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Infection Genomics for One Health: Publications

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.

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.

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.

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.

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.

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.

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.

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, 275-287.

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

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].

Lakdawala, S. S., & Brooke, C. B. (2019). What’s New with Flu? An Overview. Viruses, 11(5), [433].

Megahed, A., Aldridge, B. M., & Lowe, J. F. (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].

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.

Shah, N., Nute, M. G., Warnow, T., & Pop, M. (2019). Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinformatics (Oxford, England), 35(9), 1613-1614.

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.

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].

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.

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.

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.

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.

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.

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.

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.

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.

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].

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.

Martin, B. E., & Brooke, C. B. (2019). Flu Shows the Power of Diversity. Cell, 176(1-2), 9-10.

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.

Kaczmarek, J. L., Liu, X., Charron, C. S., Novotny, J. A., Jeffery, E. H., Seifried, H. E., ... Holscher, H. D. (2019). Broccoli consumption affects the human gastrointestinal microbiota. Journal of Nutritional Biochemistry, 63, 27-34.

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

Blair, B., & Lowe, J. F. (2019). Describing the cull sow market network in the US: A pilot project. Preventive Veterinary Medicine, 162, 107-109.

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.

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.

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.

Wang, Y., Araud, E., Shisler, J. L., Nguyen, T. H., & Yuan, B. (2019). Influence of algal organic matter on MS2 bacteriophage inactivation by ultraviolet irradiation at 220 nm and 254 nm. Chemosphere, 214, 195-202.

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.

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].

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.

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.

Mei, R., Nobu, M. K., Narihiro, T., Yu, J., Sathyagal, A., Willman, E., & Liu, W-T. (2018). Novel Geobacter species and diverse methanogens contribute to enhanced methane production in media-added methanogenic reactors. Water Research, 147, 403-412.

Surya, A., Liu, X., & Miller, M. J. (2018). Glutathione Utilization in Lactobacillus fermentum CECT 5716. Journal of Agricultural and Food Chemistry, 66(48), 12651-12656.

Yeoman, C. J., Ishaq, S. L., Bichi, E., Olivo, S. K., Lowe, J. F., & Aldridge, B. M. (2018). Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract. Scientific Reports, 8(1), [3197].

Narihiro, T., Nobu, M. K., Bocher, B. T. W., Mei, R., & Liu, W-T. (2018). Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environmental Microbiology Reports, 10(6), 673-685.

Sun, P. P., Araud, E. M., Huang, C., Shen, Y., Monroy, G. L., Zhong, S., ... Nguyen, T. H. (2018). Disintegration of simulated drinking water biofilms with arrays of microchannel plasma jets. npj Biofilms and Microbiomes, 4(1), [24].

Shen, Y., Huang, P. C., Huang, C., Sun, P., Monroy, G. L., Wu, W., ... Nguyen, T. H. (2018). Effect of divalent ions and a polyphosphate on composition, structure, and stiffness of simulated drinking water biofilms. npj Biofilms and Microbiomes, 4(1), [15].

Chen, K. L. A., Liu, X., Zhao, Y. C., Hieronymi, K., Rossi, G., Auvil, L. S., ... Madak-Erdogan, Z. (2018). Long-Term Administration of Conjugated Estrogen and Bazedoxifene Decreased Murine Fecal β-Glucuronidase Activity Without Impacting Overall Microbiome Community. Scientific Reports, 8(1), [8166].

Hidalgo-Ahumada, C. A. P., Nobu, M. K., Narihiro, T., Tamaki, H., Liu, W-T., Kamagata, Y., ... Sousa, D. Z. (2018). Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism. Environmental Microbiology, 20(12), 4503-4511.

Zhang, C., Phillips, A. P. R., Wipfler, R. L., Olsen, G. J., & Whitaker, R. (2018). The essential genome of the crenarchaeal model Sulfolobus islandicus. Nature communications, 9(1), [4908].

Diefenbacher, M., Sun, J., & Brooke, C. B. (2018). The parts are greater than the whole: the role of semi-infectious particles in influenza A virus biology. Current Opinion in Virology, 33, 42-46.

Neu, L., Bänziger, C., Proctor, C. R., Zhang, Y., Liu, W-T., & Hammes, F. (2018). Ugly ducklings - The dark side of plastic materials in contact with potable water. npj Biofilms and Microbiomes, 4(1), [7].

Gardner, A. M., Muturi, E. J., & Allan, B. F. (2018). Discovery and exploitation of a natural ecological trap for a mosquito disease vector. Proceedings of the Royal Society B: Biological Sciences, 285(1891), [20181962].

Jones, J. M., Heath, K. D., Ferrer, A., Brown, S. P., Canam, T., & Dalling, J. W. (2018). Wood decomposition in aquatic and terrestrial ecosystems in the tropics: Contrasting biotic and abiotic processes. FEMS microbiology ecology, 95(1), [fiy223].

Collins, K., & Warnow, T. (2018). PASTA for proteins. Bioinformatics, 34(22), 3939-3941.

Xu, J., Huang, C., Shi, X., Dong, S., Yuan, B., & Nguyen, T. H. (2018). Role of drinking water biofilms on residual chlorine decay and trihalomethane formation: An experimental and modeling study. Science of the Total Environment, 642, 516-525.

Gallagher, M. E., Brooke, C. B., Ke, R., & Koelle, K. (2018). Causes and Consequences of Spatial Within-Host Viral Spread. Viruses, 10(11).

Molloy, E. K., & Warnow, T. (2018). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge.

Dong, S., Massalha, N., Plewa, M. J., & Nguyen, T. H. (2018). The impact of disinfection Ct values on cytotoxicity of agricultural wastewaters: Ozonation vs. chlorination. Water Research, 144, 482-490.

Sun, J., & Brooke, C. B. (2018). Influenza A Virus Superinfection Potential Is Regulated by Viral Genomic Heterogeneity. mBio, 9(5).

Achermann, S., Falås, P., Joss, A., Mansfeldt, C. B., Men, Y., Vogler, B., & Fenner, K. (2018). Trends in Micropollutant Biotransformation along a Solids Retention Time Gradient. Environmental Science and Technology, 52(20), 11601-11611.

Keesing, F., Ostfeld, R. S., Okanga, S., Huckett, S., Bayles, B. R., Chaplin-Kramer, R., ... Allan, B. F. (2018). Consequences of integrating livestock and wildlife in an African savanna. Nature Sustainability, 1(10), 566-573.

Xing, Y., Yu, Y., & Men, Y. (2018). Emerging investigators series: Occurrence and fate of emerging organic contaminants in wastewater treatment plants with an enhanced nitrification step. Environmental Science: Water Research and Technology, 4(10), 1412-1426.

Zealand, A. M., Mei, R., Papachristodoulou, P., Roskilly, A. P., Liu, W-T., & Graham, D. W. (2018). Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure. Applied Microbiology and Biotechnology, 102(19), 8599-8612.

Holle, M. J., Ibarra-Sánchez, L. A., Liu, X., Stasiewicz, M. J., & Miller, M. J. (2018). Microbial analysis of commercially available US Queso Fresco. Journal of Dairy Science, 101(9), 7736-7745.

Shocket, M. S., Vergara, D., Sickbert, A. J., Walsman, J. M., Strauss, A. T., Hite, J. L., ... Hall, S. R. (2018). Parasite rearing and infection temperatures jointly influence disease transmission and shape seasonality of epidemics. Ecology, 99(9), 1975-1987.

Yu, Y., Han, P., Zhou, L. J., Li, Z. L., Wagner, M., & Men, Y. (2018). Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture. Environmental Science and Technology, 52(16), 9196-9205.

Pattabiraman, S., & Warnow, T. (2018). Are Profile Hidden Markov Models Identifiable? In ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 448-456). (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery, Inc.

Khan, R., Nguyen, T. H., Shisler, J. L., Lin, L. S., Jutla, A., & Colwell, R. (2018). Evaluation of risk of cholera after a natural disaster: Lessons learned from the 2015 Nepal earthquake. Journal of Water Resources Planning and Management, 144(8), [04018044].

Maradiaga, N., Aldridge, B. M., Zeineldin, M., & Lowe, J. F. (2018). Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model. Microbial Pathogenesis, 121, 27-39.

Zeineldin, M., Aldridge, B. M., Blair, B., Kancer, K., & Lowe, J. F. (2018). Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration. Microbial Pathogenesis, 121, 210-217.

Zhang, Q., Rao, S., & Warnow, T. (2018). New absolute fast converging phylogeny estimation methods with improved scalability and accuracy. In L. Parida, & E. Ukkonen (Eds.), 18th International Workshop on Algorithms in Bioinformatics, WABI 2018 [8] (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 113). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing.

Nelson, K. L., Boehm, A. B., Davies-Colley, R. J., Dodd, M. C., Kohn, T., Linden, K. G., ... Zepp, R. G. (2018). Sunlight-mediated inactivation of health-relevant microorganisms in water: a review of mechanisms and modeling approaches. Environmental Science: Processes and Impacts, 20(8), 1089-1122.

Josek, T., Walden, K. K. O., Allan, B. F., Alleyne, M., & Robertson, H. M. (2018). A foreleg transcriptome for Ixodes scapularis ticks: Candidates for chemoreceptors and binding proteins that might be expressed in the sensory Haller's organ. Ticks and Tick-borne Diseases, 9(5), 1317-1327.

Liu, G., Zhang, Y., van der Mark, E., Magic-Knezev, A., Pinto, A., van den Bogert, B., ... Medema, G. (2018). Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints. Water Research, 138, 86-96.

Borkenhagen, L. K., Mallinson, K. A., Tsao, R. W., Ha, S. J., Lim, W. H., Toh, T. H., ... Gray, G. C. (2018). Surveillance for respiratory and diarrheal pathogens at the human-pig interface in Sarawak, Malaysia. PloS one, 13(7), [e0201295].

Vachaspati, P., & Warnow, T. (2018). SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Molecular Phylogenetics and Evolution, 124, 122-136.

Halsey, S. J., Allan, B. F., & Miller, J. R. (2018). The role of Ixodes scapularis, Borrelia burgdorferi and wildlife hosts in Lyme disease prevalence: A quantitative review. Ticks and Tick-borne Diseases, 9(5), 1103-1114.

Vlčková, K., Pafčo, B., Petrželková, K. J., Modrý, D., Todd, A., Yeoman, C. J., ... Gomez, A. (2018). Relationships between gastrointestinal parasite infections and the fecal microbiome in free-ranging western lowland gorillas. Frontiers in Microbiology, 9(JUN), [1202].

Wang, Y., Jeffery, E. H., Miller, M. J., Wallig, M. A., & Wu, Y. (2018). Lightly cooked broccoli is as effective as raw broccoli in mitigating dextran sulfate sodium-induced colitis in mice. Nutrients, 10(6), [748].

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.

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.

Dong, S., Li, J., Kim, M. H., Cho, J., Park, S. J., Nguyen, T. H., & Eden, J. G. (2018). Deactivation of Legionella Pneumophila in municipal wastewater by ozone generated in arrays of microchannel plasmas. Journal of Physics D: Applied Physics, 51(25), [255501].

Ling, F., Whitaker, R., LeChevallier, M. W., & Liu, W-T. (2018). Drinking water microbiome assembly induced by water stagnation. ISME Journal, 12(6), 1520-1531.

Kosik, I., Ince, W. L., Gentles, L. E., Oler, A. J., Kosikova, M., Angel, M., ... Yewdell, J. W. (2018). Erratum: Correction: Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs (PLoS pathogens (2018) 14 1 (e1006796)). PLoS Pathogens, 14(6), e1007141.

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.

Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A., Blekhman, R., ... Johnson, T. J. (2018). The gut microbiome of nonhuman primates: Lessons in ecology and evolution. American journal of primatology, 80(6), [e22867].

Kim, J. S., Daum, M. A., Jin, Y-S., & Miller, M. J. (2018). Yeast derived lysA2 can control bacterial contamination in ethanol fermentation. Viruses, 10(6), [281].

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252].

Nute, M., Chou, J., Molloy, E. K., & Warnow, T. (2018). The performance of coalescent-based species tree estimation methods under models of missing data. BMC genomics, 19, [286].

Josek, T., Allan, B. F., & Alleyne, M. (2018). Morphometric Analysis of Chemoreception Organ in Male and Female Ticks (Acari: Ixodidae). Journal of medical entomology, 55(3), 547-552.

Luo, J., Han, L., Liu, L., Gao, L., Xue, B., Wang, Y., ... Peng, X. (2018). Catechin supplemented in a FOS diet induces weight loss by altering cecal microbiota and gene expression of colonic epithelial cells. Food and Function, 9(5), 2962-2969.

Zeineldin, M., Aldridge, B. M., Blair, B., Kancer, K., & Lowe, J. F. (2018). Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs. Microbial Pathogenesis, 118, 220-229.

Strauss, A. T., Bowling, A. M., Duffy, M. A., Caceres, C. E., & Hall, S. R. (2018). Linking host traits, interactions with competitors and disease: Mechanistic foundations for disease dilution. Functional Ecology, 32(5), 1271-1279.

Megahed, A., Aldridge, B. M., & Lowe, J. F. (2018). The microbial killing capacity of aqueous and gaseous ozone on different surfaces contaminated with dairy cattle manure. PloS one, 13(5), [e0196555].

Reznikov, E. A., Comstock, S. S., Hoeflinger, J. L., Wang, M., Miller, M. J., & Donovan, S. M. (2018). Dietary bovine Lactoferrin reduces Staphylococcus aureus in the tissues and modulates the immune response in piglets systemically infected with S. aureus. Current Developments in Nutrition, 2(4), [nzy001].

Liang, X., Lu, N., Chang, L. C., Nguyen, T. H., & Massoudieh, A. (2018). Evaluation of bacterial run and tumble motility parameters through trajectory analysis. Journal of Contaminant Hydrology, 211, 26-38.

Grenz, J. R., Chubiz, J. E. C., Thaprawat, P., & Slauch, J. M. (2018). HilE regulates HilD by blocking DNA binding in Salmonella enterica serovar Typhimurium. Journal of bacteriology, 200(8), [e00750-17].

Shocket, M. S., Strauss, A. T., Hite, J. L., Šljivar, M., Civitello, D. J., Duffy, M. A., ... Hall, S. R. (2018). Temperature drives epidemics in a zooplankton-fungus disease system: A trait-driven approach points to transmission via host foraging. American Naturalist, 191(4), 435-451.

Wang, Q., Tan, G. Y. A., Azari, M., Huang, X., Denecke, M., Men, Y., ... Lee, P. H. (2018). Insights into the roles of anammox bacteria in post-treatment of anaerobically-treated sewage. Critical Reviews in Environmental Science and Technology, 48(6), 655-684.

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2018). OCTAL: Optimal Completion of gene trees in polynomial time. Algorithms for Molecular Biology, 13(1), [6].

Massalha, N., Dong, S., Plewa, M. J., Borisover, M., & Nguyen, T. H. (2018). Spectroscopic Indicators for Cytotoxicity of Chlorinated and Ozonated Effluents from Wastewater Stabilization Ponds and Activated Sludge. Environmental Science and Technology, 52(5), 3167-3174.

Ferrando, D., Toubiana, D., Kandiyote, N. S., Nguyen, T. H., Nejidat, A., & Herzberg, M. (2018). Ambivalent role of calcium in the viscoelastic properties of extracellular polymeric substances and the consequent fouling of reverse osmosis membranes. Desalination, 429, 12-19.

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., ... Baker, W. J. (2018). A roadmap for global synthesis of the plant tree of life. American journal of botany, 105(3), 614-622.

Keesing, F., Ostfeld, R. S., Young, T. P., & Allan, B. F. (2018). Cattle and rainfall affect tick abundance in central Kenya. Parasitology, 145(3), 345-354.

Terhorst, C. P., Zee, P. C., Heath, K. D., Miller, T. E., Pastore, A. I., Patel, S., ... Walsh, M. R. (2018). Evolution in a community context: Trait responses to multiple species interactions. American Naturalist, 191(3), 368-380.

Ossler, J. N., & Heath, K. D. (2018). Shared genes but not shared genetic variation: Legume colonization by two belowground symbionts. American Naturalist, 191(3), 395-406.

Raulo, A., Ruokolainen, L., Lane, A., Amato, K., Knight, R., Leigh, S., ... Tecot, S. R. (2018). Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. Journal of Animal Ecology, 87(2), 388-399.

Molloy, E. K., & Warnow, T. (2018). To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods. Systematic biology, 67(2), 285-303.

Fang, T., Cui, Q., Huang, Y., Dong, P., Wang, H., Liu, W-T., & Ye, Q. (2018). Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: Implications for water quality management. Science of the Total Environment, 613-614, 428-438.

Zeineldin, M., Aldridge, B. M., & Lowe, J. F. (2018). Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea. Microbial Pathogenesis, 115, 123-130.

Stewart, T. E., Torchin, M. E., & Caceres, C. E. (2018). Invisible Parasites and Their Implications for Coexisting Water Fleas. Journal of Parasitology, 104(1), 101-105.

Mulder, N., Schwartz, R., Brazas, M. D., Brooksbank, C., Gaeta, B., Morgan, S. L., ... Welch, L. (2018). The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS computational biology, 14(2), [e1005772].

Bayzid, M. S., & Warnow, T. (2018). Gene tree parsimony for incomplete gene trees: Addressing true biological loss. Algorithms for Molecular Biology, 13(1), [1].

Updyke, E. A., & Allan, B. F. (2018). An experimental evaluation of cross-vane PanelTraps for the collection of SylvaticTriatomines (Hemiptera: Reduviidae). Journal of medical entomology, 55(2), 485-489.

Vlčková, K., Shutt-Phillip, K., Heisterman, M., Pafčo, B., Petrželkov, K. J., Todd, A., ... Gomez, A. (2018). Impact of stress on the gut microbiome of free-ranging western lowland gorillas. Microbiology (United Kingdom), 164(1), 40-44. [000587].

Kosik, I., Ince, W. L., Gentles, L. E., Oler, A. J., Kosikova, M., Angel, M., ... Yewdell, J. W. (2018). Influenza A virus hemagglutinin glycosylation compensates for antibody escape fitness costs. PLoS pathogens, 14(1), [e1006796].

Oh, S., Hammes, F., & Liu, W-T. (2018). Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. Water Research, 128, 278-285.

Zhang, C., & Whitaker, R. (2018). Microhomology-mediated high-throughput gene inactivation strategy for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Applied and environmental microbiology, 84(1), [e02167-17].

Molloy, E. K., & Warnow, T. (2018). NJMerge: A Generic technique for scaling phylogeny estimation methods and its application to species trees. In A. Ouangraoua, & M. Blanchette (Eds.), Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Proceedings (pp. 260-276). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11183 LNBI). Springer-Verlag.

Johnson, K. P., Nguyen, N. P., Sweet, A. D., Boyd, B. M., Warnow, T., & Allen, J. M. (2018). Simultaneous radiation of bird and mammal lice following the K-Pg boundary. Biology Letters, 14(5), [20180141].

Stewart Merrill, T. E., & Caceres, C. E. (Accepted/In press). Within-host complexity of a plankton-parasite interaction. Ecology.