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Research Areas

Infection Genomics for One Health: Publications

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

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

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

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

Chin, T. A., Cáceres, C. E., & Cristescu, M. E. (2019). The evolution of reproductive isolation in Daphnia. BMC Evolutionary Biology, 19(1), [216]. https://doi.org/10.1186/s12862-019-1542-9

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]. https://doi.org/10.1098/rspb.2019.2164

Mei, R., & Liu, W. T. (2019). Quantifying the contribution of microbial immigration in engineered water systems. Microbiome, 7(1), [144]. https://doi.org/10.1186/s40168-019-0760-0

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. https://doi.org/10.1021/acs.est.9b03734

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. https://doi.org/10.1002/ece3.5511

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. https://doi.org/10.1093/icb/icz079

One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature, 574(7780), 679-685. https://doi.org/10.1038/s41586-019-1693-2

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]. https://doi.org/10.1093/femsec/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. https://doi.org/10.1021/acs.est.9b03461

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]. https://doi.org/10.1186/s13059-019-1807-z

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. https://doi.org/10.1016/j.jmb.2019.04.038

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. https://doi.org/10.1111/1365-2435.13403

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]. https://doi.org/10.1002/ajp.23046

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. https://doi.org/10.1038/s41564-019-0494-6

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]. https://doi.org/10.1002/ajp.23060

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]. https://doi.org/10.1128/JB.00312-19

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]. https://doi.org/10.1002/ajp.23045

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]. https://doi.org/10.7554/eLife.46916

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. https://doi.org/10.1021/acssuschemeng.9b02025

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]. https://doi.org/10.1186/s13015-019-0155-6

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. https://doi.org/10.1016/j.tim.2019.04.005

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. https://doi.org/10.4230/LIPIcs.WABI.2019.4

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. https://doi.org/10.1021/acs.est.9b01037

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. https://doi.org/10.1016/j.watres.2019.05.031

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. https://doi.org/10.1016/j.lwt.2019.05.059

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. https://doi.org/10.1016/j.tim.2019.03.011

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). https://doi.org/10.1128/mSphere.00271-19

Molloy, E. K., & Warnow, T. (2019). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms for Molecular Biology, 14(1), [14]. https://doi.org/10.1186/s13015-019-0151-x

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. https://doi.org/10.1021/acs.est.8b06583

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]. https://doi.org/10.1093/bioinformatics/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]. https://doi.org/10.1093/bioinformatics/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. https://doi.org/10.1007/s12687-019-00407-w

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

Zhang, C., Wipfler, R. L., Li, Y., Wang, Z., Hallett, E. N., & Whitaker, R. J. (2019). Cell structure changes in the hyperthermophilic crenarchaeon Sulfolobus islandicus lacking the S-layer. mBio, 10(4), [e01589-19]. https://doi.org/10.1128/mBio.01589-19

Ozer, E. A., Nnah, E., Didelot, X., Whitaker, R. J., & Hauser, A. R. (2019). The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages. Genome biology and evolution, 11(1), 1780-1796. https://doi.org/10.1093/gbe/evz119

Pafčo, B., Sharma, A. K., Petrželková, K. J., Vlčková, K., Todd, A., Yeoman, C. J., ... Gomez, A. (2019). Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors. American journal of physical anthropology, 169(3), 575-585. https://doi.org/10.1002/ajpa.23842

Radin, J. N., Kelliher, J. L., Solórzano, P. K. P., Grim, K. P., Ramezanifard, R., Slauch, J. M., & Kehl-Fie, T. E. (2019). Metal-independent variants of phosphoglycerate mutase promote resistance to nutritional immunity and retention of glycolysis during infection. PLoS pathogens, 15(7), [e1007971]. https://doi.org/10.1371/journal.ppat.1007971

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

Tang, L., Zhong, L., Xue, K., Wang, S., Xu, Z., Lin, Q., ... Wang, Y. (2019). Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland. Soil Biology and Biochemistry, 134, 113-121. https://doi.org/10.1016/j.soilbio.2019.02.018

Sikora, M., Pitulko, V. V., Sousa, V. C., Allentoft, M. E., Vinner, L., Rasmussen, S., ... Willerslev, E. (2019). The population history of northeastern Siberia since the Pleistocene. Nature, 570(7760), 182-188. https://doi.org/10.1038/s41586-019-1279-z

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

Mansfeldt, C., Achermann, S., Men, Y., Walser, J. C., Villez, K., Joss, A., ... Fenner, K. (2019). Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities. ISME Journal, 13(6), 1589-1601. https://doi.org/10.1038/s41396-019-0371-6

Gao, H., Mao, Y., Zhao, X., Liu, W. T., Zhang, T., & Wells, G. (2019). Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess. Water Research, 155, 275-287. https://doi.org/10.1016/j.watres.2019.02.020

Pauly, M. D., Bautista, M. A., Black, J. A., & Whitaker, R. J. (2019). Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1772), [20180093]. https://doi.org/10.1098/rstb.2018.0093

Westra, E. R., Van Houte, S., Gandon, S., & Whitaker, R. (2019). The ecology and evolution of microbial CRISPR-Cas adaptive immune systems. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1772), [20190101]. https://doi.org/10.1098/rstb.2019.0101

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

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

Nute, M., Saleh, E., & Warnow, T. (2019). Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets. Systematic biology, 68(3), 396-411. https://doi.org/10.1093/sysbio/syy068

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

Schablitsky, J. M., Witt, K. E., Madrigal, J. R., Ellegaard, M. R., Malhi, R. S., & Schroeder, H. (2019). Ancient DNA analysis of a nineteenth century tobacco pipe from a Maryland slave quarter. Journal of Archaeological Science, 105, 11-18. https://doi.org/10.1016/j.jas.2019.02.006

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

Bader, A. C., & Malhi, R. S. (2019). How Subjectivity Strengthens Research: Developing an Integrative Approach to Investigating Human Diet in the Pacific Northwest Coast. American Anthropologist, 121(2), 476-478. https://doi.org/10.1111/aman.13218

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Alnaji, F. G., Holmes, J. R., Rendon, G., Cristobal Vera, J., Fields, C. J., Martin, B. E., & Brooke, C. B. (2019). Sequencing framework for the sensitive detection and precise mapping of defective interfering particle-associated deletions across influenza A and B viruses. Journal of virology, 93(11), [e0035419]. https://doi.org/10.1128/JVI.00354-19

Le, T., Sy, A., Molloy, E. K., Zhang, Q. R., Rao, S., & Warnow, T. (2019). Using INC Within Divide-and-Conquer Phylogeny Estimation. In M. A. Vega-Rodríguez, I. Holmes, & C. Martín-Vide (Eds.), Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings (pp. 167-178). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11488 LNBI). Springer-Verlag. https://doi.org/10.1007/978-3-030-18174-1_12

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