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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

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

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

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

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

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

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, 275-287. https://doi.org/10.1016/j.watres.2019.02.020

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]. 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

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]. https://doi.org/10.1371/journal.pone.0217428

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 (Oxford, England), 35(9), 1613-1614. https://doi.org/10.1093/bioinformatics/bty833

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

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

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

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

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

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

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

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. https://doi.org/10.1016/j.jnutbio.2018.09.015

Zeineldin, M., Lowe, J. F., & Aldridge, B. M. (2019). Contribution of the Mucosal Microbiota to Bovine Respiratory Health. Trends in Microbiology. https://doi.org/10.1016/j.tim.2019.04.005

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

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

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

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. https://doi.org/10.1016/j.chemosphere.2018.09.065

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

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

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

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

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. https://doi.org/10.1016/j.watres.2018.10.026

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. https://doi.org/10.1021/acs.jafc.8b06136

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]. https://doi.org/10.1038/s41598-018-21440-8

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. https://doi.org/10.1111/1758-2229.12689

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]. https://doi.org/10.1038/s41522-018-0063-4

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]. https://doi.org/10.1038/s41522-018-0058-1

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]. https://doi.org/10.1038/s41598-018-26506-1

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. https://doi.org/10.1111/1462-2920.14388

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]. https://doi.org/10.1038/s41467-018-07379-4

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. https://doi.org/10.1016/j.coviro.2018.07.002

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]. https://doi.org/10.1038/s41522-018-0050-9

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]. https://doi.org/10.1098/rspb.2018.1962

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]. https://doi.org/10.1093/femsec/fiy223

Collins, K., & Warnow, T. (2018). PASTA for proteins. Bioinformatics, 34(22), 3939-3941. https://doi.org/10.1093/bioinformatics/bty495

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. https://doi.org/10.1016/j.scitotenv.2018.05.363

Gallagher, M. E., Brooke, C. B., Ke, R., & Koelle, K. (2018). Causes and Consequences of Spatial Within-Host Viral Spread. Viruses, 10(11). https://doi.org/10.3390/v10110627

Molloy, E. K., & Warnow, T. (2018). Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. https://doi.org/10.1101/469130

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. https://doi.org/10.1016/j.watres.2018.07.065

Sun, J., & Brooke, C. B. (2018). Influenza A Virus Superinfection Potential Is Regulated by Viral Genomic Heterogeneity. mBio, 9(5). https://doi.org/10.1128/mBio.01761-18

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. https://doi.org/10.1021/acs.est.8b02763

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. https://doi.org/10.1038/s41893-018-0149-2

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. https://doi.org/10.1039/c8ew00278a

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. https://doi.org/10.1007/s00253-018-9243-7

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. https://doi.org/10.3168/jds.2017-14037

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. https://doi.org/10.1002/ecy.2430

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. https://doi.org/10.1021/acs.est.8b02801

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. https://doi.org/10.1145/3233547.3233563

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]. https://doi.org/10.1061/(ASCE)WR.1943-5452.0000929

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. https://doi.org/10.1016/j.micpath.2018.05.007

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. https://doi.org/10.1016/j.micpath.2018.05.028

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. https://doi.org/10.4230/LIPIcs.WABI.2018.8

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. https://doi.org/10.1039/c8em00047f

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. https://doi.org/10.1016/j.ttbdis.2018.05.013

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. https://doi.org/10.1016/j.watres.2018.03.043

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]. https://doi.org/10.1371/journal.pone.0201295

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. https://doi.org/10.1016/j.ympev.2018.03.006

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. https://doi.org/10.1016/j.ttbdis.2018.04.006

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]. https://doi.org/10.3389/fmicb.2018.01202

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]. https://doi.org/10.3390/nu10060748

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. https://doi.org/10.1016/j.fm.2017.11.013

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. https://doi.org/10.1038/s41396-018-0071-7

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]. https://doi.org/10.1088/1361-6463/aac379

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. https://doi.org/10.1038/s41396-018-0101-5

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. https://doi.org/10.1371/journal.ppat.1007141

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. https://doi.org/10.1016/j.compenvurbsys.2018.05.010

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]. https://doi.org/10.1002/ajp.22867

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]. https://doi.org/10.3390/v10060281

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252]. https://doi.org/10.1186/s12864-018-4621-1

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]. https://doi.org/10.1186/s12864-018-4619-8

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. https://doi.org/10.1093/jme/tjx232

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. https://doi.org/10.1039/c8fo00035b

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. https://doi.org/10.1016/j.micpath.2018.03.035

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. https://doi.org/10.1111/1365-2435.13066

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]. https://doi.org/10.1371/journal.pone.0196555

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. https://doi.org/10.1016/j.jconhyd.2018.03.002

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]. https://doi.org/10.1128/JB.00750-17

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. https://doi.org/10.1086/696096

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. https://doi.org/10.1080/10643389.2018.1474679

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]. https://doi.org/10.1186/s13015-018-0124-5

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. https://doi.org/10.1021/acs.est.7b05510

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. https://doi.org/10.1016/j.desal.2017.12.006

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. https://doi.org/10.1002/ajb2.1041

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. https://doi.org/10.1017/S003118201700155X

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. https://doi.org/10.1086/695835

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. https://doi.org/10.1086/695829

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. https://doi.org/10.1111/1365-2656.12781

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. https://doi.org/10.1093/sysbio/syx077

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. https://doi.org/10.1016/j.scitotenv.2017.09.008

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. https://doi.org/10.1016/j.micpath.2017.12.059

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. https://doi.org/10.1645/17-112

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]. https://doi.org/10.1371/journal.pcbi.1005772

Bayzid, M. S., & Warnow, T. (2018). Gene tree parsimony for incomplete gene trees: Addressing true biological loss. Algorithms for Molecular Biology, 13(1), [1]. https://doi.org/10.1186/s13015-017-0120-1

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. https://doi.org/10.1093/jme/tjx224

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]. https://doi.org/10.1099/mic.0.000587

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]. https://doi.org/10.1371/journal.ppat.1006796

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. https://doi.org/10.1016/j.watres.2017.10.054

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]. https://doi.org/10.1128/AEM.02167-17

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. https://doi.org/10.1007/978-3-030-00834-5_15

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]. https://doi.org/10.1098/rsbl.2018.0141

Stewart Merrill, T. E., & Caceres, C. E. (Accepted/In press). Within-host complexity of a plankton-parasite interaction. Ecology. https://doi.org/10.1002/ecy.2483