Infection Genomics for One Health: Publications

Witt, K. E., Yarlagadda, K., Allen, J. M., Bader, A. C., Simon, M. L., Kuehn, S. R., Swanson, K. S., Cross, T. W. L., Hedman, K. M., Ambrose, S. H., & Malhi, R. S. (2021). Author Correction: Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet (Scientific Reports, (2021), 11, 1, (3113), 10.1038/s41598-021-82362-6). Scientific reports, 11(1), [11445]. https://doi.org/10.1038/s41598-021-90889-x

Muturi, E. J., Njoroge, T. M., Dunlap, C., & Cáceres, C. E. (2021). Blood meal source and mixed blood-feeding influence gut bacterial community composition in Aedes aegypti. Parasites and Vectors, 14(1), [83]. https://doi.org/10.1186/s13071-021-04579-8

Brown, S. P., Grillo, M. A., Podowski, J. C., & Heath, K. D. (2021). Correction to: Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula (Microbiome, (2020), 8, 1, (139), 10.1186/s40168-020-00915-9). Microbiome, 9(1), [105]. https://doi.org/10.1186/s40168-021-01080-3

Roux, S., Paul, B. G., Bagby, S. C., Nayfach, S., Allen, M. A., Attwood, G., Cavicchioli, R., Chistoserdova, L., Gruninger, R. J., Hallam, S. J., Hernandez, M. E., Hess, M., Liu, W. T., McAllister, T. A., O’Malley, M. A., Peng, X., Rich, V. I., Saleska, S. R., & Eloe-Fadrosh, E. A. (2021). Ecology and molecular targets of hypermutation in the global microbiome. Nature communications, 12(1), [3076]. https://doi.org/10.1038/s41467-021-23402-7

Poddar, A., Azam, M. S., Kayikcioglu, T., Bobrovskyy, M., Zhang, J., Ma, X., Labhsetwar, P., Fei, J., Singh, D., Luthey-Schulten, Z., Vanderpool, C. K., & Ha, T. (2021). Effects of individual base-pairs on in vivo target search and destruction kinetics of bacterial small RNA. Nature communications, 12(1), [874]. https://doi.org/10.1038/s41467-021-21144-0

Hamed, S., Shawky, R. M., Emara, M., Slauch, J. M., & Rao, C. V. (2021). HilE is required for synergistic activation of SPI-1 gene expression in Salmonella enterica serovar Typhimurium. BMC microbiology, 21(1), [49]. https://doi.org/10.1186/s12866-021-02110-8

Sun, P. P., Won, J., Choo-Kang, G., Li, S., Chen, W., Monroy, G. L., Chaney, E. J., Boppart, S. A., Eden, J. G., & Nguyen, T. H. (2021). Inactivation and sensitization of Pseudomonas aeruginosa by microplasma jet array for treating otitis media. npj Biofilms and Microbiomes, 7(1), [48]. https://doi.org/10.1038/s41522-021-00219-2

Witt, K. E., Yarlagadda, K., Allen, J. M., Bader, A. C., Simon, M. L., Kuehn, S. R., Swanson, K. S., Cross, T. W. L., Hedman, K. M., Ambrose, S. H., & Malhi, R. S. (2021). Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet. Scientific reports, 11(1), [3113]. https://doi.org/10.1038/s41598-021-82362-6

Zhang, C., El-Kebir, M., & Ochoa, I. (2021). Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples. Nature communications, 12(1), [2204]. https://doi.org/10.1038/s41467-021-22466-9

Juma, E. O., Allan, B. F., Kim, C. H., Stone, C., Dunlap, C., & Muturi, E. (2021). The larval environment strongly influences the bacterial communities of Aedes triseriatus and Aedes japonicus (Diptera: Culicidae). Scientific reports, 11(1), [7910]. https://doi.org/10.1038/s41598-021-87017-0

Chiang, C., Pacyga, D. C., Strakovsky, R. S., Smith, R. L., James-Todd, T., Williams, P. L., Hauser, R., Meling, D. D., Li, Z., & Flaws, J. A. (2021). Urinary phthalate metabolite concentrations and serum hormone levels in pre- and perimenopausal women from the Midlife Women's Health Study. Environment international, 156, [106633]. https://doi.org/10.1016/j.envint.2021.106633

Clifton, S. M., Whitaker, R. J., & Rapti, Z. (2021). Temperate and chronic virus competition leads to low lysogen frequency. Journal of Theoretical Biology, 523, [110710]. https://doi.org/10.1016/j.jtbi.2021.110710

Smith, R. L., Gibson, L. L., Martinez, P. P., Ke, R., Mirza, A., Conte, M., Gallagher, N., Conte, A., Wang, L., Fredrickson, R., Edmonson, D. C., Baughman, M. E., Chiu, K. K., Choi, H., Jensen, T. W., Scardina, K. R., Bradley, S., Gloss, S. L., Reinhart, C., ... Brooke, C. B. (Accepted/In press). Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection. Journal of Infectious Diseases. https://doi.org/10.1101/2021.03.19.21253964, https://doi.org/10.1093/infdis/jiab337

Tan, T. J. C., Yuan, M., Kuzelka, K., Padron, G. C., Beal, J. R., Chen, X., Wang, Y., Rivera-Cardona, J., Zhu, X., Stadtmueller, B. M., Brooke, C. B., Wilson, I. A., & Wu, N. C. (2021). Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain. Nature Communications, 12(1), [3815 ]. https://doi.org/10.1101/2021.01.26.428356, https://doi.org/10.1038/s41467-021-24123-7

Zeineldin, M., Megahed, A., Blair, B., Aldridge, B., & Lowe, J. (2021). Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis. Animals, 11(6). https://doi.org/10.3390/ani11061825

Iwadate, Y., Ramezanifard, R., Golubeva, Y. A., Fenlon, L. A., & Slauch, J. M. (2021). PaeA (YtfL) protects from cadaverine and putrescine stress in Salmonella Typhimurium and E. coli. Molecular Microbiology, 115(6), 1379-1394. https://doi.org/10.1111/mmi.14686

Njoroge, T. M., Calla, B., Berenbaum, M. R., & Stone, C. M. (2021). Specific phytochemicals in floral nectar up-regulate genes involved in longevity regulation and xenobiotic metabolism, extending mosquito life span. Ecology and Evolution, 11(12), 8363-8380. https://doi.org/10.1002/ece3.7665

Warner, G. R., Pacyga, D. C., Strakovsky, R. S., Smith, R., James-Todd, T., Williams, P. L., Hauser, R., Meling, D. D., Li, Z., & Flaws, J. A. (2021). Urinary phthalate metabolite concentrations and hot flashes in women from an urban convenience sample of midlife women. Environmental Research, 197, [110891]. https://doi.org/10.1016/j.envres.2021.110891

Varga, C., John, P., Cooke, M., & Majowicz, S. E. (2021). Area-Level Clustering of Shiga Toxin–Producing Escherichia coli Infections and Their Socioeconomic and Demographic Factors in Ontario, Canada: An Ecological Study. Foodborne pathogens and disease. https://doi.org/10.1089/fpd.2020.2918

Resendiz-Moctezuma, C., Rezac, S. D., Miller, M. J., & Stasiewicz, M. J. (2021). Enabling Cost-Effective Screening for Antimicrobials against Listeria monocytogenes in Ham. Journal of Food Protection, 84(5), 802-810. https://doi.org/10.4315/JFP-20-435

Strickland, L. R., Fuller, R. C., Windsor, D., & Cáceres, C. E. (2021). A potential role for overdominance in the maintenance of colour variation in the Neotropical tortoise beetle, Chelymorpha alternans. Journal of Evolutionary Biology, 34(5), 779-791. https://doi.org/10.1111/jeb.13779

SCHUMACHER, RUSS. S., HENCE, DEANNA. A., NESBITT, STEPHEN. W., TRAPP, ROBERT. J., KOSIBA, KAREN. A., WURMAN, JOSHUA., SALIO, PAOLA., RUGNA, MARTIN., VARBLE, ADAM. C., & KELLY, NATHAN. R. (2021). Convective-storm environments in subtropical south america from high-frequency soundings during relampago-cacti. Monthly Weather Review, 149(5), 1439-1458. https://doi.org/10.1175/MWR-D-20-0293.1

Park, M., Zaharias, P., & Warnow, T. (2021). Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation. Algorithms, 14(5), [148]. https://doi.org/10.3390/a14050148

Legried, B., Molloy, E. K., Warnow, T., & Roch, S. (2021). Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. Journal of computational biology : a journal of computational molecular cell biology, 28(5), 452-468. https://doi.org/10.1089/cmb.2020.0424

Mori, J., Uprety, S., Mao, Y., Koloutsou-Vakakis, S., Nguyen, T. H., & Smith, R. L. (2021). Quantification and Comparison of Risks Associated with Wastewater Use in Spray Irrigation. Risk Analysis, 41(5), 745-760. https://doi.org/10.1111/risa.13607

Patel, S. S., Sandur, A., El-Kebir, M., Gaba, R. C., Schook, L. B., & Schachtschneider, K. M. (2021). Transcriptional Profiling of Porcine HCC Xenografts Provides Insights Into Tumor Cell Microenvironment Signaling. Frontiers in Genetics, 12, [657330]. https://doi.org/10.3389/fgene.2021.657330

Janes, J., Young, M. E., Chen, E., Rogers, N. H., Burgstaller-Muehlbacher, S., Hughes, L. D., Love, M. S., Hull, M. V., Kuhen, K. L., Woods, A. K., Joseph, S. B., Petrassi, H. M., McNamara, C. W., Tremblay, M. S., Su, A. I., Schultz, P. G., Chatterjee, A. K., & Berenbaum, M. R. (2021). Erratum: The ReFRAME library as a comprehensive drug repurposing library and its application to the treatment of cryptosporidiosis (Proceedings of the National Academy of Sciences of the United States of America (2018) 115 (10750-10755) DOI: 10.1073/pnas.1810137115). Proceedings of the National Academy of Sciences of the United States of America, 118(15), [e2104932118]. https://doi.org/10.1073/pnas.2104932118

Berenbaum, M. R. (2021). Erratum: Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise (Proceedings of the National Academy of Sciences of the United States of America (2021) 118 (e2021586118) DOI: 10.1073/pnas.2021586118). Proceedings of the National Academy of Sciences of the United States of America, 118(15), [e2105198118]. https://doi.org/10.1073/pnas.2105198118

Fu, Y., Peng, H., Liu, J., Nguyen, T. H., Hashmi, M. Z., & Shen, C. (2021). 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, 764, [142851]. https://doi.org/10.1016/j.scitotenv.2020.142851

Capodiferro, M. R., Aram, B., Raveane, A., Rambaldi Migliore, N., Colombo, G., Ongaro, L., Rivera, J., Mendizábal, T., Hernández-Mora, I., Tribaldos, M., Perego, U. A., Li, H., Scheib, C. L., Modi, A., Gòmez-Carballa, A., Grugni, V., Lombardo, G., Hellenthal, G., Pascale, J. M., ... Achilli, A. (2021). Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell, 184(7), 1706-1723.e24. https://doi.org/10.1016/j.cell.2021.02.040

Ibarra-Sánchez, L. A., Kong, W., Lu, T., & Miller, M. J. (2021). Efficacy of nisin derivatives with improved biochemical characteristics, alone and in combination with endolysin PlyP100 to control Listeria monocytogenes in laboratory-scale Queso Fresco. Food Microbiology, 94, [103668]. https://doi.org/10.1016/j.fm.2020.103668

Richards, V. P., Nigsch, A., Bitar, P. P., Sun, Q., Stuber, T., Ceres, K., Smith, R. L., Austerman, S. R., Schukken, Y., Grohn, Y. T., & Stanhope, M. J. (2021). Evolutionary Genomic and Bacterial Genome-Wide Association Study of Mycobacterium avium subsp. paratuberculosis and Dairy Cattle Johne's Disease Phenotypes. Applied and environmental microbiology, 87(8), 1-16. https://doi.org/10.1128/AEM.02570-20

Hawash, M. B. F., Sanz-Remón, J., Grenier, J. C., Kohn, J., Yotova, V., Johnson, Z., Lanford, R. E., Brinkworth, J. F., & Barreiro, L. B. (2021). Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity. Proceedings of the National Academy of Sciences of the United States of America, 118(13), [2015855118]. https://doi.org/10.1073/PNAS.2015855118

Cuevas-Maraver, J., Kevrekidis, P., Chen, Q-Y., Kevrekidis, G., Villalobos-Daniel, V., Rapti, Z., & Drossinos, Y. (Accepted/In press). Lockdown measures and their impact on single- and two-age-structured epidemic model for the COVID-19 outbreak in Mexico. Mathematical Biosciences. https://doi.org/10.1101/2020.08.11.20172833, https://doi.org/10.1016/j.mbs.2021.108590

Cabrera, S., Hiatt, D., Dillon, W. W., Clark, T., Allan, B. F., & Flory, S. L. (2021). Observations of Wild Turkey Nesting in Invasive Cogongrass. Southeastern Naturalist, 20(1), N42-N49. https://doi.org/10.1656/058.020.0119

Smirnov, V., & Warnow, T. (2021). Phylogeny Estimation Given Sequence Length Heterogeneity. Systematic biology, 70(2), 268-282. https://doi.org/10.1093/sysbio/syaa058

Brinkworth, J. F., & Valizadegan, N. (2021). Sepsis and the evolution of human increased sensitivity to lipopolysaccharide. Evolutionary anthropology, 30(2), 141-157. https://doi.org/10.1002/evan.21887

Gomez, A., Sharma, A. K., Mallott, E. K., Petrzelkova, K. J., Robinson, C. A. J., Yeoman, C. J., Carbonero, F., Pafco, B., Rothman, J. M., Ulanov, A., Vlckova, K., Amato, K. R., Schnorr, S. L., Dominy, N. J., Modry, D., Todd, A., Torralba, M., Nelson, K. E., Burns, M. B., ... Leigh, S. R. (2021). Erratum for Gomez et al., “Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints”. mSphere, 6(2), [e00168]. https://doi.org/10.1128/mSphere.00168-21

Ueki, Y., Amarasiri, M., Kamio, S., Sakagami, A., Ito, H., Uprety, S., Umam, A. N., Miura, T., Nguyen, T. H., & Sano, D. (2021). Human norovirus disease burden of consuming Crassostrea gigas oysters: A case-study from Japan. Food Control, 121, [107556]. https://doi.org/10.1016/j.foodcont.2020.107556

Varga, C. (2021). DEMOGRAPHIC CHARACTERISTICS, AND HUSBANDRY AND BIOSECURITY PRACTICES OF SMALL POULTRY FLOCKS IN ONTARIO, CANADA. Avian Diseases. https://doi.org/10.1637/aviandiseases-d-20-00108

Sashittal, P., Zhang, C., Peng, J., & El-Kebir, M. (2021). Jumper Enables Discontinuous Transcript Assembly in Coronaviruses. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2021.02.12.431026

Perri, A. R., Feuerborn, T. R., Frantz, L. A. F., Larson, G., Malhi, R. S., Meltzer, D. J., & Witt, K. E. (2021). Dog domestication and the dual dispersal of people and dogs into the Americas. Proceedings of the National Academy of Sciences of the United States of America, 118(6), [e2010083118]. https://doi.org/10.1073/pnas.2010083118

de Flamingh, A., Coutu, A., Sealy, J., Chirikure, S., Bastos, A. D. S., Libanda-Mubusisi, N. M., Malhi, R. S., & Roca, A. L. (2021). Sourcing Elephant Ivory from a Sixteenth-Century Portuguese Shipwreck. Current Biology, 31(3), 621-628.e4. https://doi.org/10.1016/j.cub.2020.10.086

Dong, X., Hu, X., Bao, Y., Li, G., Yang, X. D., Slauch, J. M., & Chen, L. F. (2021). Brd4 regulates NLRC4 inflammasome activation by facilitating IRF8-mediated transcription of Naips. Journal of Cell Biology, 220(3), [e202005148]. https://doi.org/10.1083/JCB.202005148

Berenbaum, M. R., Bush, D. S., & Liao, L. H. (2021). Cytochrome P450-mediated mycotoxin metabolism by plant-feeding insects. Current Opinion in Insect Science, 43, 85-91. https://doi.org/10.1016/j.cois.2020.11.007

Mao, Y., Zeineldin, M., Usmani, M., Uprety, S., Shisler, J. L., Jutla, A., Unnikrishnan, A., & Nguyen, T. H. (2021). Distribution and Antibiotic Resistance Profiles of Salmonella enterica in Rural Areas of North Carolina After Hurricane Florence in 2018. GeoHealth, 5(2), [e2020GH000294]. https://doi.org/10.1029/2020GH000294

Berenbaum, M., & Calla, B. (2021). Editorial overview: Cytochrome P450s in plant–insect interactions: new insights on gut reactions. Current Opinion in Insect Science, 43, vi-ix. https://doi.org/10.1016/j.cois.2021.03.006

Hedman, H. D., Krawczyk, E., Helmy, Y. A., Zhang, L., & Varga, C. (2021). Host Diversity and Potential Transmission Pathways of SARS-CoV-2 at the Human-Animal Interface. Pathogens. https://doi.org/10.3390/pathogens10020180

Stewart Merrill, T. E., Hall, S. R., & Cáceres, C. E. (2021). Parasite exposure and host susceptibility jointly drive the emergence of epidemics. Ecology, 102(2), e03245. [e03245]. https://doi.org/10.1002/ecy.3245

Althaus, S. L., Berenbaum, M. R., Jordan, J., & Shalmon, D. A. (2021). No buzz for bees: Media coverage of pollinator decline. Proceedings of the National Academy of Sciences, 118(2), [e2002552117]. https://doi.org/10.1073/pnas.2002552117

Wagner, D. L., Grames, E. M., Forister, M. L., Berenbaum, M. R., & Stopak, D. (2021). Insect decline in the Anthropocene: Death by a thousand cuts. Proceedings of the National Academy of Sciences of the United States of America, 118(2), [e202398918]. https://doi.org/10.1073/PNAS.2023989118

Berenbaum, M. R., & Calla, B. (2021). Honey as a Functional Food for Apis mellifera. Annual Review of Entomology, 66, 185-208. https://doi.org/10.1146/annurev-ento-040320-074933

Calla, B., Demkovich, M., Siegel, J. P., Viana, J. P. G., Walden, K. K. O., Robertson, H. M., & Berenbaum, M. R. (2021). Selective sweeps in a nutshell: the genomic footprint of rapid insecticide resistance evolution in the almond agroecosystem. Genome biology and evolution, 13(1). https://doi.org/10.1093/gbe/evaa234

Uelmen, J. A., Irwin, P., Bartlett, D., Brown, W., Karki, S., O'Hara, M. S., Fraterrigo, J. M., Li, B., & Smith, R. L. (2021). Effects of scale on modeling west nile virus disease risk. American Journal of Tropical Medicine and Hygiene, 104(1), 151-165. https://doi.org/10.4269/AJTMH.20-0416

Zhang, G., St Clair, A. L., Dolezal, A. G., Toth, A. L., & O'Neal, M. E. (2021). North American Prairie Is a Source of Pollen for Managed Honey Bees (Hymenoptera: Apidae). Journal of insect science (Online), 21(1). https://doi.org/10.1093/jisesa/ieab001

Pattabiraman, S., & Warnow, T. (2021). Profile Hidden Markov Models Are Not Identifiable. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(1), 162-172. [8798655]. https://doi.org/10.1109/TCBB.2019.2933821

Le, T., Sy, A., Molloy, E. K., Zhang, Q., Rao, S., & Warnow, T. (2021). Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18(1), 2-15. [9093990]. https://doi.org/10.1109/TCBB.2020.2990867

Holle, M. J., & Miller, M. J. (2021). Designing asynchronous online fermentation science materials including using a home fermented foods project to engage online learners. Journal of Food Science Education, 20(1), 57-62. https://doi.org/10.1111/1541-4329.12212

Demkovich, M. R., Calla, B., Ngumbi, E., Higbee, B. S., Siegel, J. P., & Berenbaum, M. R. (2021). Differential regulation of cytochrome P450 genes associated with biosynthesis and detoxification in bifenthrin-resistant populations of navel orangewom (Amyelois transitella). PloS one, 16(1 January), [e0245803]. https://doi.org/10.1371/journal.pone.0245803

Gibson, D. J., Nemeth, N. M., Beaufrère, H., Varga, C., Garner, M. M., & Susta, L. (Accepted/In press). Lymphoma in Psittacine Birds: A Histological and Immunohistochemical Assessment. Veterinary pathology. https://doi.org/10.1177/03009858211002180

Muturi, E. J., Dunlap, C., & Caceres, C. E. (2021). Microbial communities of container aquatic habitats shift in response to Culex restuans larvae. FEMS microbiology ecology, 96(7), [fiaa112]. https://doi.org/10.1093/FEMSEC/FIAA112

Warnow, T., & Mirarab, S. (2021). Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP. In Methods in Molecular Biology (pp. 99-119). (Methods in Molecular Biology; Vol. 2231). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-1036-7_7

Warnow, T. (2021). Revisiting Evaluation of Multiple Sequence Alignment Methods. In Methods in Molecular Biology (pp. 299-317). (Methods in Molecular Biology; Vol. 2231). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-1036-7_17

Berenbaum, M. R. (2021). What Does It Mean, This Plague? (with Apologies to Albert Camus). American Entomologist, 67(1), 10-13. https://doi.org/10.1093/ae/tmab015

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 Sciences, 287(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 Sciences, 287(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. mSystems, 5(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 Science, 7, [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 biology. https://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 Microbiology, 11, [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 Protection. https://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 Microbiology, 334, [108834]. https://doi.org/10.1016/j.ijfoodmicro.2020.108834

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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 entomology, 113(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 Genetics, 21(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 Development, 10(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 Medicine, 51(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. mSystems, 5(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 Journal. https://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. Viruses, 12(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 Journal. https://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 Journal. https://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. PNAS, 117(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 Technology, 54(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 America, 117(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 ecology, 29(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 Ecology, 34(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. Oecologia, 193(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 Health, 226, [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 pathogens, 16(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 one, 15(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 America, 117(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 genomics, 21, [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 Journal. https://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 Biology, 490, [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 Chemistry, 295(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 Journal. https://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, Genetics, 10(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 bacteriology, 202(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 Reports, 12(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 Analysis, 40(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 Microbiology, 113(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 International, 137, [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. LWT, 124, [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 Environment, 709, [135344]. https://doi.org/10.1016/j.scitotenv.2019.135344

Berenbaum, M. (2020). Weed Whackers. American Entomologist, 66(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 Technology, 54(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 Research, 170, [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. mBio, 11(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 Science, 103(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 Medicine, 176, [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 Science, 7, [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 Journal, 382, [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. Microbiome, 8(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 genomics, 21(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 C, 124(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 Ecology, 46(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 Journal, 14(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 botany, 107(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 botany, 107(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 Entomology, 45(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 Biology, 29(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 microbiology, 86(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. Nature, 577(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 America, 117(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 Journal. https://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 Biology, 15(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 Research, 168, [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 Ecology, 46(1), 40-47. https://doi.org/10.1007/s10886-019-01129-6

Golding, I. (2020). Revisiting Replication-Induced Transcription in Escherichia coli. BioEssays, 42(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 Microbiology, 5(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 Science, 103(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 health, 17(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 Insights, 14. https://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 Anthropology. https://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 Nano, 14(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 Biocomputing, 25(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 Analysis. https://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 Chip, 20, 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 one, 15(3), [e0230736]. https://doi.org/10.1371/journal.pone.0230736

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]. https://doi.org/10.1038/s41598-019-49996-z

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]. https://doi.org/10.1038/s41598-019-50187-z

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. https://doi.org/10.1038/s41564-019-0553-z

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. https://doi.org/10.1016/j.tpb.2019.07.009

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]. https://doi.org/10.1016/j.chemosphere.2019.124727

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