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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.

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.

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].

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].

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.

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].

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 biology

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.

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].

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 Protection

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].

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].

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].

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].

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 Biology

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].

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.

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].

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].

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.

Smirnov, V., & Warnow, T. (2020). MAGUS: Multiple Sequence Alignment using Graph Clustering. Bioinformatics (Oxford, England)

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].

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 Diseases

Stewart Merrill, T. E., Hall, S. R., & Cáceres, C. E. (2020). Parasite exposure and host susceptibility jointly drive the emergence of epidemics. Ecology, e03245.

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.

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].

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).

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 evolution

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 Hygiene

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.

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.

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].

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].

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].

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 & technology

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].

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.

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 Evolution

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].

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.

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].

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].

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.

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].

Devarakonda, S., Korobskiy, D., Warnow, T., & Chacko, G. (2020). Viewing computer science through citation analysis: Salton and Bergmark Redux. Scientometrics125(1), 271-287.

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].

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].

Berenbaum, M. R. (2020). Crabby Days. American Entomologist66(3), 10-13.

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 Journal

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].

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 Journal

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.

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].

Yang, Q., & Warnow, T. (2020). An improved mode of running PASTA. Unknown Journal

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

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].

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.

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.

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].

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.

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.

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.

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.

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].

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.

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.

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.

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.

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].

Berenbaum, M. R. (2020). PNAS and prejudice. Proceedings of the National Academy of Sciences of the United States of America117(29), 16710-16712.

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.

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.

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

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.

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).

Sashittal, P., & El-Kebir, M. (2020). Sampling and summarizing transmission trees with multi-strain infections. Bioinformatics (Oxford, England)36(1), i362-i370.

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].

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].

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].

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 Journal

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.

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 entomology

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.

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.

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 Journal

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].

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.

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.

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.

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.

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].

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 Journal

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

Yu, X., Le, T., Christensen, S. A., Molloy, E. K., & Warnow, T. (2020). Advancing divide-and-conquer phylogeny estimation using Robinson-Foulds supertrees. Unknown Journal

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.

Sashittal, P., Luo, Y., Peng, J., & El-Kebir, M. (2020). Characterization of SARS-CoV-2 viral diversity within and across hosts. Unknown Journal

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.

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.

Berenbaum, M. R. (2020). PNAS and the pandemic. Proceedings of the National Academy of Sciences of the United States of America117(18), 9650-9651.

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.

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.

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.

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].

Alnaji, F. G., & Brooke, C. B. (2020). Influenza virus di particles: Defective interfering or delightfully interesting? PLoS pathogens16(5), [e1008436].

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].

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.

Smirnov, V., & Warnow, T. (2020). Unblended disjoint tree merging using GTM improves species tree estimation. BMC genomics21, [235].

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 Journal

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].

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.

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 Journal

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.

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].

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.

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.

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.

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].

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].

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].

Berenbaum, M. (2020). Weed Whackers. American Entomologist66(1), 10-13.

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.

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].

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].

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.

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].

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].

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].

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].

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].

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.

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.

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.

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.

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.

Holmes, C. J., & Cáceres, C. E. (2020). Predation differentially structures immature mosquito populations in stormwater ponds. Ecological Entomology45(1), 97-108.

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.

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].

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.

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.

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 Journal

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].

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].

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.

Golding, I. (2020). Revisiting Replication-Induced Transcription in Escherichia coli. BioEssays42(1), [1900193].

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.

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.

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].

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.

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 Insights14

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 Anthropology

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].

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.

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 Analysis

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.

Gorin, G., Wang, M., Golding, I., & Xu, H. (2020). Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics. PloS one15(3), [e0230736].

Yamamoto, K., Hackley, K. C., Kelly, W. R., Panno, S. V., Sekiguchi, Y., Sanford, R. A., ... Tamaki, H. (2019). Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States. Scientific reports, 9(1), [13484].

Megahed, A., Zeineldin, M., Evans, K., Maradiaga, N., Blair, B., Aldridge, B., & Lowe, J. (2019). Impacts of environmental complexity on respiratory and gut microbiome community structure and diversity in growing pigs. Scientific reports, 9(1), [13773].

Wang, M., Zhang, J., Xu, H., & Golding, I. (2019). Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality. Nature Microbiology, 4(12), 2118-2127.

Rapti, Z., Stewart Merrill, T. E., Mueller-Brennan, B., Kavouras, J. H., & Cáceres, C. E. (2019). Indirect effects in a planktonic disease system. Theoretical Population Biology, 130, 132-142.

Wu, X., Tang, A., Bi, X., Nguyen, T. H., & Yuan, B. (2019). Influence of algal organic matter of Microcystis aeruginosa on ferrate decay and MS2 bacteriophage inactivation. Chemosphere, 236, [124727].

Chin, T. A., Cáceres, C. E., & Cristescu, M. E. (2019). The evolution of reproductive isolation in Daphnia. BMC Evolutionary Biology, 19(1), [216].

Strauss, A. T., Hite, J. L., Civitello, D. J., Shocket, M. S., Cáceres, C. E., & Hall, S. R. (2019). Genotypic variation in parasite avoidance behaviour and other mechanistic, nonlinear components of transmission. Proceedings of the Royal Society B: Biological Sciences, 286(1915), [20192164].

Mei, R., & Liu, W. T. (2019). Quantifying the contribution of microbial immigration in engineered water systems. Microbiome, 7(1), [144].

Samineni, L., Xiong, B., Chowdhury, R., Pei, A., Kuehster, L., Wang, H., ... Velegol, S. (2019). 7 Log Virus Removal in a Simple Functionalized Sand Filter. Environmental Science and Technology, 53(21), 12706-12714.

Morrison, B. D., Heath, K., & Greenberg, J. A. (2019). Spatial scale affects novel and disappeared climate change projections in Alaska. Ecology and Evolution, 9(21), 12026-12044.

Stewart Merrill, T. E., Hall, S. R., Merrill, L., & Cáceres, C. E. (2019). Variation in Immune Defense Shapes Disease Outcomes in Laboratory and Wild Daphnia. Integrative and comparative biology, 59(5), 1203-1219.

One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780), 679-685.

Landesman, W. J., Mulder, K., Page Fredericks, L., & Allan, B. F. (2019). Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load. FEMS microbiology ecology, 95(12), [fiz167].

Fuzawa, M., Araud, E., Li, J., Shisler, J. L., & Nguyen, T. H. (2019). Free Chlorine Disinfection Mechanisms of Rotaviruses and Human Norovirus Surrogate Tulane Virus Attached to Fresh Produce Surfaces. Environmental Science and Technology, 53(20), 11999-12006.

Amato, K. R., Mallott, E. K., McDonald, D., Dominy, N. J., Goldberg, T., Lambert, J. E., ... Knight, R. (2019). Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. Genome biology, 20(1), [201].

Lakdawala, S. S., Lee, N., & Brooke, C. B. (2019). Teaching an Old Virus New Tricks: A Review on New Approaches to Study Age-Old Questions in Influenza Biology. Journal of Molecular Biology, 431(21), 4247-4258.

Shocket, M. S., Magnante, A., Duffy, M. A., Cáceres, C. E., & Hall, S. R. (2019). Can hot temperatures limit disease transmission? A test of mechanisms in a zooplankton–fungus system. Functional Ecology, 33(10), 2017-2029.

Donohue, M. E., Asangba, A. E., Ralainirina, J., Weisrock, D. W., Stumpf, R. M., & Wright, P. C. (2019). Extensive variability in the gut microbiome of a highly-specialized and critically endangered lemur species across sites. American journal of primatology, 81(10-11), [e23046].

Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., ... Dutilh, B. E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nature Microbiology, 4(10), 1727-1736.

Amato, K. R., & Stumpf, R. M. (2019). Moving forward with the primate microbiome: Introduction to a special issue of the American Journal of Primatology. American journal of primatology, 81(10-11), [e23060].

Kim, K., Palmer, A. D., Vanderpool, C., & Slauch, J. M. (2019). The small RNA pint contributes to phop-mediated regulation of the salmonella pathogenicity island 1 type III secretion system in salmonella enterica serovar typhimurium. Journal of bacteriology, 201(19), [e00312-19].

Asangba, A. E., Donohue, M. E., Lamb, A., Wright, P. C., Halajian, A., Leigh, S. R., & Stumpf, R. M. (2019). Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity. American journal of primatology, 81(10-11), [e23045].

Ladinsky, M. S., Khamaikawin, W., Jung, Y., Lin, S., Lam, J., An, D. S., ... Kieffer, C. (2019). Mechanisms of virus dissemination in bone marrow of HIV-1–infected humanized BLT mice. eLife, 8, [e46916].

Razavi, S. M. R., Oh, J., Haasch, R. T., Kim, K., Masoomi, M., Bagheri, R., ... Miljkovic, N. (2019). Environment-Friendly Antibiofouling Superhydrophobic Coatings. ACS Sustainable Chemistry and Engineering, 7(17), 14509-14520.

Qi, Y., Pradhan, D., & El-Kebir, M. (2019). Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors. Algorithms for Molecular Biology, 14(1), [19].

Zeineldin, M., Lowe, J. F., & Aldridge, B. M. (2019). Contribution of the Mucosal Microbiota to Bovine Respiratory Health. Trends in Microbiology, 27(9), 753-770.

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2019). Traction: Fast non-parametric improvement of estimated gene trees. In K. T. Huber, & D. Gusfield (Eds.), 19th International Workshop on Algorithms in Bioinformatics, WABI 2019 [4] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 143). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing.

Han, P., Yu, Y., Zhou, L., Tian, Z., Li, Z., Hou, L., ... Men, Y. (2019). Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata. Environmental Science and Technology, 53(15), 8695-8705.

Zhou, L. J., Han, P., Yu, Y., Wang, B., Men, Y., Wagner, M., & Wu, Q. L. (2019). Cometabolic biotransformation and microbial-mediated abiotic transformation of sulfonamides by three ammonia oxidizers. Water Research, 159, 444-453.

Feng, Y., Ibarra-Sánchez, L. A., Luu, L., Miller, M. J., & Lee, Y. (2019). Co-assembly of nisin and zein in microfluidics for enhanced antilisterial activity in Queso Fresco. LWT, 111, 355-362.

Hull, N. M., Ling, F., Pinto, A. J., Albertsen, M., Jang, H. G., Hong, P. Y., ... Liu, W-T. (2019). Drinking Water Microbiome Project: Is it Time? Trends in Microbiology, 27(8), 670-677.

Gomez, A., Sharma, A. K., Mallott, E. K., Petrzelkova, K. J., Jost Robinson, C. A., Yeoman, C. J., ... Mcmahon, K. (2019). Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints. mSphere, 4(4).

Molloy, E. K., & Warnow, T. (2019). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms for Molecular Biology, 14(1), [14].

Bauza, V., Madadi, V., Ocharo, R. M., Nguyen, T. H., & Guest, J. S. (2019). Microbial source tracking using 16S rRNA amplicon sequencing identifies evidence of widespread contamination from young children's feces in an Urban Slum of Nairobi, Kenya. Environmental Science and Technology, 53(14), 8271-8281.

Aguse, N., Qi, Y., & El-Kebir, M. (2019). Summarizing the solution space in tumor phylogeny inference by multiple consensus trees. Bioinformatics, 35(14), i408-i416. [btz312].

Molloy, E. K., & Warnow, T. (2019). TreeMerge: A new method for improving the scalability of species tree estimation methods. Bioinformatics, 35(14), i417-i426. [btz344].

Fogleman, A. J., Zahnd, W. E., Lipka, A. E., Malhi, R. S., Ganai, S., Delfino, K. R., & Jenkins, W. D. (2019). Knowledge, attitudes, and perceived barriers towards genetic testing across three rural Illinois communities. Journal of Community Genetics, 10(3), 417-423.

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.

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Munson-Mcgee, J. H., Peng, S., Dewerff, S., Stepanauskas, R., Whitaker, R., Weitz, J. S., & Young, M. J. (2018). A virus or more in (nearly) every cell: Ubiquitous networks of virus-host interactions in extreme environments. ISME Journal, 12(7), 1706-1714.

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Soliman, A., MacKay, A. J., Schmidt, A., Allan, B., & Wang, S. (Accepted/In press). Quantifying the geographic distribution of building coverage across the US for urban sustainability studies. Computers, Environment and Urban Systems.

Ibarra-Sánchez, L. A., Van Tassell, M. L., & Miller, M. J. (2018). Antimicrobial behavior of phage endolysin PlyP100 and its synergy with nisin to control Listeria monocytogenes in Queso Fresco. Food Microbiology, 72, 128-134.

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