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Illinois IGB

Research Areas

Infection Genomics for One Health: Publications

Christensen, S., Kim, J., Chia, N., Koyejo, O., & El-Kebir, M. (2020). Detecting evolutionary patterns of cancers using consensus trees. Bioinformatics (Oxford, England)36(Supplement_2), i684-i691. https://doi.org/10.1093/bioinformatics/btaa801

Gardner, A. M., Pawlikowski, N. C., Hamer, S. A., Hickling, G. J., Miller, J. R., Schotthoefer, A. M., Tsao, J. I., & Allan, B. F. (2020). Landscape features predict the current and forecast the future geographic spread of Lyme disease. Proceedings of the Royal Society B: Biological Sciences287(1941), 20202278. https://doi.org/10.1098/rspb.2020.2278

Gardner, A. M., Pawlikowski, N. C., Hamer, S. A., Hickling, G. J., Miller, J. R., Schotthoefer, A. M., Tsao, J. I., & Allan, B. F. (2020). Landscape features predict the current and forecast the future geographic spread of Lyme disease: Landscape predicts Lyme disease spread. Proceedings of the Royal Society B: Biological Sciences287(1941), [20202278]. https://doi.org/10.1098/rspb.2020.2278rspb20202278

Sharma, A. K., Petrzelkova, K., Pafco, B., Robinson, C. A. J., Fuh, T., Wilson, B. A., Stumpf, R. M., Torralba, M. G., Blekhman, R., White, B., Nelson, K. E., Leigh, S. R., & Gomez, A. (2020). Traditional human populations and nonhuman primates show parallel gut microbiome adaptations to analogous ecological conditions. mSystems5(6), [e00815-20]. https://doi.org/10.1128/mSystems.00815-20

Hoffmann, M. A. G., Kieffer, C., & Bjorkman, P. J. (2020). In vitro characterization of engineered red blood cells as potent viral traps against HIV-1 and SARS-CoV-2. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.12.20.423607

Gutema, F. D., Agga, G. E., Makita, K., Smith, R. L., Mourits, M., Tufa, T. B., Leta, S., Beyene, T. J., Asefa, Z., Urge, B., & Ameni, G. (2020). Evaluation of the Control Options of Bovine Tuberculosis in Ethiopia Using a Multi-Criteria Decision Analysis. Frontiers in Veterinary Science7, [586056]. https://doi.org/10.3389/fvets.2020.586056

Legried, B., Molloy, E. K., Warnow, T., & Roch, S. (2020). Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. Journal of computational biology : a journal of computational molecular cell biologyhttps://doi.org/10.1089/cmb.2020.0424

Goswami, N., He, Y. R., Deng, Y-H., Oh, C., Sobh, N., Valera, E., Bashir, R., Ismail, N., Kong, H. J., Nguyen, T. H., Best-Popescu, C., & Popescu, G. (2020). Rapid SARS-CoV-2 Detection and Classification Using Phase Imaging with Computational Specificity. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.12.14.422601

Megahed, A., Aldridge, B., & Lowe, J. (2020). Antimicrobial Efficacy of Aqueous Ozone and Ozone–Lactic Acid Blend on Salmonella-Contaminated Chicken Drumsticks Using Multiple Sequential Soaking and Spraying Approaches. Frontiers in Microbiology11, [593911]. https://doi.org/10.3389/fmicb.2020.593911

Resendiz-Moctezuma, C., Rezac, S. D., Miller, M. J., & Stasiewicz, M. J. (2020). Enabling cost-effective screening for antimicrobials against Listeria monocytogenes in ham. Journal of Food Protectionhttps://doi.org/10.4315/JFP-20-435

Palma-Salgado, S., Ku, K. M., Dong, M., Nguyen, T. H., Juvik, J. A., & Feng, H. (2020). Adhesion and removal of E. coli K12 as affected by leafy green produce epicuticular wax composition, surface roughness, produce and bacterial surface hydrophobicity, and sanitizers. International Journal of Food Microbiology334, [108834]. https://doi.org/10.1016/j.ijfoodmicro.2020.108834

Kim, J., Mei, R., Wilson, F. P., Yuan, H., Bocher, B. T. W., & Liu, W. T. (2020). Ecogenomics-Based Mass Balance Model Reveals the Effects of Fermentation Conditions on Microbial Activity. Frontiers in Microbiology11, [595036]. https://doi.org/10.3389/fmicb.2020.595036

Buonasera, T., Eerkens, J., de Flamingh, A., Engbring, L., Yip, J., Li, H., Haas, R., DiGiuseppe, D., Grant, D., Salemi, M., Nijmeh, C., Arellano, M., Leventhal, A., Phinney, B., Byrd, B. F., Malhi, R. S., & Parker, G. (2020). A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation. Scientific reports10(1), [11897]. https://doi.org/10.1038/s41598-020-68550-w

Juma, E. O., Allan, B. F., Kim, C. H., Stone, C., Dunlap, C., & Muturi, E. J. (2020). Effect of life stage and pesticide exposure on the gut microbiota of Aedes albopictus and Culex pipiens L. Scientific reports10(1), [9489]. https://doi.org/10.1038/s41598-020-66452-5

De Flamingh, A., Coutu, A., Sealy, J., Chirikure, S., Bastos, A. D. S., Libanda-Mubusisi, N. M., Malhi, R. S., & Roca, A. L. (Accepted/In press). Sourcing Elephant Ivory from a Sixteenth-Century Portuguese Shipwreck. Current Biologyhttps://doi.org/10.1016/j.cub.2020.10.086

Kim, H., Seiler, P., Jones, J. C., Ridout, G., Camp, K. P., Fabrizio, T. P., Jeevan, T., Miller, L. A., Throm, R. E., Ferrara, F., Fredrickson, R. L., Lowe, J. F., Wang, L., Odemuyiwa, S. O., Wan, X-F., & Webby, R. J. (2020). Antibody Responses to SARS-CoV-2 Antigens in Humans and Animals. Vaccines8(4), 1-15. [684]. https://doi.org/10.3390/vaccines8040684

Martínez-Ramos, A. R., Ibarra-Sánchez, L. A., Amaya-Llano, S. L., & Miller, M. J. (2020). Evaluation of combinations of nisin, lauric arginate, and ε-polylysine to control Listeria monocytogenes in queso fresco. Journal of Dairy Science103(12), 11152-11162. https://doi.org/10.3168/jds.2020-19001

Hedman, H. D., Varga, C., Duquette, J., Novakofski, J., & Mateus-Pinilla, N. E. (2020). Food Safety Considerations Related to the Consumption and Handling of Game Meat in North America. Veterinary Sciences7(4), 1-13. [188]. https://doi.org/10.3390/vetsci7040188

Liao, L. H., Pearlstein, D. J., Wu, W. Y., Kelley, A. G., Montag, W. M., Hsieh, E. M., & Berenbaum, M. R. (2020). Increase in longevity and amelioration of pesticide toxicity by natural levels of dietary phytochemicals in the honey bee, Apis mellifera. PloS one15(12 December), [e0243364]. https://doi.org/10.1371/journal.pone.0243364

Bogler, A., Packman, A., Furman, A., Gross, A., Kushmaro, A., Ronen, A., Dagot, C., Hill, C., Vaizel-Ohayon, D., Morgenroth, E., Bertuzzo, E., Wells, G., Kiperwas, H. R., Horn, H., Negev, I., Zucker, I., Bar-Or, I., Moran-Gilad, J., Balcazar, J. L., ... Bar-Zeev, E. (2020). Rethinking wastewater risks and monitoring in light of the COVID-19 pandemic. Nature Sustainability3(12), 981-990. https://doi.org/10.1038/s41893-020-00605-2

Smirnov, V., & Warnow, T. (2020). MAGUS: Multiple Sequence Alignment using Graph Clustering. Bioinformatics (Oxford, England)https://doi.org/10.1093/bioinformatics/btaa992

Rezac, S. D., Resendiz-Moctezuma, C., Boler, D. D., Stasiewicz, M. J., & Miller, M. J. (2020). Non-Destructive Luminescence-Based Screening Tool for Listeria monocytogenes Growth on Ham. Foods9(11), [1700]. https://doi.org/10.3390/foods9111700

Hedman, H. D., Varga, C., Brown, W. M., Shelton, P., Roca, A. L., Novakofski, J. E., & Mateus‐Pinilla, N. E. (2020). Spatial analysis of chronic wasting disease in free‐ranging white‐tailed deer ( Odocoileus virginianus ) in Illinois, 2008–2019. Transboundary and Emerging Diseaseshttps://doi.org/10.1111/tbed.13901

Stewart Merrill, T. E., Hall, S. R., & Cáceres, C. E. (2020). Parasite exposure and host susceptibility jointly drive the emergence of epidemics. Ecology, e03245. https://doi.org/10.1002/ecy.3245

Park, J., Jayaraman, A., Schrader, A. W., Hwang, G. W., & Han, H-S. (2020). Controllable modulation of precursor reactivity using chemical additives for systematic synthesis of high-quality quantum dots. Nature communications11(1), 5748. https://doi.org/10.1038/s41467-020-19573-4

Lin, C. Y., Carroll, M. Q., Miller, M. J., Rabot, R., & Swanson, K. S. (2020). Supplementation of Yeast Cell Wall Fraction Tends to Improve Intestinal Health in Adult Dogs Undergoing an Abrupt Diet Transition. Frontiers in Veterinary Science7, [597939]. https://doi.org/10.3389/fvets.2020.597939

Urtecho, G., Campbell, D. E., Hershey, D. M., Hussain, F. A., Whitaker, R. J., & O'Toole, G. A. (2020). Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18. mSphere5(6). https://doi.org/10.1128/mSphere.00898-20

Calla, B., Demkovich, M., Siegel, J. P., Viana, J. P. G., Walden, K. K. O., Robertson, H. M., & Berenbaum, M. R. (2020). Selective sweeps in a nutshell: the genomic footprint of rapid insecticide resistance evolution in the almond agroecosystem. Genome biology and evolutionhttps://doi.org/10.1093/gbe/evaa234

Uelmen, J. A., Irwin, P., Bartlett, D., Brown, W., Karki, S., Ruiz, M. OH., Fraterrigo, J., Li, B., & Smith, R. L. (2020). Effects of Scale on Modeling West Nile Virus Disease Risk. American Journal of Tropical Medicine and Hygienehttps://doi.org/10.4269/ajtmh.20-0416

Peng, H., Zhang, Y., Wang, R., Liu, J., & Liu, W. T. (2020). Assessing the contribution of biofilm to bacterial growth during stagnation in shower hoses. Water Science and Technology: Water Supply20(7), 2564-2576. https://doi.org/10.2166/ws.2020.161

Hatcher, K. M., Smith, R. L., Chiang, C., Li, Z., Flaws, J. A., & Mahoney, M. M. (2020). Association of phthalate exposure and endogenous hormones with self-reported sleep disruptions: results from the Midlife Women's Health Study. Menopause27(11), 1251-1264. https://doi.org/10.1097/GME.0000000000001614

Oh, C., Sun, P. P., Araud, E., & Nguyen, T. H. (2020). Mechanism and efficacy of virus inactivation by a microplasma UV lamp generating monochromatic UV irradiation at 222 nm. Water Research186, [116386]. https://doi.org/10.1016/j.watres.2020.116386

Shaw, C. L., Hall, S. R., Overholt, E. P., Cáceres, C. E., Williamson, C. E., & Duffy, M. A. (2020). Shedding light on environmentally transmitted parasites: lighter conditions within lakes restrict epidemic size. Ecology101(11), [e03168]. https://doi.org/10.1002/ecy.3168

Crist, S., Mori, J., & Smith, R. L. (2020). Flooding on Beef and Swine Farms: A Scoping Review of Effects in the Midwestern United States. Preventive Veterinary Medicine184, [105158]. https://doi.org/10.1016/j.prevetmed.2020.105158

Huang, C., Sun, P. P., Won, J., Wang, Y., Boppart, S. A., & Nguyen, T. H. (2020). Effect of Nonphosphorus Corrosion Inhibitors on Biofilm Pore Structure and Mechanical Properties. Environmental science & technologyhttps://doi.org/10.1021/acs.est.0c04645

Mei, R., Nobu, M. K., Narihiro, T., & Liu, W. T. (2020). Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters. Frontiers in Microbiology11, [593006]. https://doi.org/10.3389/fmicb.2020.593006

Juma, E. O., Kim, C-H., Dunlap, C., Allan, B. F., & Stone, C. M. (2020). Culex pipiens and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues. Parasites and Vectors13(1), 532. https://doi.org/10.1186/s13071-020-04408-4

Pilosof, S., Alcalá-Corona, S. A., Wang, T., Kim, T., Maslov, S., Whitaker, R., & Pascual, M. (2020). The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification. Nature Ecology and Evolutionhttps://doi.org/10.1038/s41559-020-01312-z

Martin, B. E., Harris, J. D., Sun, J., Koelle, K., & Brooke, C. B. (2020). Cellular co-infection can modulate the efficiency of influenza A virus production and shape the interferon response. PLoS pathogens16(10), [e1008974]. https://doi.org/10.1371/journal.ppat.1008974

Nicole, A. L. V., Adamovicz, L., Willeford, B., Allan, B. F., & Allender, M. C. (2020). Lack of molecular detection of frog virus 3-like ranavirus (FV3) in mosquitoes during natural outbreak and nonoutbreak conditions. Facets5(1), 812-820. https://doi.org/10.1139/FACETS-2020-0024

Manivannan, B., Massalha, N., Halahlih, F., Eltzov, E., Nguyen, T. H., Sabbah, I., & Borisover, M. (2020). Water toxicity evaluations: Comparing genetically modified bioluminescent bacteria and CHO cells as biomonitoring tools. Ecotoxicology and Environmental Safety203, [110984]. https://doi.org/10.1016/j.ecoenv.2020.110984

Hsieh, E. M., Berenbaum, M. R., & Dolezal, A. G. (2020). Ameliorative Effects of Phytochemical Ingestion on Viral Infection in Honey Bees. Insects11(10), 1-18. [698]. https://doi.org/10.3390/insects11100698

Olmez, S. Y., Mori, J., Miehling, E., Basar, T., Smith, R. L., West, M., & Mehta, P. G. (2020). A Data-Informed Approach for Analysis, Validation, and Identification of COVID-19 Models. (medRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.10.03.20206250

Weber, L. L., Aguse, N., Chia, N., & El-Kebir, M. (2020). PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. PLoS computational biology16(10), [e1008240]. https://doi.org/10.1371/journal.pcbi.1008240

Devarakonda, S., Korobskiy, D., Warnow, T., & Chacko, G. (2020). Viewing computer science through citation analysis: Salton and Bergmark Redux. Scientometrics125(1), 271-287. https://doi.org/10.1007/s11192-020-03624-0

Fuzawa, M., Bai, H., Shisler, J. L., & Nguyen, T. H. (2020). The basis of peracetic acid inactivation mechanisms for rotavirus and tulane virus under conditions relevant for vegetable sanitation. Applied and environmental microbiology86(19), [e01095-20]. https://doi.org/10.1128/AEM.01095-20

Brown, S. P., Grillo, M. A., Podowski, J. C., & Heath, K. D. (2020). Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula. Microbiome8(1), [139]. https://doi.org/10.1186/s40168-020-00915-9

Berenbaum, M. R. (2020). Crabby Days. American Entomologist66(3), 10-13. https://doi.org/10.1093/ae/tmaa048

Ruzic, D. N., Oh, C., Puthussery, J. V., Patel, D., Jeckell, Z., Verma, V., & Nguyen, T. H. (2020). Converting microwave ovens into plasma-generating decontamination units for N-95 respirators. Unknown Journalhttps://doi.org/10.1101/2020.09.15.297630

Metras, B. N., Holle, M. J., Parker, V. J., Miller, M. J., & Swanson, K. S. (2020). Assessment of Commercial Companion Animal Kefir Products for Label Accuracy of Microbial Composition and Quantity. Journal of animal science98(9), [skaa301]. https://doi.org/10.1093/jas/skaa301

Ruzic, D. N., Oh, C., Puthussery, J. V., Verma, V., & Nguyen, T. H. (2020). Converting microwave ovens into plasma-generating decontamination units for N-95 respirators. Unknown Journalhttps://doi.org/10.1101/2020.07.28.20163915

Oh, C., Araud, E., Puthussery, J. V., Bai, H., Clark, G. G., Wang, L., Verma, V., & Nguyen, T. H. (2020). Dry Heat as a Decontamination Method for N95 Respirator Reuse. Environmental Science and Technology Letters7(9), 677-682. https://doi.org/10.1021/acs.estlett.0c00534

Stone, C. M., Zuo, Z., Li, B., Ruiz, M., Swanson, J., Hunt, J., Kim, C. H., & Smith, R. L. (2020). Spatial, Temporal, and Genetic Invasion Dynamics of Aedes albopictus (Diptera: Culicidae) in Illinois. Journal of medical entomology57(5), 1488-1500. [tjaa047]. https://doi.org/10.1093/jme/tjaa047

Yang, Q., & Warnow, T. (2020). An improved mode of running PASTA. Unknown Journalhttps://doi.org/10.1101/2020.08.30.274217

Parker, A. T., McGill, K., & Allan, B. F. (2020). Container type affects mosquito (diptera: culicidae) oviposition choice. Journal of medical entomology57(5), 1459-1467. https://doi.org/10.1093/jme/tjaa045

Ferrer, A., Heath, K. D., Canam, T., Flores, H. D., & Dalling, J. W. (2020). Contribution of fungal and invertebrate communities to wood decay in tropical terrestrial and aquatic habitats. Ecology101(9), [e03097]. https://doi.org/10.1002/ecy.3097

Drayman, N., Jones, K. A., Azizi, S-A., Froggatt, H. M., Tan, K., Ivanova Maltseva, N., Chen, S., Nicolaescu, V., Dvorkin, S., Furlong, K., Kathayat, R. S., Firpo, M. R., Mastrodomenico, V., Bruce, E. A., Schmidt, M. M., Jedrzejczak, R., Munoz-Alia, M. A., Schuster, B., Nair, V., ... Tay, S. (2020). Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.08.31.274639

Lampe, R., Foss, K. D., Hague, D. W., Oliveira, C. R., & Smith, R. (2020). Dynamic MRI is reliable for evaluation of the lumbosacral spine in healthy dogs. Veterinary Radiology and Ultrasound61(5), 555-565. https://doi.org/10.1111/vru.12891

Palmer, A. D., & Slauch, J. M. (2020). Envelope stress and regulation of the salmonella pathogenicity Island 1 type III secretion system. Journal of bacteriology202(17), [e00272-20]. https://doi.org/10.1128/JB.00272-20

Holmes, C. J., Rapti, Z., Pantel, J. H., Schulz, K. L., & Cáceres, C. E. (2020). Patch centrality affects metapopulation dynamics in small freshwater ponds. Theoretical Ecology13(3), 435-448. https://doi.org/10.1007/s12080-020-00463-w

Yao, L., Witt, K., Li, H., Rice, J., Salinas, N. R., Martin, R. D., Huerta-Sánchez, E., & Malhi, R. S. (2020). Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens. American journal of physical anthropology173(1), 21-33. https://doi.org/10.1002/ajpa.24099

Azam, M. S., & Vanderpool, C. K. (2020). Translation inhibition from a distance: The small RNA SgrS silences a ribosomal protein S1-dependent enhancer. Molecular Microbiology114(3), 391-408. https://doi.org/10.1111/mmi.14514

Brinkworth, J. F., & Alvarado, A. S. (2020). Cell-Autonomous Immunity and The Pathogen-Mediated Evolution of Humans: Or How Our Prokaryotic and Single-Celled Origins Affect The Human Evolutionary Story. Quarterly Review of Biology95(3), 215-246. https://doi.org/10.1086/710389

Eve, A. A., Liu, X., Wang, Y., Miller, M. J., Jeffery, E. H., & Madak-Erdogan, Z. (2020). Biomarkers of Broccoli Consumption: Implications for Glutathione Metabolism and Liver Health. Nutrients12(9), [2514]. https://doi.org/10.3390/nu12092514

Cuevas-Maraver, J., Kevrekidis, P., Chen, Q-Y., Kevrekidis, G., Villalobos-Daniel, V., Rapti, Z., & Drossinos, Y. (2020). Lockdown Measures and their Impact on Single- and Two-age-structured Epidemic Model for the COVID-19 Outbreak in Mexico. (medRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.08.11.20172833

Yu, X., Le, T., Christensen, S., Molloy, E. K., & Warnow, T. (2020). Advancing divide-and-conquer phylogeny estimation using robinson-foulds supertrees. In C. Kingsford, & N. Pisanti (Eds.), 20th International Workshop on Algorithms in Bioinformatics, WABI 2020 [15] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 172). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.WABI.2020.15

Weber, L. L., & El-Kebir, M. (2020). Phyolin: Identifying a linear perfect phylogeny in single-cell DNA sequencing data of tumors. In C. Kingsford, & N. Pisanti (Eds.), 20th International Workshop on Algorithms in Bioinformatics, WABI 2020 [5] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 172). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.WABI.2020.5

TRAPP, ROBERT. J., KOSIBA, KAREN. A., MARQUIS, JAMES. N., KUMJIAN, MATTHEW. R., NESBITT, STEPHEN. W., WURMAN, JOSHUA., SALIO, PAOLA., GROVER, MAXWELL. A., ROBINSON, PAUL., & HENCE, DEANNA. A. (2020). Multiple-platform and multiple-doppler radar observations of a supercell thunderstorm in south america during relampago. Monthly Weather Review148(8), 3225-3241. https://doi.org/10.1175/MWR-D-20-0125.1

Chandrasekharan, S., Zaka, M., Gallo, S., Warnow, T., & Chacko, G. (2020). Finding scientific communities in citation graphs: Convergent clustering. Unknown Journal.

Nobu, M. K., Narihiro, T., Mei, R., Kamagata, Y., Lee, P. K. H., Lee, P. H., McInerney, M. J., & Liu, W. T. (2020). Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses. Microbiome8(1), [111]. https://doi.org/10.1186/s40168-020-00885-y

Berenbaum, M. R. (2020). PNAS and prejudice. Proceedings of the National Academy of Sciences of the United States of America117(29), 16710-16712. https://doi.org/10.1073/pnas.2012747117

Gaba, R. C., Elkhadragy, L., Edward Boas, F., Chaki, S., Chen, H. H., El-Kebir, M., Garcia, K. D., Giurini, E. F., Guzman, G., LoBianco, F. V., Neto, M. F., Newson, J. L., Qazi, A., Regan, M., Rund, L. A., Schwind, R. M., Stewart, M. C., Thomas, F. M., Whiteley, H. E., ... Schachtschneider, K. M. (2020). Development and comprehensive characterization of porcine hepatocellular carcinoma for translational liver cancer investigation. Oncotarget11(28), 2686-2701. https://doi.org/10.18632/oncotarget.27647

Zhang, X., Lardizabal, A., Silverman, A. I., Vione, D., Kohn, T., Nguyen, T. H., & Guest, J. S. (2020). Global Sensitivity Analysis of Environmental, Water Quality, Photoreactivity, and Engineering Design Parameters in Sunlight Inactivation of Viruses. Environmental Science and Technology54(13), 8401-8410. https://doi.org/10.1021/acs.est.0c01214

Wu, J., & El-Kebir, M. (2020). ClonArch: visualizing the spatial clonal architecture of tumors. Bioinformatics (Oxford, England)36(1), i161-i168. https://doi.org/10.1093/bioinformatics/btaa471

Molloy, E. K., & Warnow, T. (2020). FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. Bioinformatics (Oxford, England)36(1), i57-i65. https://doi.org/10.1093/bioinformatics/btaa444

Muturi, E. J., Dunlap, C., & Cáceres, C. E. (2020). Microbial communities of container aquatic habitats shift in response to Culex restuans larvae. FEMS microbiology ecology96(7). https://doi.org/10.1093/femsec/fiaa112

Sashittal, P., & El-Kebir, M. (2020). Sampling and summarizing transmission trees with multi-strain infections. Bioinformatics (Oxford, England)36(1), i362-i370. https://doi.org/10.1093/bioinformatics/btaa438

Lam, T. Y. C., Mei, R., Wu, Z., Lee, P. K. H., Liu, W. T., & Lee, P. H. (2020). Superior resolution characterisation of microbial diversity in anaerobic digesters using full-length 16S rRNA gene amplicon sequencing. Water Research178, [115815]. https://doi.org/10.1016/j.watres.2020.115815

Sun, J., Vera, J. C., Drnevich, J., Lin, Y. T., Ke, R., & Brooke, C. B. (2020). Single cell heterogeneity in influenza A virus gene expression shapes the innate antiviral response to infection. PLoS pathogens16(7), [e1008671]. https://doi.org/10.1371/journal.ppat.1008671

Varga, C., John, P., Cooke, M., & Majowicz, S. E. (2020). Spatial and space-time clustering and demographic characteristics of human nontyphoidal Salmonella infections with major serotypes in Toronto, Canada. PloS one15(7), [e0235291]. https://doi.org/10.1371/journal.pone.0235291

Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Brooke, C. B., Burke, M. D., Fan, T. M., & Hergenrother, P. J. (2020). Saliva-based molecular testing for SARS-CoV-2 that bypasses RNA extraction. Unknown Journalhttps://doi.org/10.1101/2020.06.18.159434

Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Brooke, C. B., Burke, M., Fan, T. M., & Hergenrother, P. (2020). Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.06.18.159434

Mader, E. M., Ganser, C., Geiger, A., Harrington, L. C., Foley, J., Smith, R. L., Mateus-Pinilla, N., Teel, P. D., Eisen, R. J., & Gaff, H. (2020). A Survey of Tick Surveillance and Control Practices in the United States. Journal of medical entomologyhttps://doi.org/10.1093/jme/tjaa094

Zhang, L., Zhang, L., Zhang, L., Chichlowski, M., Chichlowski, M., Gross, G., Gross, G., Holle, M. J., Lbarra-Sánchez, L. A., Wang, S., & Miller, M. J. (2020). Milk Fat Globule Membrane Protects Lactobacillus rhamnosus GG from Bile Stress by Regulating Exopolysaccharide Production and Biofilm Formation. Journal of Agricultural and Food Chemistry68(24), 6646-6655. https://doi.org/10.1021/acs.jafc.0c02267

St Clair, A. L., St Clair, A. L., Zhang, G., Dolezal, A. G., O'Neal, M. E., Toth, A. L., & Toth, A. L. (2020). Diversified Farming in a Monoculture Landscape: Effects on Honey Bee Health and Wild Bee Communities. Environmental entomology49(3), 753-764. https://doi.org/10.1093/ee/nvaa031

Oh, C., Araud, E., Puthussery, J. V., Bai, H., Clark, G. G., Verma, V., & Nguyen, T. H. (2020). Dry heat as a decontamination method for N95 respirator reuse. Unknown Journalhttps://doi.org/10.26434/chemrxiv.12290621.v2

St. Clair, A. L., Dolezal, A. G., O’Neal, M. E., & Toth, A. L. (2020). Pan Traps for Tracking Honey Bee Activity-Density: A Case Study in Soybeans. Insects11(6), [366]. https://doi.org/10.3390/insects11060366

Zhang, G., St. Clair, A. L., Dolezal, A., Toth, A. L., & O'Neal, M. (2020). Honey Bee (Hymenoptera: Apidea) Pollen Forage in a Highly Cultivated Agroecosystem: Limited Diet Diversity and Its Relationship to Virus Resistance. Journal of economic entomology113(3), 1062-1072. https://doi.org/10.1093/jee/toaa055

Hudson, M., Garrison, N. A., Sterling, R., Caron, N. R., Fox, K., Yracheta, J., Anderson, J., Wilcox, P., Arbour, L., Brown, A., Taualii, M., Kukutai, T., Haring, R., Te Aika, B., Baynam, G. S., Dearden, P. K., Chagné, D., Malhi, R. S., Garba, I., ... Carroll, S. R. (2020). Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data. Nature Reviews Genetics21(6), 377-384. https://doi.org/10.1038/s41576-020-0228-x

Wu, C. F., Piedra, L. M., Matthew, L. E., Rhodes, E. C., & Nguyen, T. H. (2020). Water treatment in rural guatemala: Factors associated with the use of biosand water filters. Journal of Water Sanitation and Hygiene for Development10(2), 286-297. https://doi.org/10.2166/washdev.2020.147

Landolfi, J. A., Adkesson, M. J., Ahmed, N., Smith, C. R., Smith, R. L., Snyder, T., & Terio, K. A. (2020). A QPCR ASSAY and TESTING GUIDELINES for the MOLECULAR DIAGNOSIS of SYSTEMIC ISOSPOROSIS (FORMERLY ATOXPLASMOSIS) in PASSERINE BIRDS. Journal of Zoo and Wildlife Medicine51(2), 391-397. https://doi.org/10.1638/2019-0176

Barelli, C., Barelli, C., Barelli, C., Albanese, D., Stumpf, R. M., Stumpf, R. M., Asangba, A., Donati, C., Rovero, F., Rovero, F., & Hauffe, H. C. (2020). The gut microbiota communities of wild arboreal and ground-feeding tropical primates are affected differently by habitat disturbance. mSystems5(3), [e00061-20]. https://doi.org/10.1128/mSystems.00061-20

Juma, E. O., Kim, C. H., Dunlap, C., Allan, B. F., & Stone, C. M. (2020). Culex pipiens L. And Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues. Unknown Journalhttps://doi.org/10.1101/2020.05.23.112128

Harwood, G. P., & Dolezal, A. G. (2020). Pesticide–Virus Interactions in Honey Bees: Challenges and Opportunities for Understanding Drivers of Bee Declines. Viruses12(5). https://doi.org/10.3390/v12050566

Yu, X., Le, T., Christensen, S. A., Molloy, E. K., & Warnow, T. (2020). Advancing divide-and-conquer phylogeny estimation using Robinson-Foulds supertrees. Unknown Journalhttps://doi.org/10.1101/2020.05.16.099895

Sashittal, P., Luo, Y., Peng, J., & El-Kebir, M. (2020). Characterization of SARS-CoV-2 viral diversity within and across hosts. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.05.07.083410

Sashittal, P., Luo, Y., Peng, J., & El-Kebir, M. (2020). Characterization of SARS-CoV-2 viral diversity within and across hosts. Unknown Journalhttps://doi.org/10.1101/2020.05.07.083410

Geffre, A. C., Gernat, T., Harwood, G. P., Jones, B. M., Morselli Gysi, D., Hamilton, A. R., Bonning, B. C., Toth, A. L., Robinson, G. E., & Dolezal, A. G. (2020). Honey bee virus causes context-dependent changes in host social behavior. PNAS117(19), 10406-10413. https://doi.org/10.1073/pnas.2002268117

Devarakonda, S., Bradley, J., Korobskiy, D., Warnow, T., & Chacko, G. (2020). Frequently co-cited publications: Features and kinetics. Unknown Journal.

Kevrekidis, P. G., Cuevas-Maraver, J., Drossinos, Y., Rapti, Z., & Kevrekidis, G. A. (2020). Spatial Modeling of COVID-19: Greece and Andalusia as Case Examples. Unknown Journal.

Liu, G., Zhang, Y., Liu, X., Hammes, F., Liu, W. T., Medema, G., Wessels, P., & Van Der Meer, W. (2020). 360-Degree Distribution of Biofilm Quantity and Community in an Operational Unchlorinated Drinking Water Distribution Pipe. Environmental Science and Technology54(9), 5619-5628. https://doi.org/10.1021/acs.est.9b06603

Berenbaum, M. R. (2020). PNAS and the pandemic. Proceedings of the National Academy of Sciences of the United States of America117(18), 9650-9651. https://doi.org/10.1073/pnas.2006488117

Loog, L., Thalmann, O., Sinding, M. H. S., Schuenemann, V. J., Perri, A., Germonpré, M., Bocherens, H., Witt, K. E., Samaniego Castruita, J. A., Velasco, M. S., Lundstrøm, I. K. C., Wales, N., Sonet, G., Frantz, L., Schroeder, H., Budd, J., Jimenez, E. L., Fedorov, S., Gasparyan, B., ... Manica, A. (2020). Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia. Molecular ecology29(9), 1596-1610. https://doi.org/10.1111/mec.15329

Jones, J. M., Heath, K. D., Ferrer, A., & Dalling, J. W. (2020). Habitat-specific effects of bark on wood decomposition: Influences of fragmentation, nitrogen concentration and microbial community composition. Functional Ecology34(5), 1123-1133. https://doi.org/10.1111/1365-2435.13547

Crawford, J. W., Schrader, M., Hall, S. R., & Cáceres, C. E. (2020). Intraspecific variation in resource use is not explained by population persistence or seasonality. Oecologia193(1), 135-142. https://doi.org/10.1007/s00442-020-04651-7

Uprety, S., Dangol, B., Nakarmi, P., Dhakal, I., Sherchan, S. P., Shisler, J. L., Jutla, A., Amarasiri, M., Sano, D., & Nguyen, T. H. (2020). Assessment of microbial risks by characterization of Escherichia coli presence to analyze the public health risks from poor water quality in Nepal. International Journal of Hygiene and Environmental Health226, [113484]. https://doi.org/10.1016/j.ijheh.2020.113484

Alnaji, F. G., & Brooke, C. B. (2020). Influenza virus di particles: Defective interfering or delightfully interesting? PLoS pathogens16(5), [e1008436]. https://doi.org/10.1371/journal.ppat.1008436

Karki, S., Brown, W. M., Uelmen, J., O’Hara Ruiz, M., & Smith, R. L. (2020). The drivers of West Nile virus human illness in the Chicago, Illinois, USA area: Fine scale dynamic effects of weather, mosquito infection, social, and biological conditions. PloS one15(5), [e0227160]. https://doi.org/10.1371/journal.pone.0227160

Berenbaum, M. R. (2020). On Mr. Hyslop’s prediction, content archives, and preprint servers. Proceedings of the National Academy of Sciences of the United States of America117(17), 9131-9134. https://doi.org/10.1073/pnas.2005725117

Smirnov, V., & Warnow, T. (2020). Unblended disjoint tree merging using GTM improves species tree estimation. BMC genomics21, [235]. https://doi.org/10.1186/s12864-020-6605-1

Urtecho, G., Campbell, D. E., Hershey, D. M., Whitaker, R. J., & O’Toole, G. A. (2020). Discovering the Molecular Determinants of Phaeobacter inhibens susceptibility to Phaeobacter phage MD18. Unknown Journalhttps://doi.org/10.1101/2020.04.13.038638

Suarez, G. P., Udiani, O., Allan, B. F., Price, C., Ryan, S. J., Lofgren, E., Coman, A., Stone, C. M., Gallos, L. K., & Fefferman, N. H. (2020). A generic arboviral model framework for exploring trade-offs between vector control and environmental concerns. Journal of Theoretical Biology490, [110161]. https://doi.org/10.1016/j.jtbi.2020.110161

Weitzel, C. S., Li, L., Zhang, C., Eilts, K. K., Bretz, N. M., Gatten, A. L., Whitaker, R. J., & Martinis, S. A. (2020). Duplication of leucyl-tRNA synthetase in an archaeal extremophile may play a role in adaptation to variable environmental conditions. Journal of Biological Chemistry295(14), 4563-4576. https://doi.org/10.1074/jbc.RA118.006481

Roux, S., Paul, B. G., Bagby, S. C., Allen, M. A., Attwood, G., Cavicchioli, R., Chistoserdova, L., Hallam, S. J., Hernandez, M. E., Hess, M., Liu, W. T., O’Malley, M. A., Peng, X., Rich, V. I., Saleska, S., & Eloe-Fadrosh, E. A. (2020). Ecology and molecular targets of hypermutation in the global microbiome. Unknown Journalhttps://doi.org/10.1101/2020.04.01.020958

Flamingh, A., Coutu, A., Roca, A. L., & Malhi, R. S. (2020). Accurate sex identification of ancient elephant and other animal remains using low-coverage DNA shotgun sequencing data. G3: Genes, Genomes, Genetics10(4), 1427-1432. https://doi.org/10.1534/g3.119.400833

Narm, K. E., Kalafatis, M., & Slauch, J. M. (2020). HilD, HilC, and RtsA form homodimers and heterodimers to regulate expression of the salmonella pathogenicity island i type iii secretion system. Journal of bacteriology202(9), [e00012-20]. https://doi.org/10.1128/JB.00012-20

Mei, R., Nobu, M. K., & Liu, W. T. (2020). Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments. Environmental Microbiology Reports12(2), 173-184. https://doi.org/10.1111/1758-2229.12821

Fuzawa, M., Smith, R. L., Ku, K. M., Shisler, J. L., Feng, H., Juvik, J. A., & Nguyen, T. H. (2020). Roles of Vegetable Surface Properties and Sanitizer Type on Annual Disease Burden of Rotavirus Illness by Consumption of Rotavirus-Contaminated Fresh Vegetables: A Quantitative Microbial Risk Assessment. Risk Analysis40(4), 741-757. https://doi.org/10.1111/risa.13426

Rowland, E. F., Bautista, M. A., Zhang, C., & Whitaker, R. J. (2020). Surface resistance to SSVs and SIRVs in pilin deletions of Sulfolobus islandicus. Molecular Microbiology113(4), 718-727. https://doi.org/10.1111/mmi.14435

Huang, C., Shen, Y., Smith, R. L., Dong, S., & Nguyen, T. H. (2020). Effect of disinfectant residuals on infection risks from Legionella pneumophila released by biofilms grown under simulated premise plumbing conditions. Environment International137, [105561]. https://doi.org/10.1016/j.envint.2020.105561

Hernández-Barrueta, T., Martínez-Bustos, F., Castaño-Tostado, E., Lee, Y., Miller, M. J., & Amaya-Llano, S. L. (2020). Encapsulation of probiotics in whey protein isolate and modified huauzontle's starch: An approach to avoid fermentation and stabilize polyphenol compounds in a ready-to-drink probiotic green tea. LWT124, [109131]. https://doi.org/10.1016/j.lwt.2020.109131

Bauza, V., Madadi, V., Ocharo, R., Nguyen, T. H., & Guest, J. S. (2020). Enteric pathogens from water, hands, surface, soil, drainage ditch, and stream exposure points in a low-income neighborhood of Nairobi, Kenya. Science of the Total Environment709, [135344]. https://doi.org/10.1016/j.scitotenv.2019.135344

Berenbaum, M. (2020). Weed Whackers. American Entomologist66(1), 10-13. https://doi.org/10.1093/ae/tmaa016

Massalha, N., Plewa, M. J., Nguyen, T. H., & Dong, S. (2020). Influence of Anaerobic Mesophilic and Thermophilic Digestion on Cytotoxicity of Swine Wastewaters. Environmental Science and Technology54(5), 3032-3038. https://doi.org/10.1021/acs.est.9b07066

Sun, H., Mei, R., Zhang, X. X., Ren, H., Liu, W. T., & Ye, L. (2020). Bacterial enrichment in highly-selective acetate-fed bioreactors and its application in rapid biofilm formation. Water Research170, [115359]. https://doi.org/10.1016/j.watres.2019.115359

Dewerff, S. J., Bautista, M. A., Pauly, M., Zhang, C., & Whitaker, R. J. (2020). Killer archaea: Virus-mediated antagonism to CRISPR-immune populations results in emergent virus-host mutualism. mBio11(2), [e00404-20]. https://doi.org/10.1128/mBio.00404-20

Ibarra-Sánchez, L. A., El-Haddad, N., Mahmoud, D., Miller, M. J., & Karam, L. (2020). Invited review: Advances in nisin use for preservation of dairy products. Journal of Dairy Science103(3), 2041-2052. https://doi.org/10.3168/jds.2019-17498

Verteramo Chiu, L. J., Tauer, L. W., Gröhn, Y. T., & Smith, R. L. (2020). Ranking disease control strategies with stochastic outcomes. Preventive Veterinary Medicine176, [104906]. https://doi.org/10.1016/j.prevetmed.2020.104906

Zeineldin, M., Lowe, J., & Aldridge, B. (2020). Effects of Tilmicosin Treatment on the Nasopharyngeal Microbiota of Feedlot Cattle With Respiratory Disease During the First Week of Clinical Recovery. Frontiers in Veterinary Science7, [115]. https://doi.org/10.3389/fvets.2020.00115

Straub, A. P., Asa, E., Zhang, W., Nguyen, T. H., & Herzberg, M. (2020). In-situ graft-polymerization modification of commercial ultrafiltration membranes for long-term fouling resistance in a pilot-scale membrane bioreactor. Chemical Engineering Journal382, [122865]. https://doi.org/10.1016/j.cej.2019.122865

Ye, L., Mei, R., Liu, W. T., Ren, H., & Zhang, X. X. (2020). Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes. Microbiome8(1), [16]. https://doi.org/10.1186/s40168-020-0794-3

Nute, M., Chou, J., Molloy, E. K., & Warnow, T. (2020). Erratum: The performance of coalescent-based species tree estimation methods under models of missing data (BMC Genomics DOI: 10.1186/s12864-018-4619-8). BMC genomics21(1), [133]. https://doi.org/10.1186/s12864-020-6540-1

Dardir, K., Wang, H., Martin, B. E., Atzampou, M., Brooke, C. B., & Fabris, L. (2020). SERS Nanoprobe for Intracellular Monitoring of Viral Mutations. Journal of Physical Chemistry C124(5), 3211-3217. https://doi.org/10.1021/acs.jpcc.9b09253

Ngumbi, E. N., Hanks, L. M., Suarez, A. V., Millar, J. G., & Berenbaum, M. R. (2020). Author Correction: Factors Associated with Variation in Cuticular Hydrocarbon Profiles in the Navel Orangeworm, Amyelois transitella (Lepidoptera: Pyralidae) (Journal of Chemical Ecology, (2020), 46, 1, (40-47), 10.1007/s10886-019-01129-6). Journal of Chemical Ecology46(2), 232. https://doi.org/10.1007/s10886-020-01155-9

Mann, A. E., Mazel, F., Lemay, M. A., Morien, E., Billy, V., Kowalewski, M., Di Fiore, A., Link, A., Goldberg, T. L., Tecot, S., Baden, A. L., Gomez, A., Sauther, M. L., Cuozzo, F. P., Rice, G. A. O., Dominy, N. J., Stumpf, R., Lewis, R. J., Swedell, L., ... Wegener Parfrey, L. (2020). Biodiversity of protists and nematodes in the wild nonhuman primate gut. ISME Journal14(2), 609-622. https://doi.org/10.1038/s41396-019-0551-4

Heath, K. D., Podowski, J. C., Heniff, S., Klinger, C. R., Burke, P. V., Weese, D. J., Yang, W. H., & Lau, J. A. (2020). Light availability and rhizobium variation interactively mediate the outcomes of legume–rhizobium symbiosis. American journal of botany107(2), 229-238. https://doi.org/10.1002/ajb2.1435

Baucom, R. S., Heath, K. D., & Chambers, S. M. (2020). Plant–environment interactions from the lens of plant stress, reproduction, and mutualisms. American journal of botany107(2), 175-178. https://doi.org/10.1002/ajb2.1437

Holmes, C. J., & Cáceres, C. E. (2020). Predation differentially structures immature mosquito populations in stormwater ponds. Ecological Entomology45(1), 97-108. https://doi.org/10.1111/een.12783

Calla, B., Wu, W. Y., Dean, C. A. E., Schuler, M. A., & Berenbaum, M. R. (2020). Substrate-specificity of cytochrome P450-mediated detoxification as an evolutionary strategy for specialization on furanocoumarin-containing hostplants: CYP6AE89 in parsnip webworms. Insect Molecular Biology29(1), 112-123. https://doi.org/10.1111/imb.12612

Araud, E., Fuzawa, M., Shisler, J. L., Li, J., & Nguyen, T. H. (2020). UV inactivation of rotavirus and tulane virus targets different components of the virions. Applied and environmental microbiology86(4), [e02436]. https://doi.org/10.1128/AEM.02436-19

Athukoralage, J. S., McMahon, S. A., Zhang, C., Grüschow, S., Graham, S., Krupovic, M., Whitaker, R. J., Gloster, T. M., & White, M. F. (2020). An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature577(7791), 572-575. https://doi.org/10.1038/s41586-019-1909-5

Rhodes, J. A., Nute, M. G., & Warnow, T. (2020). NJst and ASTRID are not statistically consistent under a random model of missing data. Unknown Journal.

Berenbaum, M. R. (2020). On a subject no one wants to read about (about which no one wants to read?). Proceedings of the National Academy of Sciences of the United States of America117(1), 4-6. https://doi.org/10.1073/pnas.1920932117

Fernandez, M. C., Hu, F. S., Gavin, D. G., deLafontaine, G., & Heath, K. D. (2020). Postglacial migration across a large dispersal barrier outpaces regional expansion from glacial refugia: Evidence from two conifers in the Pacific Northwest. Unknown Journalhttps://doi.org/10.1101/2020.01.05.895193

Christensen, S., Molloy, E. K., Vachaspati, P., Yammanuru, A., & Warnow, T. (2020). Non-parametric correction of estimated gene trees using TRACTION. Algorithms for Molecular Biology15(1), [1]. https://doi.org/10.1186/s13015-019-0161-8

Chen, L., Ling, F., Bakker, G., Liu, W. T., Medema, G., van der Meer, W., & Liu, G. (2020). Assessing the transition effects in a drinking water distribution system caused by changing supply water quality: an indirect approach by characterizing suspended solids. Water Research168, [115159]. https://doi.org/10.1016/j.watres.2019.115159

Ngumbi, E. N., Hanks, L. M., Suarez, A. V., Millar, J. G., & Berenbaum, M. R. (2020). Factors Associated with Variation in Cuticular Hydrocarbon Profiles in the Navel Orangeworm, Amyelois transitella (Lepidoptera: Pyralidae). Journal of Chemical Ecology46(1), 40-47. https://doi.org/10.1007/s10886-019-01129-6

Golding, I. (2020). Revisiting Replication-Induced Transcription in Escherichia coli. BioEssays42(1), [1900193]. https://doi.org/10.1002/bies.201900193

Tsai, C. L., Tripp, P., Sivabalasarma, S., Zhang, C., Rodriguez-Franco, M., Wipfler, R. L., Chaudhury, P., Banerjee, A., Beeby, M., Whitaker, R. J., Tainer, J. A., & Albers, S. V. (2020). The structure of the periplasmic FlaG–FlaF complex and its essential role for archaellar swimming motility. Nature Microbiology5(1), 216-225. https://doi.org/10.1038/s41564-019-0622-3

Van Tassell, M. L., Ibarra-Sánchez, L. A., Takhar, S. R., Amaya-Llano, S. L., & Miller, M. J. (2020). Corrigendum to “Use of a miniature laboratory fresh cheese model for investigating antimicrobial activities” (J. Dairy Sci. 98:8515–8524)(S002203021500733X)(10.3168/jds.2015-9967). Journal of Dairy Science103(1), 1048. https://doi.org/10.3168/jds.2020-103-1-1048

Scott-Richardson, M., Ruiz, M. OH., & Smith, R. L. (2020). Erratum to: Florida arsenic distribution index: Quantifying the distribution of past and present arsenic usage (Int. J. Environ. Res. Public Health, (2019), 16, 10.3390/ijerph16050744). International journal of environmental research and public health17(1), [270]. https://doi.org/10.3390/ijerph17010270

Ruzic, D. N., Oh, C., Puthussery, J. V., Patel, D., Jeckell, Z., Verma, V., & Nguyen, T. H. (2020). Converting Microwave Ovens into Plasma-Generating Decontamination Units for N-95 Respirators. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.09.15.297630

Scott-Richardson, M., Ruiz, M. OH., & Smith, R. L. (2020). Examining the Relationship Between Low Birth Weight Occurrence and Passive Measures of Environmental Arsenic by Census Tract in Escambia and Santa Rosa Counties, Florida. Environmental Health Insights14https://doi.org/10.1177/1178630220913053

Guardado Torrez, C., & Moodie, E. (Accepted/In press). La línea, los Indignados, and the Post-Postwar Generation in El Salvador. Journal of Latin American and Caribbean Anthropologyhttps://doi.org/10.1111/jlca.12498

Park, J., Wang, X., Zhao, J., & Han, H. S. (2020). Nanocrystal Precursor Incorporating Separated Reaction Mechanisms for Nucleation and Growth to Unleash the Potential of Heat-up Synthesis. ACS Nano14(9), 11579-11593.

Fu, Y., Peng, H., Liu, J., Nguyen, T. H., Hashmi, M. Z., & Shen, C. (Accepted/In press). Occurrence and quantification of culturable and viable but non-culturable (VBNC) pathogens in biofilm on different pipes from a metropolitan drinking water distribution system. Science of the Total Environment, [142851]. https://doi.org/10.1016/j.scitotenv.2020.142851

Christensen, S., Leiserson, M. D. M., & El-Kebir, M. (2020). PhySigs: Phylogenetic inference of mutational signature dynamics. Pacific Symposium on Biocomputing25(2020), 226-237.

Legried, B., Molloy, E. K., Warnow, T., & Roch, S. (2020). Polynomial-time statistical estimation of species trees under gene duplication and loss. In R. Schwartz (Ed.), Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings (pp. 120-135). (Lecture Notes in Computer Science; Vol. 12074 LNBI). Springer. https://doi.org/10.1007/978-3-030-45257-5_8

Mori, J., Uprety, S., Mao, Y., Koloutsou-Vakakis, S., Nguyen, T. H., & Smith, R. L. (Accepted/In press). Quantification and Comparison of Risks Associated with Wastewater Use in Spray Irrigation. Risk Analysishttps://doi.org/10.1111/risa.13607

Cowell, T. W., Valera, E., Jankelow, A., Park, J., Schrader, A. W., Ding, R., Berger, J., Bashir, R., & Han, H. S. (2020). Rapid, Multiplexed Electrical Detection of Biomolecules using Electrically Distinct Hydrogel Beads. Lab on a Chip20, 2274-2283.

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Zhang, Y., & Liu, W-T. (2019). The application of molecular tools to study the drinking water microbiome–Current understanding and future needs. Critical Reviews in Environmental Science and Technology, 49(13), 1188-1235. https://doi.org/10.1080/10643389.2019.1571351

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Zhang, L., Holle, M. J., Kim, J. S., Daum, M. A., & Miller, M. J. (2019). Nisin incorporation enhances the inactivation of lactic acid bacteria during the acid wash step of bioethanol production from sugarcane juice. Letters in Applied Microbiology, 69(1), 50-56. https://doi.org/10.1111/lam.13165

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Zhang, Y., Ahn, J. W., Green, K. J., Vann, K. R., Black, J., Brooke, C. B., & Kutateladze, T. G. (2019). MORC3 Is a Target of the Influenza A Viral Protein NS1. Structure, 27(6), 1029-1033.e3. https://doi.org/10.1016/j.str.2019.03.015

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Lakdawala, S. S., & Brooke, C. B. (2019). What’s New with Flu? An Overview. Viruses, 11(5), [433]. https://doi.org/10.3390/v11050433

Parker, A. T., Gardner, A. M., Perez, M., Allan, B. F., & Muturi, E. J. (2019). Container Size Alters the Outcome of Interspecific Competition between Aedes aegypti (Diptera: Culicidae) and Aedes albopictus. Journal of medical entomology, 56(3), 708-715. https://doi.org/10.1093/jme/tjy215

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Shah, N., Nute, M. G., Warnow, T., & Pop, M. (2019). Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinformatics, 35(9), 1613-1614. https://doi.org/10.1093/bioinformatics/bty833

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Megahed, A., Aldridge, B., & Lowe, J. (2019). Comparative study on the efficacy of sodium hypochlorite, aqueous ozone, and peracetic acid in the elimination of Salmonella from cattle manure contaminated various surfaces supported by Bayesian analysis. PloS one, 14(5), [e0217428]. https://doi.org/10.1371/journal.pone.0217428

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Malhi, R. S., Antón, S. C., & Fuentes, A. (2019). Increasing Diversity in Evolutionary Anthropological Sciences—the IDEAS Program. American Anthropologist, 121(2), 478-479. https://doi.org/10.1111/aman.13226

Napier, J. D., de Lafontaine, G., Heath, K. D., & Hu, F. S. (2019). Rethinking long-term vegetation dynamics: multiple glacial refugia and local expansion of a species complex. Ecography, 42(5), 1056-1067. https://doi.org/10.1111/ecog.04243

Mei, R., Kim, J., Wilson, F. P., Bocher, B. T. W., & Liu, W-T. (2019). Coupling growth kinetics modeling with machine learning reveals microbial immigration impacts and identifies key environmental parameters in a biological wastewater treatment process. Microbiome, 7(1), [65]. https://doi.org/10.1186/s40168-019-0682-x

Bentel, M. J., Yu, Y., Xu, L., Li, Z. L., Wong, B. M., Men, Y., & Liu, J. (2019). Defluorination of Per- and Polyfluoroalkyl Substances (PFASs) with Hydrated Electrons: Structural Dependence and Implications to PFAS Remediation and Management. Environmental Science and Technology, 53(7), 3718-3728. https://doi.org/10.1021/acs.est.8b06648

Landesman, W. J., Mulder, K., Allan, B. F., Bashor, L. A., Keesing, F., LoGiudice, K., & Ostfeld, R. S. (2019). Potential effects of blood meal host on bacterial community composition in Ixodes scapularis nymphs. Ticks and Tick-borne Diseases, 10(3), 523-527. https://doi.org/10.1016/j.ttbdis.2019.01.002

Amato, K. R., G. Sanders, J., Song, S. J., Nute, M., Metcalf, J. L., Thompson, L. R., ... R. Leigh, S. (2019). Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME Journal, 13(3), 576-587. https://doi.org/10.1038/s41396-018-0175-0

Roch, S., Nute, M., & Warnow, T. (2019). Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods. Systematic biology, 68(2), 281-297. https://doi.org/10.1093/sysbio/syy061

Parker, A. T., & Allan, B. F. (2019). Do gutter guards affect mosquito production in roof gutter habitats? Journal of the American Mosquito Control Association, 35(1), 67-70. https://doi.org/10.2987/18-6782.1

Welsh, E. C., Keesing, F., & Allan, B. F. (2019). Oxpecker (Buphagus erythrorhynchus, Buphagus africanus) and tick abundances in acaricide-treated livestock areas. African Journal of Ecology, 57(1), 155-159. https://doi.org/10.1111/aje.12560

Kim, K., Golubeva, Y. A., Vanderpool, C., & Slauch, J. M. (2019). Oxygen-dependent regulation of SPI1 type three secretion system by small RNAs in Salmonella enterica serovar Typhimurium. Molecular Microbiology, 111(3), 570-587. https://doi.org/10.1111/mmi.14174

Zhang, Q., Rao, S., & Warnow, T. (2019). Constrained incremental tree building: New absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Algorithms for Molecular Biology, 14(1), [2]. https://doi.org/10.1186/s13015-019-0136-9

Kosik, I., Angeletti, D., Gibbs, J. S., Angel, M., Takeda, K., Kosikova, M., ... Yewdell, J. W. (2019). Neuraminidase inhibition contributes to influenza A virus neutralization by anti-hemagglutinin stem antibodies. Journal of Experimental Medicine, 216(2), 304-316. https://doi.org/10.1084/jem.20181624

Martin, B. E., & Brooke, C. B. (2019). Flu Shows the Power of Diversity. Cell, 176(1-2), 9-10. https://doi.org/10.1016/j.cell.2018.12.017

Zeineldin, M., Aldridge, B., & Lowe, J. (2019). Antimicrobial effects on swine gastrointestinal microbiota and their accompanying antibiotic resistome. Frontiers in Microbiology, 10(MAY), [1035]. https://doi.org/10.3389/fmicb.2019.01035

Barreiro, A. K., Bronski, J. C., & Rapti, Z. (2019). Applications of a class of Herglotz operator pencils. SIAM Journal on Mathematical Analysis, 51(1), 256-275. https://doi.org/10.1137/18M1185673

Mann, A. E., Mazel, F., Lemay, M. A., Morien, E., Billy, V., Kowalewski, M., ... Wegener Parfrey, L. (Accepted/In press). Biodiversity of protists and nematodes in the wild nonhuman primate gut. ISME Journal. https://doi.org/10.1038/s41396-019-0551-4

Blair, B., & Lowe, J. F. (2019). Describing the cull sow market network in the US: A pilot project. Preventive Veterinary Medicine, 162, 107-109. https://doi.org/10.1016/j.prevetmed.2018.11.005

Zeineldin, M., Megahed, A., Burton, B., Blair, B., Aldridge, B., & Lowe, J. F. (2019). Effect of single dose of antimicrobial administration at birth on fecal microbiota development and prevalence of antimicrobial resistance genes in piglets. Frontiers in Microbiology, 10(JUN), [1414]. https://doi.org/10.3389/fmicb.2019.01414

Josek, T., Gardner, A. M., Hedlund, T. J., Parker, A. T., Allmann Updyke, E., & Allan, B. F. (2019). Fatal attraction: lone star ticks (Amblyomma americanum) exhibit preference for human female breath over male breath. Experimental and Applied Acarology, 77(1), 59-64. https://doi.org/10.1007/s10493-018-00338-0

Madak-Erdogan, Z., Band, S., Zhao, Y. C., Smith, B. P., Kulkoyluoglu-Cotul, E., Zuo, Q., ... Flaws, J. A. (2019). Free fatty acids rewire cancer metabolism in obesity-associated breast cancer via estrogen receptor and mTOR signaling. Cancer Research, 79(10), 2494-2510. https://doi.org/10.1158/0008-5472.CAN-18-2849

Clifton, S. M., Kim, T., Chandrashekhar, J. H., O'Toole, G. A., Rapti, Z., & Whitaker, R. J. (2019). Lying in wait: Modeling the control of bacterial infections via antibiotic-induced proviruses. mSystems, 4(5), [e00221-19]. https://doi.org/10.1128/mSystems.00221-19

Zealand, A. M., Mei, R., Roskilly, A. P., Liu, W. T., & Graham, D. W. (2019). Molecular microbial ecology of stable versus failing rice straw anaerobic digesters. Microbial Biotechnology, 12(5), 879-891. https://doi.org/10.1111/1751-7915.13438

Zeineldin, M. M., Megahed, A., Blair, B., Burton, B., Aldridge, B., & Lowe, J. (2019). Negligible impact of perinatal tulathromycin metaphylaxis on the developmental dynamics of fecal microbiota and their accompanying antimicrobial resistome in piglets. Frontiers in Microbiology, 10(APR), [726]. https://doi.org/10.3389/fmicb.2019.00726

Warnow, T. (2019). New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation. In M. A. Vega-Rodríguez, I. Holmes, & C. Martín-Vide (Eds.), Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings (pp. 3-21). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11488 LNBI). Springer-Verlag. https://doi.org/10.1007/978-3-030-18174-1_1

Yuan, H., Mei, R., Liao, J., & Liu, W. T. (2019). Nexus of stochastic and deterministic processes on microbial community assembly in biological systems. Frontiers in Microbiology, 10(JULY), [1536]. https://doi.org/10.3389/fmicb.2019.01536

Golding, I. (Accepted/In press). Revisiting Replication-Induced Transcription in Escherichia coli. BioEssays, [1900193]. https://doi.org/10.1002/bies.201900193

Fuzawa, M., Smith, R. L., Ku, K. M., Shisler, J. L., Feng, H., Juvik, J. A., & Nguyen, T. H. (Accepted/In press). Roles of Vegetable Surface Properties and Sanitizer Type on Annual Disease Burden of Rotavirus Illness by Consumption of Rotavirus-Contaminated Fresh Vegetables: A Quantitative Microbial Risk Assessment. Risk Analysis. https://doi.org/10.1111/risa.13426

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