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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Bauza, V., Ocharo, R. M., Nguyen, T. H., & Guest, J. S. (2017). Soil ingestion is associated with child diarrhea in an urban slum of Nairobi, Kenya. American Journal of Tropical Medicine and Hygiene, 96(3), 569-575. DOI: 10.4269/ajtmh.16-0543
 
Mao, W., Schuler, M. A., & Berenbaum, M. R. (2017). Disruption of quercetin metabolism by fungicide affects energy production in honey bees (Apis mellifera). Proceedings of the National Academy of Sciences of the United States of America, 114(10), 2538-2543. DOI: 10.1073/pnas.1614864114
 
Liao, L. H., Wu, W. Y., & Berenbaum, M. R. (2017). Impacts of dietary phytochemicals in the presence and absence of pesticides on longevity of honey bees (Apis mellifera). Insects, 8(1), [22]. DOI: 10.3390/insects8010022
 
Lu, R., Zhang, C., Piatkovsky, M., Ulbricht, M., Herzberg, M., & Nguyen, T. H. (2017). Improvement of virus removal using ultrafiltration membranes modified with grafted zwitterionic polymer hydrogels. Water Research, 116, 86-94. DOI: 10.1016/j.watres.2017.03.023
 
Nute, M., & Warnow, T. (2016). Scaling statistical multiple sequence alignment to large datasets. BMC Genomics, 17, [764]. DOI: 10.1186/s12864-016-3101-8
 
Dong, S., Li, J., Kim, M. H., Park, S. J., Eden, J. G., Guest, J. S., & Nguyen, T. H. (2017). Human health trade-offs in the disinfection of wastewater for landscape irrigation: Microplasma ozonation: Vs. chlorination. Environmental Science: Water Research and Technology, 3(1), 106-118. DOI: 10.1039/c6ew00235h
 
Hansen, T. A., Mollerup, S., Nguyen, N. P., White, N. E., Coghlan, M., Alquezar-Planas, D. E., ... Hansen, A. J. (2016). High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerging microbes & infections, 5(8), e90. DOI: 10.1038/emi.2016.90
 
Amato, K. R., van Belle, S., Di Fiore, A., Estrada, A., Stumpf, R., White, B., ... Leigh, S. R. (2017). Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate. Microbial Ecology, 1-9. DOI: 10.1007/s00248-017-0938-6
 
Bagchi, V. A., Siegel, J. P., Demkovich, M. R., Zehr, L. N., & Berenbaum, M. R. (2016). Impact of Pesticide Resistance on Toxicity and Tolerance of Hostplant Phytochemicals in Amyelois Transitella (Lepidoptera: Pyralidae). Journal of insect science (Online), 16(1). DOI: 10.1093/jisesa/iew063
 
Uricchio, L. H., Warnow, T., & Rosenberg, N. A. (2016). An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees. BMC Bioinformatics, 17, [417]. DOI: 10.1186/s12859-016-1266-4
 
Randrianandrasana, M., Wu, W. Y., Carney, D. A., Wagoner Johnson, A. J., & Berenbaum, M. R. (2017). Structural and Mechanical Properties of Cocoons of Antherina suraka (Saturniidae, Lepidoptera), an Endemic Species Used for Silk Production in Madagascar. Journal of insect science (Online), 17(1). DOI: 10.1093/jisesa/iew112
 
Wang, H., Li, M., Brockman, K., & Nguyen, T. H. (2016). Reduction of MS2 bacteriophage and rotavirus in biosand filters. Environmental Science: Water Research and Technology, 2(3), 483-491. DOI: 10.1039/c5ew00297d
 
Tarver, J. E., Dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O'Reilly, J. E., ... Pisani, D. (2016). The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biology and Evolution, 8(2), 330-344. DOI: 10.1093/gbe/evv261
 
Nguyen, N. P., Nute, M., Mirarab, S., & Warnow, T. (2016). HIPPI: Highly accurate protein family classification with ensembles of HMMs. BMC Genomics, 17, [765]. DOI: 10.1186/s12864-016-3097-0
 
Polk, J. D., Stumpf, R. M., & Rosengren, K. S. (2017). Limb dominance, foot orientation and functional asymmetry during walking gait. Gait and Posture, 52, 140-146. DOI: 10.1016/j.gaitpost.2016.11.028
 
Dong, S., Lu, J., Plewa, M. J., & Nguyen, T. H. (2016). Comparative Mammalian Cell Cytotoxicity of Wastewaters for Agricultural Reuse after Ozonation. Environmental Science and Technology, 50(21), 11752-11759. DOI: 10.1021/acs.est.6b04796
 
Fuzawa, M., Ku, K. M., Palma-Salgado, S. P., Nagasaka, K., Feng, H., Juvik, J. A., ... Nguyen, T. H. (2016). Effect of leaf surface chemical properties on efficacy of sanitizer for rotavirus inactivation. Applied and Environmental Microbiology, 82(20), 6214-6222. DOI: 10.1128/AEM.01778-16
 
Feng, Z., Lu, R., Yuan, B., Zhou, Z., Wu, Q., & Nguyen, T. H. (2016). Influence of solution chemistry on the inactivation of particle-associated viruses by UV irradiation. Colloids and Surfaces B: Biointerfaces, 148, 622-628. DOI: 10.1016/j.colsurfb.2016.09.025
 
Berenbaum, M. R. (2016). Speaking of insects⋯. Science, 353(6306), 1343. DOI: 10.1126/science.aaj2166
 
Liang, X., Chang, L. C., Massoudieh, A., Lu, N., & Nguyen, T. H. (2016). Quantitative inference of bacterial motility behavior. In Proceedings - 2015 International Conference on Computational Science and Computational Intelligence, CSCI 2015 (pp. 368-373). [7424119] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/CSCI.2015.97
 
Mirarab, S., Bayzid, M. S., & Warnow, T. (2016). Evaluating summarymethods for multilocus species tree estimation in the presence of incomplete lineage sorting. Systematic Biology, 65(3), 366-380. DOI: 10.1093/sysbio/syu063
 
Bennett, G., Malone, M., Sauther, M. L., Cuozzo, F. P., White, B., Nelson, K. E., ... Amato, K. R. (2016). Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta). American Journal of Primatology, 78(8), 883-892. DOI: 10.1002/ajp.22555
 
Whitaker, R. J., & Vanderpool, C. K. (2016). CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done. Cell Host and Microbe, 19(2), 135-137. DOI: 10.1016/j.chom.2016.01.015
 
Welch, L., Brooksbank, C., Schwartz, R., Morgan, S. L., Gaeta, B., Kilpatrick, A. M., ... Warnow, T. (2016). Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee). PLoS Computational Biology, 12(5), [e1004943]. DOI: 10.1371/journal.pcbi.1004943
 
Harrison, T., Dean, C. A. E., Parks, K., & Berenbaum, M. R. (2016). Depressaria depressana (fabricius) (depressariidae), new to the Midwestern USA. Journal of the Lepidopterists' Society, 70(2), 169-173. DOI: 10.18473/lepi.70i2.a15
 
Randrianandrasana, M., Berlocher, S. H., Rougerie, R., & Berenbaum, M. R. (2016). Intraspecific Variation in Antherina suraka (Lepidoptera: Saturniidae), an Endemic Resident of Endangered Forests in Madagascar. Annals of the Entomological Society of America, 109(3), 384-395. DOI: 10.1093/aesa/saw006
 
Stumpf, R. M., Gomez, A., Amato, K. R., Yeoman, C. J., Polk, J. D., Wilson, B. A., ... Leigh, S. R. (2016). Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biological Conservation, 199, 56-66. DOI: 10.1016/j.biocon.2016.03.035
 
Zhang, C., She, Q., Bi, H., & Whitaker, R. J. (2016). The apt/6-methylpurine counterselection system and its applications in genetic studies of the hyperthermophilic archaeon Sulfolobus islandicus. Applied and Environmental Microbiology, 82(10), 3070-3081. DOI: 10.1128/AEM.00455-16
 
Ampt, E. A., Bush, D. S., Siegel, J. P., & Berenbaum, M. R. (2016). Larval preference and performance of amyelois transitella (navel orangeworm, lepidoptera: Pyralidae) in relation to the fungus aspergillus flavus. Environmental Entomology, 45(1), 155-162. DOI: 10.1093/ee/nvv160
 
Vlčková, K., Gomez, A., Petrželková, K. J., Whittier, C. A., Todd, A. F., Yeoman, C. J., ... Leigh, S. R. (2016). Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla). Microbial Ecology, 72(4), 943-954. DOI: 10.1007/s00248-016-0745-5
 
Gomez, A., Petrzelkova, K. J., Burns, M. B., Yeoman, C. J., Amato, K. R., Vlckova, K., ... Blekhman, R. (2016). Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Reports, 14(9), 2142-2153. DOI: 10.1016/j.celrep.2016.02.013
 
Amato, K. R., Martinez-Mota, R., Righini, N., Raguet-Schofield, M., Corcione, F. P., Marini, E., ... Leigh, S. R. (2016). Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species. Oecologia, 180(3), 717-733. DOI: 10.1007/s00442-015-3507-z
 
Shen, Y., Huang, C., Monroy, G. L., Janjaroen, D., Derlon, N., Lin, J., ... Nguyen, T. H. (2016). Response of Simulated Drinking Water Biofilm Mechanical and Structural Properties to Long-Term Disinfectant Exposure. Environmental Science and Technology, 50(4), 1779-1787. DOI: 10.1021/acs.est.5b04653
 
Gomez, A., Rothman, J. M., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Umaña, J. D., ... Leigh, S. R. (2016). Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME Journal, 10(2), 514-526. DOI: 10.1038/ismej.2015.146
 
Berenbaum, M. R. (2016). Does the Honey Bee "risk Cup" Runneth Over? Estimating Aggregate Exposures for Assessing Pesticide Risks to Honey Bees in Agroecosystems. Journal of Agricultural and Food Chemistry, 64(1), 13-20. DOI: 10.1021/acs.jafc.5b01067
 
Lu, R., Li, Q., & Nguyen, T. H. (2016). Random sequential adsorption of human adenovirus 2 onto polyvinylidene fluoride surface influenced by extracellular polymeric substances. Journal of Colloid and Interface Science, 466, 120-127. DOI: 10.1016/j.jcis.2015.12.017
 
Lu, R., Li, Q., Yin, Z., Xagoraraki, I., Tarabara, V. V., & Nguyen, T. H. (2016). Effect of virus influent concentration on its removal by microfiltration: The case of human adenovirus 2. Journal of Membrane Science, 497, 120-127. DOI: 10.1016/j.memsci.2015.08.065