zhang, G., St. Clair, A. L., Dolezal, A. G., Toth, A. L., & O'Neal, M. E. (2022). Can Native Plants Mitigate Climate-related Forage Dearth for Honey Bees (Hymenoptera: Apidae)? Journal of economic entomology, 115(1), 1-9. https://doi.org/10.1093/jee/toab202
Blaxter, M., Archibald, J. M., Childers, A. K., Coddington, J. A., Crandall, K. A., Di Palma, F., Durbin, R., Edwards, S. V., Graves, J. A. M., Hackett, K. J., Hall, N., Jarvis, E. D., Johnson, R. N., Karlsson, E. K., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Lindblad-Toh, K., Lopez, J. V., ... Lewin, H. A. (2022). Why sequence all eukaryotes? Proceedings of the National Academy of Sciences of the United States of America, 119(4), [e2115636118]. https://doi.org/10.1073/pnas.2115636118
Ma, L., Smith, A. M., & Tu, C. (2022). Compact and homogeneous quantum dots and methods of making the same. (U.S. Patent No. 11226336).
Dolezal, A. G. (2022). Carryover insecticide exposure reduces bee reproduction across years. Proceedings of the National Academy of Sciences of the United States of America, 119(1), [e2120128118]. https://doi.org/10.1073/pnas.2120128118
Haynes, E., Stanford, K., Gramhofer, M., Vivirito, K., Durante, K., Wright, A., Varga, C., & Allender, M. C. (2022). EPIDEMIOLOGY OF OPHIDIOMYCOSIS IN LAKE ERIE WATERSNAKES (NERODIA SIPEDON INSULARUM). Journal of wildlife diseases, 58(1), 100-113. https://doi.org/10.7589/JWD-D-21-00111
El-Kebir, M., Morris, Q., Oesper, L., & Sahinalp, S. C. (2022). Emerging Topics in Cancer Evolution. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 27, 397-401.
Liu, X., Ibarra-Sánchez, L. A., Miller, M. J., & Lee, Y. (2022). Fabrication of zein-modified starch nanoparticle complexes via microfluidic chip and encapsulation of nisin. Current Research in Food Science, 5, 1110-1117. https://doi.org/10.1016/j.crfs.2022.07.005
Kim, H. W., Kim, N. K., Phillips, A. P. R., Parker, D. A., Liu, P., Whitaker, R. J., Rao, C. V., & Mackie, R. I. (2022). Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction. Microorganisms, 10(1), [142]. https://doi.org/10.3390/microorganisms10010142
Taylor, A. J., Cardenas-Torres, E., Miller, M. J., Zhao, S. D., & Engeseth, N. J. (2022). Microbes associated with spontaneous cacao fermentations - A systematic review and meta-analysis. Current Research in Food Science, 5, 1452-1464. https://doi.org/10.1016/j.crfs.2022.08.008
Zaharias, P., Grosshauser, M., & Warnow, T. (2022). Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling. Journal of Computational Biology, 29(1), 74-89. https://doi.org/10.1089/cmb.2021.0383
Murray, C. E., Varga, C., Ouckama, R., & Guerin, M. T. (2022). Temporal Study of Salmonella enterica Serovars Isolated from Fluff Samples from Ontario Poultry Hatcheries between 2009 and 2018. Pathogens, 11(1), [9]. https://doi.org/10.3390/pathogens11010009
Cakar, F., Golubeva, Y. A., Vanderpool, C. K., & Slauch, J. M. (2022). The Small RNA MicC Downregulates hilD Translation to Control the Salmonella Pathogenicity Island 1 Type III Secretion System in Salmonella enterica Serovar Typhimurium. Journal of bacteriology, 204(1), [e00378-21]. https://doi.org/10.1128/JB.00378-21
Berenbaum, M. R. (2022). A Hard Pill to Swallow. American Entomologist, 68(4), 14-17. https://doi.org/10.1093/ae/tmac063
Zhang, C., Taluja, S. M., Hallett, E. N., & Whitaker, R. J. (2022). A Rapid Targeted Gene Inactivation Approach in Sulfolobus islandicus. In Methods in Molecular Biology (pp. 145-162). (Methods in Molecular Biology; Vol. 2522). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-2445-6_9
Cass, R. P., Hodgson, E. W., O'Neal, M. E., Toth, A. L., & Dolezal, A. G. (2022). Attitudes about Honey Bees and Pollinator-Friendly Practices: A Survey of Iowan Beekeepers, Farmers, and Landowners. Journal of Integrated Pest Management, 13(1), [30]. https://doi.org/10.1093/jipm/pmac027
Kevrekidis, G. A., Rapti, Z., Drossinos, Y., Kevrekidis, P. G., Barmann, M. A., Chen, Q. Y., & Cuevas-Maraver, J. (2022). Backcasting COVID-19: A physics-informed estimate for early case incidence. Royal Society Open Science, 9(12), [220329]. https://doi.org/10.1098/rsos.220329
Berenbaum, M. R. (2022). Bowl Games. American Entomologist, 68(1), 12-15. https://doi.org/10.1093/ae/tmac006
Epstein, B., Burghardt, L. T., Heath, K. D., Grillo, M. A., Kostanecki, A., Hämälä, T., Young, N. D., & Tiffin, P. (Accepted/In press). Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis. Molecular ecology. https://doi.org/10.1111/mec.16602
Zhang, C., Sashittal, P., & El-Kebir, M. (2022). CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. In I. Pe’er (Ed.), Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, Proceedings (pp. 360-362). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 13278 LNBI). Springer. https://doi.org/10.1007/978-3-031-04749-7_28
Kowalski, R., Miller, M. J., Jawde, D., Xie, Z., & Gonzalez De Mejia, E. (2022). Effect of Fermentation on Phenolic Composition and Antioxidant Capacity of Blackcurrant Juice using Lactobacillus with Different ß-Glucosidase Activities. In M. H. Tunick, & E. G. de Meji´a (Eds.), ACS Symposium Series (pp. 91-113). (ACS Symposium Series; Vol. 1406). American Chemical Society. https://doi.org/10.1021/bk-2022-1406.ch007
Blair, B. W., & Lowe, J. F. (2022). Exploración descriptiva de los movimientos de animales dentro de la red de mercadeo de cerdas de desecho de los Estados Unidos. Journal of Swine Health and Production, 30(2), 72-78. https://doi.org/10.54846/jshap/1245
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
Applegate, C. C., Deng, H., Kleszynski, B. L., Cross, T. W. L., Konopka, C. J., Dobrucki, L. W., Nelson, E. R., Wallig, M. A., Smith, A. M., & Swanson, K. S. (2022). Impact of administration route on nanocarrier biodistribution in a murine colitis model. Journal of Experimental Nanoscience, 17(1), 599-616. https://doi.org/10.1080/17458080.2022.2134563
Jackson-Gordo, R., Dariotis, J. K., Fisher, B. S., & Dickman-Burnet, V. (2022). Implementing Sexual Violence Primary Prevention Programs: A Case Study of Implementer Perspectives. Journal of Youth Development, 17(4), 126-144. https://doi.org/10.5195/jyd.2022.1272
Dewerff, S. J., Zhang, C., Schneider, J., & Whitaker, R. J. (2022). Intraspecific antagonism through viral toxin encoded by chronic Sulfolobus spindle-shaped virus. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1842), [20200476]. https://doi.org/10.1098/rstb.2020.0476
Zaharias, P., Smirnov, V., & Warnow, T. (Accepted/In press). Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1-13. https://doi.org/10.1109/TCBB.2022.3191848
Xiong, Y., Huang, Q., Canady, T. D., Barya, P., Liu, S., Arogundade, O. H., Race, C. M., Wang, X., Zhou, L., Wang, X., Kohli, M., Smith, A. M., & Cunningham, B. T. (2022). Photonic Crystal Enhanced Emission and Blinking Suppression for Single Quantum Dot Digital Resolution Biosensing of Cancer-associated miRNA Biomarkers. In CLEO: Science and Innovations, S and I 2022 [JTh6A.2] (Optics InfoBase Conference Papers). Optica Publishing Group (formerly OSA).
Xiong, Y., Huang, Q., Canady, T. D., Barya, P., Liu, S., Arogundade, O. H., Race, C. M., Wang, X., Zhou, L., Wang, X., Kohli, M., Smith, A. M., & Cunningham, B. T. (2022). Photonic Crystal Enhanced Emission and Blinking Suppression for Single Quantum Dot Digital Resolution Biosensing of Cancer-associated miRNA Biomarkers. In 2022 Conference on Lasers and Electro-Optics, CLEO 2022 - Proceedings [JTh6A.2] (2022 Conference on Lasers and Electro-Optics, CLEO 2022 - Proceedings). Institute of Electrical and Electronics Engineers Inc..
Xiong, Y., Huang, Q., Canady, T. D., Barya, P., Liu, S., Arogundade, O. H., Race, C. M., Che, C., Wang, X., Zhou, L., Igarashi, A., Wang, X., Kohli, M., Smith, A. M., & Cunningham, B. T. (2022). Photonic Crystal Enhanced Quantum Dot Biosensor for Cancer-associated miRNA Detection. In 2022 IEEE Sensors, SENSORS 2022 - Conference Proceedings (Proceedings of IEEE Sensors; Vol. 2022-October). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/SENSORS52175.2022.9967032
Berenbaum, M. R. (2022). Sew-Sew Jokes. American Entomologist, 68(2), 12-15. https://doi.org/10.1093/ae/tmac025
Montag, W., Liao, L. H., & Berenbaum, M. R. (Accepted/In press). Sexually dimorphic responses to monofloral honeys in the small hive beetle, Aethina tumida Murray (Coleoptera: Nitidulidae). Journal of Apicultural Research. https://doi.org/10.1080/00218839.2022.2147712
Dariotis, J. K., & Chen, F. R. (2022). Stress Coping Strategies as Mediators: Toward a Better Understanding of Sexual, Substance, and Delinquent Behavior-Related Risk-Taking among Transition-Aged Youth. Deviant Behavior, 43(4), 397-414. https://doi.org/10.1080/01639625.2020.1796210
Han, Z., Vaidya, R. M., Arogundade, O. H., Ma, L., Zahid, M. U., Sarkar, S., Kuo, C. W., Selvin, P. R., & Smith, A. M. (Accepted/In press). Structural Design of Multidentate Copolymers as Compact Quantum Dot Coatings for Live-Cell Single-Particle Imaging. Chemistry of Materials. https://doi.org/10.1021/acs.chemmater.2c00498
Berenbaum, M. R. (2022). Terms of Art and Terms of Arthropods. American Entomologist, 68(3), 12-15. https://doi.org/10.1093/ae/tmac051
Zhang, C., & Whitaker, R. J. (2022). Transposon Insertion Mutagenesis in Hyperthermophilic Crenarchaeon Sulfolobus islandicus. In Methods in Molecular Biology (pp. 163-176). (Methods in Molecular Biology; Vol. 2522). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-2445-6_10
1.3. 2021
