Skip to main content

Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Yeoman, C. J., Ishaq, S. L., Bichi, E., Olivo, S. K., Lowe, J., & 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]. DOI: 10.1038/s41598-018-21440-8

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]. DOI: 10.1038/s41598-018-26506-1

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]. DOI: 10.1038/s41522-018-0050-9

Khan, R., Nguyen, T. H., Shisler, J., 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]. DOI: 10.1061/(ASCE)WR.1943-5452.0000929

Maradiaga, N., Aldridge, B., Zeineldin, M., & Lowe, J. (2018). Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model. Microbial Pathogenesis, 121, 27-39. DOI: 10.1016/j.micpath.2018.05.007

Zeineldin, M., Aldridge, B., Blair, B., Kancer, K., & Lowe, J. (2018). Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration. Microbial Pathogenesis, 121, 210-217. DOI: 10.1016/j.micpath.2018.05.028

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. DOI: 10.1016/j.watres.2018.03.043

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. DOI: 10.1016/

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. DOI: 10.1038/s41396-018-0101-5

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]. DOI: 10.3390/v10060281

Vachaspati, P., & Warnow, T. (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC genomics, 19, [252]. DOI: 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]. DOI: 10.1186/s12864-018-4619-8

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. DOI: 10.1039/c8fo00035b

Zeineldin, M., Aldridge, B., Blair, B., Kancer, K., & Lowe, J. (2018). Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs. Microbial Pathogenesis, 118, 220-229. DOI: 10.1016/j.micpath.2018.03.035

Strauss, A. T., Bowling, A. M., Duffy, M. A., Cáceres, 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. DOI: 10.1111/1365-2435.13066

Farrell, A. K., Slatcher, R. B., Tobin, E. T., Imami, L., Wildman, D. E., Luca, F., & Zilioli, S. (2018). Socioeconomic status, family negative emotional climate, and anti-inflammatory gene expression among youth with asthma. Psychoneuroendocrinology, 91, 62-67. DOI: 10.1016/j.psyneuen.2018.02.011

Megahed, A., Aldridge, B., & Lowe, J. (2018). The microbial killing capacity of aqueous and gaseous ozone on different surfaces contaminated with dairy cattle manure. PloS one, 13(5), [e0196555]. DOI: 10.1371/journal.pone.0196555

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. DOI: 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]. DOI: 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. DOI: 10.1086/696096

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]. DOI: 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. DOI: 10.1021/acs.est.7b05510

Duncan, L. E., Ratanatharathorn, A., Aiello, A. E., Almli, L. M., Amstadter, A. B., Ashley-Koch, A. E., ... Koenen, K. C. (2018). Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability. Molecular Psychiatry, 23(3), 666-673. DOI: 10.1038/mp.2017.77

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. DOI: 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. DOI: 10.1093/sysbio/syx077

Munson-McGee, J. H., Peng, S., Dewerff, S., Stepanauskas, R., Whitaker, R. J., Weitz, J. S., & Young, M. J. (Accepted/In press). A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments. ISME Journal, 1-9. DOI: 10.1038/s41396-018-0071-7

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. DOI: 10.1016/j.scitotenv.2017.09.008

Zeineldin, M., Aldridge, B., & Lowe, J. (2018). Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea. Microbial Pathogenesis, 115, 123-130. DOI: 10.1016/j.micpath.2017.12.059

Stewart, T. E., Torchin, M. E., & Cáceres, C. E. (2018). Invisible Parasites and Their Implications for Coexisting Water Fleas. Journal of Parasitology, 104(1), 101-105. DOI: 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]. DOI: 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]. DOI: 10.1186/s13015-017-0120-1

Josek, T., Walden, K. K. O., Allan, B. F., Alleyne, M., & Robertson, H. M. (Accepted/In press). 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. DOI: 10.1016/j.ttbdis.2018.05.013

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. DOI: 10.1093/jme/tjx224

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., ... Baker, W. J. (Accepted/In press). A roadmap for global synthesis of the plant tree of life. American journal of botany. DOI: 10.1002/ajb2.1041

Armstrong, D., & Wildman, D. E. (2018). Extracellular vesicles and the promise of continuous liquid biopsies. Journal of Pathology and Translational Medicine, 52(1), 1-8. DOI: 10.4132/jptm.2017.05.21

Bustamante, A. C., Aiello, A. E., Guffanti, G., Galea, S., Wildman, D. E., & Uddin, M. (2018). FKBP5 DNA methylation does not mediate the association between childhood maltreatment and depression symptom severity in the Detroit Neighborhood Health Study. Journal of Psychiatric Research, 96, 39-48. DOI: 10.1016/j.jpsychires.2017.09.016

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]. DOI: 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]. DOI: 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. DOI: 10.1016/j.watres.2017.10.054

Zhang, C., & Whitaker, R. J. (2018). Microhomology-mediated high-throughput gene inactivation strategy for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Applied and Environmental Microbiology, 84(1), [e02167-17]. DOI: 10.1128/AEM.02167-17

Halsey, S. J., Allan, B. F., & Miller, J. R. (Accepted/In press). The role of Ixodes scapularis, Borrelia burgdorferi and wildlife hosts in Lyme disease prevalence: A quantitative review. Ticks and Tick-borne Diseases. DOI: 10.1016/j.ttbdis.2018.04.006


Strauss, A. T., Hite, J. L., Shocket, M. S., Cáceres, C. E., Duffy, M. A., & Hall, S. R. (2017). Rapid evolution rescues hosts from competition and disease but—despite a dilution effect—increases the density of infected hosts. Proceedings of the Royal Society B: Biological Sciences, 284(1868), [20171970]. DOI: 10.1098/rspb.2017.1970

Uprety, S., Hong, P. Y., Sadik, N., Dangol, B., Adhikari, R., Jutla, A., ... Nguyen, T. H. (2017). The effect of the 2015 earthquake on the bacterial community compositions in water in Nepal. Frontiers in Microbiology, 8(DEC), [2380]. DOI: 10.3389/fmicb.2017.02380

Weckle, A., McGowen, M. R., Xing, J., Chen, C., Sterner, K. N., Hou, Z. C., ... Wildman, D. E. (2017). Ancestral resurrection of anthropoid estrogen receptor β demonstrates functional consequences of positive selection. Molecular Phylogenetics and Evolution, 117, 2-9. DOI: 10.1016/j.ympev.2017.09.007

Hawley, A. K., Nobu, M. K., Wright, J. J., Durno, W. E., Morgan-Lang, C., Sage, B., ... Hallam, S. J. (2017). Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nature Communications, 8(1), [1507]. DOI: 10.1038/s41467-017-01376-9

Zimmer, E., & Wildman, D. (2017). Editorial for 25th Anniversary Issue of Molecular Phylogenetics and Evolution. Molecular Phylogenetics and Evolution, 117. DOI: 10.1016/j.ympev.2017.10.024

VanderWaal, K., Gilbertson, M., Okanga, S., Allan, B. F., & Craft, M. E. (2017). Seasonality and pathogen transmission in pastoral cattle contact networks. Royal Society Open Science, 4(12), [170808]. DOI: 10.1098/rsos.170808

for The Psychiatric Genomics Consortium Posttraumatic Stress Disorder Workgroup (2017). A putative causal relationship between genetically determined female body shape and posttraumatic stress disorder. Genome Medicine, 9(1), [99]. DOI: 10.1186/s13073-017-0491-4

Palmer, A. D., & Slauch, J. M. (2017). Mechanisms of Salmonella pathogenesis in animal models. Human and Ecological Risk Assessment, 23(8), 1877-1892. DOI: 10.1080/10807039.2017.1353903

KEESING, F. E. L. I. C. I. A., OSTFELD, R. I. C. H. A. R. D. S., YOUNG, T. R. U. M. A. N. P., & ALLAN, B. R. I. A. N. F. (2017). Cattle and rainfall affect tick abundance in central Kenya. Parasitology, 1-10. DOI: 10.1017/S003118201700155X

Hite, J. L., Penczykowski, R. M., Shocket, M. S., Griebel, K. A., Strauss, A. T., Duffy, M. A., ... Hall, S. R. (2017). Allocation, not male resistance, increases male frequency during epidemics: a case study in facultatively sexual hosts. Ecology, 98(11), 2773-2783. DOI: 10.1002/ecy.1976

Klein, J. A., Grenz, J. R., Slauch, J. M., & Knodler, L. A. (2017). Controlled activity of the Salmonella invasion-associated injectisome reveals its intracellular role in the cytosolic population. mBio, 8(6), [e01931-17]. DOI: 10.1128/mBio.01931-17

Boyd, B. M., Allen, J. M., Nguyen, N. P., Sweet, A. D., Warnow, T., Shapiro, M. D., ... Johnson, K. P. (2017). Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola). Systematic Biology, 66(6), 896-911. DOI: 10.1093/sysbio/syx027

Brooke, C. B. (2017). Population diversity and collective interactions during influenza virus infection. Journal of Virology, 91(22), [e01164-17]. DOI: 10.1128/JVI.01164-17

Matthew, L. E., Piedra, L. M., Wu, C. F., Kramer Diaz, A., Wang, H., Straub, A. P., & Nguyen, T. H. (2017). Social work and engineering: Lessons from a water filtration project in Guatemala. International Social Work, 60(6), 1578-1590. DOI: 10.1177/0020872816655869

Nobu, M. K., Narihiro, T., Liu, M., Kuroda, K., Mei, R., & Liu, W. T. (2017). Thermodynamically diverse syntrophic aromatic compound catabolism. Environmental Microbiology, 19(11), 4576-4586. DOI: 10.1111/1462-2920.13922

Zhang, Y., Kitajima, M., Whittle, A. J., & Liu, W. T. (2017). Benefits of genomic insights and CRISPR-Cas signatures to monitor potential pathogens across drinking water production and distribution systems. Frontiers in Microbiology, 8(OCT). DOI: 10.3389/fmicb.2017.02036

Lau, J. A., Lennon, J. T., & Heath, K. D. (2017). Trees harness the power of microbes to survive climate change. Proceedings of the National Academy of Sciences of the United States of America, 114(42), 11009-11011. DOI: 10.1073/pnas.1715417114

Liu, X., Turchi, B., Mok, K. C., Taga, M. E., & Miller, M. J. (2017). HM2-phage resistant solventogenic Clostridium saccharoperbutylacetonicum N1-4 shows increased exopolysaccharide production. FEMS Microbiology Letters, 364(19), [fnx191]. DOI: 10.1093/femsle/fnx191

Thongaram, T., Hoeflinger, J. L., Chow, J. M., & Miller, M. J. (2017). Human milk oligosaccharide consumption by probiotic and human-associated bifidobacteria and lactobacilli. Journal of Dairy Science, 100(10), 7825-7833. DOI: 10.3168/jds.2017-12753

Oh, S., Yap, G. C., Hong, P. Y., Huang, C. H., Aw, M. M., Shek, L. P. C., ... Lee, B. W. (2017). Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema. PLoS ONE, 12(10), [e0184955]. DOI: 10.1371/journal.pone.0184955

Titcomb, G., Allan, B. F., Ainsworth, T., Henson, L., Hedlund, T., Pringle, R. M., ... Young, H. S. (2017). Interacting effects of wildlife loss and climate on ticks and tick-borne disease. Proceedings of the Royal Society B: Biological Sciences, 284(1862), [20170475]. DOI: 10.1098/rspb.2017.0475

Athreya, A. P., Armstrong, D., Gundling, W., Wildman, D., Kalbarczyk, Z. T., & Iyer, R. K. (2017). Prediction of adenocarcinoma development using game theory. In 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings (pp. 1668-1671). [8037161] Institute of Electrical and Electronics Engineers Inc.. DOI: 10.1109/EMBC.2017.8037161

Zeineldin, M., Lowe, J., de Godoy, M., Maradiaga, N., Ramirez, C., Ghanem, M., ... Aldridge, B. (2017). Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease. Veterinary microbiology, 208, 30-37. DOI: 10.1016/j.vetmic.2017.07.006

Stanton, S. C. E., Zilioli, S., Briskin, J. L., Imami, L., Tobin, E. T., Wildman, D. E., ... Slatcher, R. B. (2017). Mothers’ Attachment is Linked to Their Children’s Anti-Inflammatory Gene Expression via Maternal Warmth. Social Psychological and Personality Science, 8(7), 796-805. DOI: 10.1177/1948550616687125

Allen, J. M., Boyd, B., Nguyen, N. P., Vachaspati, P., Warnow, T., Huang, D. I., ... Johnson, K. P. (2017). Phylogenomics from whole genome sequences using aTRAM. Systematic Biology, 66(5), 786-798. DOI: 10.1093/sysbio/syw105

Armstrong, D. L., McGowen, M. R., Weckle, A., Pantham, P., Caravas, J., Agnew, D., ... Wildman, D. E. (2017). The core transcriptome of mammalian placentas and the divergence of expression with placental shape. Placenta, 57, 71-78. DOI: 10.1016/j.placenta.2017.04.015

Dong, S., Masalha, N., Plewa, M. J., & Nguyen, T. H. (2017). Toxicity of Wastewater with Elevated Bromide and Iodide after Chlorination, Chloramination, or Ozonation Disinfection. Environmental Science and Technology, 51(16), 9297-9304. DOI: 10.1021/acs.est.7b02345

The Genome Standards Consortium (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature biotechnology, 35(8), 725-731. DOI: 10.1038/nbt.3893

Gardner, A. M., Muturi, E. J., Overmier, L. D., & Allan, B. F. (2017). Large-Scale Removal of Invasive Honeysuckle Decreases Mosquito and Avian Host Abundance. EcoHealth, 1-12. DOI: 10.1007/s10393-017-1265-6

Allan, B. F., Tallis, H., Chaplin-Kramer, R., Huckett, S., Kowal, V. A., Musengezi, J., ... Keesing, F. (2017). Can integrating wildlife and livestock enhance ecosystem services in central Kenya? Frontiers in Ecology and the Environment, 15(6), 328-335. DOI: 10.1002/fee.1501

Dong, S., Nguyen, T. H., & Plewa, M. J. (2017). Comparative mammalian cell cytotoxicity of wastewater with elevated bromide and iodide after chlorination, chloramination, or ozonation. Journal of Environmental Sciences, 58, 296-301. DOI: 10.1016/j.jes.2017.03.030

Bayzid, M. S., & Warnow, T. (2017). Gene tree parsimony for incomplete gene trees. In 17th International Workshop on Algorithms in Bioinformatics, WABI 2017 (Vol. 88). [2] Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. DOI: 10.4230/LIPIcs.WABI.2017.2

Zhang, Y., Oh, S., & Liu, W. T. (2017). Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance's perspective. Environmental Microbiology, 19(8), 3163-3174. DOI: 10.1111/1462-2920.13800

Wagner, A., Whitaker, R. J., Krause, D. J., Heilers, J. H., Van Wolferen, M., Van Der Does, C., & Albers, S. V. (2017). Mechanisms of gene flow in archaea. Nature Reviews Microbiology, 15(8), 492-501. DOI: 10.1038/nrmicro.2017.41

Christensen, S., Molloy, E. K., Vachaspati, P., & Warnow, T. (2017). Optimal completion of incomplete gene trees in polynomial time using OCTAL. In 17th International Workshop on Algorithms in Bioinformatics, WABI 2017 (Vol. 88). [27] Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. DOI: 10.4230/LIPIcs.WABI.2017.27

Schieltz, J. M., Okanga, S., Allan, B. F., & Rubenstein, D. I. (2017). GPS tracking cattle as a monitoring tool for conservation and management. African Journal of Range and Forage Science, 34(3), 173-177. DOI: 10.2989/10220119.2017.1387175

Liao, J., Fang, C., Yu, J., Sathyagal, A., Willman, E., & Liu, W. T. (2017). Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics. Applied Microbiology and Biotechnology, 101(14), 5925-5936. DOI: 10.1007/s00253-017-8326-1

Duka, T., Collins, Z., Anderson, S. M., Raghanti, M. A., Ely, J. J., Hof, P. R., ... Sherwood, C. C. (2017). Divergent lactate dehydrogenase isoenzyme profile in cellular compartments of primate forebrain structures. Molecular and Cellular Neuroscience, 82, 137-142. DOI: 10.1016/j.mcn.2017.04.007

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, 74(1), 250-258. DOI: 10.1007/s00248-017-0938-6

Boyd, B. M., Allen, J. M., Nguyen, N. P., Vachaspati, P., Quicksall, Z. S., Warnow, T., ... Reed, D. L. (2017). Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice. Molecular biology and evolution, 34(7), 1743-1757. DOI: 10.1093/molbev/msx117

Zeineldin, M. M., Lowe, J. F., Grimmer, E. D., De Godoy, M. R. C., Ghanem, M. M., Abd El-Raof, Y. M., & Aldridge, B. M. (2017). Relationship between nasopharyngeal and bronchoalveolar microbial communities in clinically healthy feedlot cattle. BMC Microbiology, 17(1), [138]. DOI: 10.1186/s12866-017-1042-2

Campbell, K. M., Kouris, A., England, W., Anderson, R. E., McCleskey, R. B., Nordstrom, D. K., & Whitaker, R. J. (2017). Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs. Environmental Microbiology, 19(6), 2334-2347. DOI: 10.1111/1462-2920.13728

Thongaram, T., Hoeflinger, J. L., Chow, J., & Miller, M. J. (2017). Prebiotic Galactooligosaccharide Metabolism by Probiotic Lactobacilli and Bifidobacteria. Journal of Agricultural and Food Chemistry, 65(20), 4184-4192. DOI: 10.1021/acs.jafc.7b00851

Bautista, M. A., Black, J. A., Youngblut, N. D., & Whitaker, R. J. (2017). Differentiation and structure in Sulfolobus islandicus rod-shaped virus populations. Viruses, 9(5), [120]. DOI: 10.3390/v9050120

Parker, C. M., Miller, J. R., Allan, B. F., & Ginsberg, H. (2017). Avian and habitat characteristics influence tick infestation among birds in Illinois. Journal of Medical Entomology, 54(3), 550-558. DOI: 10.1093/jme/tjw235

Gao, H., Liu, M., Griffin, J. S., Xu, L., Xiang, D., Scherson, Y. D., ... Wells, G. F. (2017). Complete Nutrient Removal Coupled to Nitrous Oxide Production as a Bioenergy Source by Denitrifying Polyphosphate-Accumulating Organisms. Environmental Science and Technology, 51(8), 4531-4540. DOI: 10.1021/acs.est.6b04896

Rushmore, J., Allison, A. B., Edwards, E. E., Bagal, U., Altizer, S., Cranfield, M. R., ... Yabsley, M. J. (2017). Erratum to: Screening wild and semi-free ranging great apes for putative sexually transmitted diseases: Evidence of Trichomonadidae infections ((2015), 10.1002/ajp.22442). American Journal of Primatology, 79(4), 1-2. DOI: 10.1002/ajp.22645

Van Tassell, M. L., Ibarra-Sánchez, L. A., Hoepker, G. P., & Miller, M. J. (2017). Hot topic: Antilisterial activity by endolysin PlyP100 in fresh cheese. Journal of Dairy Science, 100(4), 2482-2487. DOI: 10.3168/jds.2016-11990

Ibarra-Sánchez, L. A., Van Tassell, M. L., & Miller, M. J. (2017). Invited review: Hispanic-style cheeses and their association with Listeria monocytogenes. Journal of Dairy Science, 100(4), 2421-2432. DOI: 10.3168/jds.2016-12116

Men, Y., Yu, K., Bælum, J., Gao, Y., Tremblay, J., Prestat, E., ... Alvarez-Cohen, L. (2017). Metagenomic and metatranscriptomic analyses reveal the structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoidproviding microorganisms under cobalaminlimited conditions. Applied and Environmental Microbiology, 83(8), [e03508-16]. DOI: 10.1128/AEM.03508-16

Liu, X., Wang, Y., Hoeflinger, J. L., Neme, B. P., Jeffery, E. H., & Miller, M. J. (2017). Dietary broccoli alters rat cecal microbiota to improve glucoraphanin hydrolysis to bioactive isothiocyanates. Nutrients, 9(3), [262]. DOI: 10.3390/nu9030262

Boddy, A. M., Harrison, P. W., Montgomery, S. H., Caravas, J. A., Raghanti, M. A., Phillips, K. A., ... Wildman, D. E. (2017). Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates. Genome biology and evolution, 9(3), 700-713. DOI: 10.1093/gbe/evx028

Yang, J., Vittori, N., Wang, W., Shi, Y. C., Hoeflinger, J. L., Miller, M. J., & Pan, Y. (2017). Molecular weight distribution and fermentation of mechanically pre-treated konjac enzymatic hydrolysates. Carbohydrate Polymers, 159, 58-65. DOI: 10.1016/j.carbpol.2016.12.014

Hoeflinger, J. L., & Miller, M. J. (2017). Cronobacter sakazakii ATCC 29544 autoaggregation requires flic flagellation, not motility. Frontiers in Microbiology, 8(FEB), [301]. DOI: 10.3389/fmicb.2017.00301

Shen, Y., Huang, C., Lin, J., Wu, W., Ashbolt, N. J., Liu, W. T., & Nguyen, T. H. (2017). Effect of Disinfectant Exposure on Legionella pneumophila Associated with Simulated Drinking Water Biofilms: Release, Inactivation, and Infectivity. Environmental Science and Technology, 51(4), 2087-2095. DOI: 10.1021/acs.est.6b04754

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

Men, Y., Achermann, S., Helbling, D. E., Johnson, D. R., & Fenner, K. (2017). Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation. Water Research, 109, 217-226. DOI: 10.1016/j.watres.2016.11.048

Hoeflinger, J. L., Hoeflinger, D. E., & Miller, M. J. (2017). A dynamic regression analysis tool for quantitative assessment of bacterial growth written in Python. Journal of Microbiological Methods, 132, 83-85. DOI: 10.1016/j.mimet.2016.11.015

Amarasiri, M., Kitajima, M., Nguyen, T. H., Okabe, S., & Sano, D. (2017). Bacteriophage removal efficiency as a validation and operational monitoring tool for virus reduction in wastewater reclamation: Review. Water Research, 121, 258-269. DOI: 10.1016/j.watres.2017.05.035

Li, C., Ling, F., Zhang, M., Liu, W. T., Li, Y., & Liu, W. (2017). Characterization of bacterial community dynamics in a full-scale drinking water treatment plant. Journal of Environmental Sciences (China), 51, 21-30. DOI: 10.1016/j.jes.2016.05.042

Fenlon, L. A., & Slauch, J. M. (2017). Cytoplasmic copper detoxification in Salmonella can contribute to SodC metalation but is dispensable during systemic infection. Journal of Bacteriology, 199(24), [e00437-17]. DOI: 10.1128/JB.00437-17

Herman, N. A., Li, J., Bedi, R., Turchi, B., Liu, X., Miller, M. J., & Zhang, W. (2017). Development of a high-efficiency transformation method and implementation of rational metabolic engineering for the industrial butanol hyperproducer clostridium saccharoperbutylacetonicum strain N1-4. Applied and Environmental Microbiology, 83(2), [e02942-16]. DOI: 10.1128/AEM.02942-16

Vachaspati, P., & Warnow, T. (2017). Enhancing searches for optimal trees using SIESTA. In Comparative Genomics - 15th International Workshop, RECOMB CG 2017, Proceedings (Vol. 10562 LNBI, pp. 232-255). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 10562 LNBI). Springer Verlag. DOI: 10.1007/978-3-319-67979-2_13

Vachaspati, P., & Warnow, T. (2017). FastRFS: Fast and accurate Robinson-Foulds Supertrees using constrained exact optimization. Bioinformatics, 33(5), 631-639. DOI: 10.1093/bioinformatics/btw600

Browne, P., Tamaki, H., Kyrpides, N., Woyke, T., Goodwin, L., Imachi, H., ... Cadillo-Quiroz, H. (2017). Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments. ISME Journal, 11(1), 87-99. DOI: 10.1038/ismej.2016.104

Liu, G., Tao, Y., Zhang, Y., Lut, M., Knibbe, W. J., van der Wielen, P., ... van der Meer, W. (2017). Hotspots for selected metal elements and microbes accumulation and the corresponding water quality deterioration potential in an unchlorinated drinking water distribution system. Water Research, 124, 435-445. DOI: 10.1016/j.watres.2017.08.002

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

Paez-Espino, D., Chen, I. M. A., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., ... Kyrpides, N. C. (2017). IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses. Nucleic Acids Research, 45(D1), D457-D465. DOI: 10.1093/nar/gkw1030

Liu, M., Wang, S., Nobu, M. K., Bocher, B. T. W., Kaley, S. A., & Liu, W. T. (2017). Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater. Water Research, 122, 308-316. DOI: 10.1016/j.watres.2017.06.008

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

Liang, J., Bai, Y., Men, Y., & Qu, J. (2017). Microbe-microbe interactions trigger Mn(II)-oxidizing gene expression. ISME Journal, 11(1), 67-77. DOI: 10.1038/ismej.2016.106

Mei, R., Nobu, M. K., Narihiro, T., Kuroda, K., Muñoz Sierra, J., Wu, Z., ... Liu, W. T. (2017). Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome. Water Research, 124, 77-84. DOI: 10.1016/j.watres.2017.07.050

Liu, G., Zhang, Y., Knibbe, W. J., Feng, C., Liu, W., Medema, G., & van der Meer, W. (2017). Potential impacts of changing supply-water quality on drinking water distribution: A review. Water Research, 116, 135-148. DOI: 10.1016/j.watres.2017.03.031

Fritz, E., & Miller, M. J. (2017). Draft genome sequence of the murine bacterial isolate Lactobacillus murinus EF-1. Genome Announcements, 5(12), [e00077-17]. DOI: 10.1128/genomeA.00077-17

Shoaib, T., Carmichael, A., Corman, R. E., Shen, Y., Nguyen, T. H., Ewoldt, R. H., & Espinosa-Marzal, R. M. (2017). Self-adaptive hydrogels to mineralization. Soft Matter, 13(32), 5469-5480. DOI: 10.1039/c7sm01058c

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

Kuroda, K., Nobu, M. K., Mei, R., Narihiro, T., Bocher, B. T. W., Yamaguchi, T., & Liu, W. T. (2016). A single-granule-level approach reveals ecological heterogeneity in an upflow anaerobic sludge blanket reactor. PLoS ONE, 11(12), [e0167788]. DOI: 10.1371/journal.pone.0167788

Bustamante, A. C., Aiello, A. E., Galea, S., Ratanatharathorn, A., Noronha, C., Wildman, D. E., & Uddin, M. (2016). Glucocorticoid receptor DNA methylation, childhood maltreatment and major depression. Journal of Affective Disorders, 206, 181-188. DOI: 10.1016/j.jad.2016.07.038

Wildman, D. E. (2016). IFPA award in placentology lecture: Phylogenomic origins and evolution of the mammalian placenta. Placenta, 48, S31-S39. DOI: 10.1016/j.placenta.2016.04.004

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

Grillo, M. A., De Mita, S., Burke, P. V., Solórzano-Lowell, K. L. S., & Heath, K. D. (2016). Intrapopulation genomics in a model mutualist: Population structure and candidate symbiosis genes under selection in Medicago truncatula. Evolution, 70(12), 2704-2717. DOI: 10.1111/evo.13095

Heath, K. D., & Grillo, M. A. (2016). Rhizobia: tractable models for bacterial evolutionary ecology. Environmental Microbiology, 18(12), 4307-4311. DOI: 10.1111/1462-2920.13492

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

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

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., 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

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

Mei, R., Narihiro, T., Nobu, M. K., & Liu, W. T. (2016). Effects of heat shocks on microbial community structure and microbial activity of a methanogenic enrichment degrading benzoate. Letters in Applied Microbiology, 63(5), 356-362. DOI: 10.1111/lam.12629

Strauss, A. T., Shocket, M. S., Civitello, D. J., Hite, J. L., Penczykowski, R. M., Duffy, M. A., ... Hall, S. R. (2016). Habitat, predators, and hosts regulate disease in Daphnia through direct and indirect pathways. Ecological Monographs, 86(4), 393-411. DOI: 10.1002/ecm.1222

Singh, P., Yeong, H. C., Zhang, H., Rapti, Z., & Namachchivaya, N. S. (2016). Stochastic stability and dynamics of a two-dimensional structurally nonlinear airfoil in turbulent flow. Meccanica, 51(11), 2665-2688. DOI: 10.1007/s11012-016-0445-8

Nobu, M. K., Narihiro, T., Kuroda, K., Mei, R., & Liu, W. T. (2016). Chasing the elusive Euryarchaeota class WSA2: Genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME Journal, 10(10), 2478-2487. DOI: 10.1038/ismej.2016.33

Wrobel, K., Zhao, Y. C., Kulkoyluoglu, E., Chen, K. L. A., Hieronymi, K., Holloway, J., ... Madak-Erdogan, Z. (2016). ERα-XPO1 cross talk controls tamoxifen sensitivity in tumors by altering ERK5 cellular localization. Molecular Endocrinology, 30(10), 1029-1045. DOI: 10.1210/me.2016-1101

Oh, S., Zhang, R., Wu, Q. L., & Liu, W. T. (2016). Evolution and adaptation of SAR11 and cyanobium in a saline Tibetan lake. Environmental Microbiology Reports, 8(5), 595-604. DOI: 10.1111/1758-2229.12408

Mei, R., Narihiro, T., Nobu, M. K., Kuroda, K., & Liu, W. T. (2016). Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity. Scientific Reports, 6, [34090]. DOI: 10.1038/srep34090

Bayles, B. R., Brauman, K. A., Adkins, J. N., Allan, B. F., Ellis, A. M., Goldberg, T. L., ... Ristaino, J. B. (2016). Ecosystem Services Connect Environmental Change to Human Health Outcomes. EcoHealth, 13(3), 443-449. DOI: 10.1007/s10393-016-1137-5

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

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

Holmes, C. J., Figary, S., Schulz, K. L., & Cáceres, C. E. (2016). Effects of diversity on community assembly in newly formed pond communities. Ecosphere, 7(7), [e01377]. DOI: 10.1002/ecs2.1377

Guerra, A. S., Eckerlin, R. P., Dowling, A. P. G., Durden, L. A., Robbins, R. G., Dittmar, K., ... Young, H. S. (2016). Host-Parasite Associations in Small Mammal Communities in Semiarid Savanna Ecosystems of East Africa. Journal of Medical Entomology, 53(4), 851-860. DOI: 10.1093/jme/tjw048

Holmes, C. J., Pantel, J. H., Schulz, K. L., & Cáceres, C. E. (2016). Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation. Molecular ecology, 25(14), 3299-3308. DOI: 10.1111/mec.13672

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

Oh, S., Yoo, D., & Liu, W. T. (2016). Metagenomics reveals a novel virophage population in a Tibetan mountain lake. Microbes and Environments, 31(2), 173-177. DOI: 10.1264/jsme2.ME16003

Baker, J. L., Dunn, K. A., Mingrone, J., Wood, B. A., Karpinski, B. A., Sherwood, C. C., ... Bielawski, J. P. (2016). Functional divergence of the nuclear receptor NR2C1 as a modulator of pluripotentiality during hominid evolution. Genetics, 203(2), 905-922. DOI: 10.1534/genetics.115.183889

Men, Y., Han, P., Helbling, D. E., Jehmlich, N., Herbold, C., Gulde, R., ... Fenner, K. (2016). Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis. Environmental Science and Technology, 50(9), 4682-4692. DOI: 10.1021/acs.est.5b06016

Feinstein, L., Ferrando-Martínez, S., Leal, M., Zhou, X., Sempowski, G. D., Wildman, D. E., ... Aiello, A. E. (2016). Population Distributions of Thymic Function in Adults: Variation by Sociodemographic Characteristics and Health Status. Biodemography and Social Biology, 62(2), 208-221. DOI: 10.1080/19485565.2016.1172199

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

Aiello, A. E., Dowd, J. B., Jayabalasingham, B., Feinstein, L., Uddin, M., Simanek, A. M., ... Pawelec, G. (2016). PTSD is associated with an increase in aged T cell phenotypes in adults living in Detroit. Psychoneuroendocrinology, 67, 133-141. DOI: 10.1016/j.psyneuen.2016.01.024

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

Springer, Y. P., Hoekman, D., Johnson, P. T. J., Duffy, P. A., Hufft, R. A., Barnett, D. T., ... Yabsley, M. J. (2016). Tick-, mosquito-, and rodent-borne parasite sampling designs for the National Ecological Observatory Network. Ecosphere, 7(5), [e01271]. DOI: 10.1002/ecs2.1271

Nguyen, N. P., Warnow, T., Pop, M., & White, B. (2016). A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. npj Biofilms and Microbiomes, 2, [16004]. DOI: 10.1038/npjbiofilms.2016.4

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

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

Wingo, A. P., Almli, L. M., Stevens, J. S., Klengel, T., Uddin, M., Li, Y., ... Ressler, K. J. (2016). Erratum: DICER1 and microRNA regulation in post-traumatic stress disorder with comorbid depression (Nature Communications (2015) 6 (10106) DOI: 10.1038/ncomms10106). Nature Communications, 7, [10958]. DOI: 10.1038/ncomms10958

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

Ling, F., Hwang, C., LeChevallier, M. W., Andersen, G. L., & Liu, W. T. (2016). Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system. ISME Journal, 10(3), 582-595. DOI: 10.1038/ismej.2015.136

Gordon, B. R., Klinger, C. R., Weese, D. J., Lau, J. A., Burke, P. V., Dentinger, B. T. M., & Heath, K. D. (2016). Decoupled genomic elements and the evolution of partner quality in nitrogen-fixing rhizobia. Ecology and Evolution, 6(5), 1317-1327. DOI: 10.1002/ece3.1953

Kim, N. K., Oh, S., & Liu, W. T. (2016). Enrichment and characterization of microbial consortia degrading soluble microbial products discharged from anaerobic methanogenic bioreactors. Water Research, 90, 395-404. DOI: 10.1016/j.watres.2015.12.021

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

Zhang, M., Sun, Y., Liu, Y., Qiao, F., Chen, L., Liu, W. T., ... Li, E. (2016). Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference. Aquaculture, 454, 72-80. DOI: 10.1016/j.aquaculture.2015.12.014

Golubeva, Y. A., Ellermeier, J. R., Chubiz, J. E. C., & Slauch, J. M. (2016). Intestinal long-chain fatty acids act as a direct signal to modulate expression of the Salmonella pathogenicity island 1 type III secretion system. mBio, 7(1), [e02170-15]. DOI: 10.1128/mBio.02170-15

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

Liu, G., Ling, F. Q., Van Der Mark, E. J., Zhang, X. D., Knezev, A., Verberk, J. Q. J. C., ... Van Dijk, J. C. (2016). Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources. Scientific Reports, 6, [20367]. DOI: 10.1038/srep20367

Van Tassell, M. L., Angela Daum, M., Kim, J. S., & Miller, M. J. (2016). Creative lysins: Listeria and the engineering of antimicrobial enzymes. Current Opinion in Biotechnology, 37, 88-96. DOI: 10.1016/j.copbio.2015.10.006

Rapti, Z., & Cáceres, C. E. (2016). Effects of Intrinsic and Extrinsic Host Mortality on Disease Spread. Bulletin of Mathematical Biology, 78(2), 235-253. DOI: 10.1007/s11538-016-0141-9

Gomez, A., Rothman, J. M., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Umaña, J. D., ... Leigh, S. R. (2016). Erratum: Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp (The ISME Journal (2016) 10, 532; (DOI:10.1038/ismej.2015.252)). ISME Journal, 10(2). DOI: 10.1038/ismej.2015.252

Lu, H., Ulanov, A. V., Nobu, M., & Liu, W. T. (2016). Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns. Applied Microbiology and Biotechnology, 100(4), 1843-1852. DOI: 10.1007/s00253-015-7095-y

Lipovich, L., Hou, Z. C., Jia, H., Sinkler, C., Mcgowen, M., Sterner, K. N., ... Wildman, D. E. (2016). High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. Journal of Comparative Neurology, 524(2), 288-308. DOI: 10.1002/cne.23843

Hite, J. L., Penczykowski, R. M., Shocket, M. S., Strauss, A. T., Orlando, P. A., Duffy, M. A., ... Hall, S. R. (2016). Parasites destabilize host populations by shifting stage-structured interactions. Ecology, 97(2), 439-449. DOI: 10.1890/15-1065.1

Nobu, M. K., Dodsworth, J. A., Murugapiran, S. K., Rinke, C., Gies, E. A., Webster, G., ... Hedlund, B. P. (2016). Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. ISME Journal, 10(2), 273-286. DOI: 10.1038/ismej.2015.97

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

MacKay, A. J., Muturi, E. J., Ward, M. P., & Allan, B. F. (2016). Cascade of ecological consequences for West Nile virus transmission when aquatic macrophytes invade stormwater habitats. Ecological Applications, 26(1), 219-232. DOI: 10.1890/15-0050/suppinfo

Shinzato, N., Aoyama, H., Saitoh, S., Nikoh, N., Nakano, K., Shimoji, M., ... Kamagata, Y. (2016). Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum. Genome Announcements, 4(5), [e01032-16]. DOI: 10.1128/genomeA.01032-16

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

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

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

Liu, Y. Q., Zhang, X., Zhang, R., Liu, W. T., & Tay, J. H. (2016). Effects of hydraulic retention time on aerobic granulation and granule growth kinetics at steady state with a fast start-up strategy. Applied Microbiology and Biotechnology, 100(1), 469-477. DOI: 10.1007/s00253-015-6993-3

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

Lu, H., Xue, Z., Saikaly, P., Nunes, S. P., Bluver, T. R., & Liu, W. T. (2016). Membrane biofouling in a wastewater nitrification reactor: Microbial succession from autotrophic colonization to heterotrophic domination. Water Research, 88, 337-345. DOI: 10.1016/j.watres.2015.10.013

Berding, K., Wang, M., Monaco, M. H., Alexander, L. S., Mudd, A. T., Chichlowski, M., ... Donovan, S. M. (2016). Prebiotics and bioactive milk fractions affect gut development, microbiota, and neurotransmitter expression in piglets. Journal of Pediatric Gastroenterology and Nutrition, 63(6), 688-697. DOI: 10.1097/MPG.0000000000001200

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

Li, Y., Lin, Q., Wang, S., Li, X., Liu, W., Luo, C., ... Li, X. (2016). Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow. FEMS Microbiology Ecology, 92(1). DOI: 10.1093/femsec/fiv152

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

Fredericks, L. P., Forgacs, D., Yu, J., & Allan, B. F. (2016). An expanded reverse line blot hybridization protocol for the simultaneous detection of numerous tick-borne pathogens in North America. Journal of Medical Entomology, 53(3), 721-726. DOI: 10.1093/jme/tjv251

Narihiro, T., Nobu, M. K., Tamaki, H., Kamagata, Y., Sekiguchi, Y., & Liu, W. T. (2016). Comparative genomics of syntrophic branched-chain fatty acid degrading bacteria. Microbes and Environments, 31(3), 288-292. DOI: 10.1264/jsme2.ME16057

Wooten, J., Liu, X., & Miller, M. J. (2016). Draft genome sequence of Lactobacillus crispatus JCM5810, which can reduce Campylobacter jejuni colonization in chicken intestine. Genome Announcements, 4(2), [e00255-16]. DOI: 10.1128/genomeA.00255-16

Narihiro, T., Nobu, M. K., Tamaki, H., Kamagata, Y., & Liu, W. T. (2016). Draft genome sequence of Syntrophomonas wolfei subsp. methylbutyratica strain 4J5T (JCM 14075), a mesophilic butyrate- and 2-methylbutyrate-degrading syntroph. Genome Announcements, 4(2), [e00047-16]. DOI: 10.1128/genomeA.00047-16

Crawford, J. W., Redlinski, I., Steiner, C. F., & Caceres, C. E. (2015). Life-history evolution in a Daphnia ambigua population during community assembly. Journal of Plankton Research, 37(2), 409-416. DOI: 10.1093/plankt/fbu110

Wingo, A. P., Almli, L. M., Stevens, J. J., Klengel, T., Uddin, M., Li, Y., ... Ressler, K. J. (2015). DICER1 and microRNA regulation in post-traumatic stress disorder with comorbid depression. Nature Communications, 6, [10106]. DOI: 10.1038/ncomms10106

Sanz-sáez, Á., Heath, K. D., Burke, P. V., & Ainsworth, E. A. (2015). Inoculation with an enhanced N2-fixing Bradyrhizobium japonicum strain (USDA110) does not alter soybean (Glycine max Merr.) response to elevated [CO2]. Plant Cell and Environment, 38(12), 2589-2602. DOI: 10.1111/pce.12577

Nobu, M. K., Narihiro, T., Hideyuki, T., Qiu, Y. L., Sekiguchi, Y., Woyke, T., ... Liu, W. T. (2015). The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environmental Microbiology, 17(12), 4861-4872. DOI: 10.1111/1462-2920.12444

Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., ... Heath, K. (2015). The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics, 47(12), 1435-1442. DOI: 10.1038/ng.3435

Mota, N., Sumner, J. A., Lowe, S. R., Neumeister, A., Uddin, M., Aiello, A. E., ... Pietrzak, R. H. (2015). The rs1049353 polymorphism in the CNR1 gene interacts with childhood abuse to predict posttraumatic threat symptoms. Journal of Clinical Psychiatry, 76(12), e1622-e1623. DOI: 10.4088/JCP.15l10084

Van Tassell, M. L., Ibarra-Sánchez, L. A., Takhar, S. R., Amaya-Llano, S. L., & Miller, M. J. (2015). Use of a miniature laboratory fresh cheese model for investigating antimicrobial activities. Journal of Dairy Science, 98(12), 8515-8524. DOI: 10.3168/jds.2015-9967

Weckle, A., Aiello, A. E., Uddin, M., Galea, S., Coulborn, R. M., Soliven, R., ... Wildman, D. E. (2015). Rapid fractionation and isolation of whole blood components in samples obtained from a community-based setting. Journal of Visualized Experiments, 2015(105), [e52227]. DOI: 10.3791/52227

Amato, K. R., Yeoman, C. J., Cerda, G., Schmitt, C. A., Cramer, J. D., Miller, M. E. B., ... Leigh, S. R. (2015). Variable responses of human and non-human primate gut microbiomes to a Western diet. Microbiome, 3. DOI: 10.1186/s40168-015-0120-7

Krause, D. J., & Whitaker, R. J. (2015). Inferring speciation processes from patterns of natural variation in microbial genomes. Systematic Biology, 64(6), 926-935. DOI: 10.1093/sysbio/syv050

Tobin, E. T., Kane, H. S., Saleh, D. J., Wildman, D. E., Breen, E. C., Secord, E., & Slatcher, R. B. (2015). Asthma-related immune responses in youth with asthma: Associations with maternal responsiveness and expressions of positive and negative affect in daily life. Psychosomatic Medicine, 77(8), 892-902. DOI: 10.1097/PSY.0000000000000236

Mirarab, S., Bayzid, M. S., Boussau, B., & Warnow, T. (2015). Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science, 350(6257), [171]. DOI: 10.1126/science.aaa7719

Angelino, D., Dosz, E. B., Sun, J., Hoeflinger, J. L., Van Tassell, M. L., Chen, P., ... Jeffery, E. H. (2015). Myrosinase-dependent and –independent formation and control of isothiocyanate products of glucosinolate hydrolysis. Frontiers in Plant Science, 6(OCTOBER), [831]. DOI: 10.3389/fpls.2015.00831

Cracraft, J., Houde, P., Ho, S. Y. W., Mindell, D. P., Fjeldså, J., Lindow, B., ... Jarvis, E. D. (2015). Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science, 349(6255), 1460-b. DOI: 10.1126/science.aab1578

Ramirez, C. R., Harding, A. L., Forteguerri, E. B. R., Aldridge, B. M., & Lowe, J. F. (2015). Limited efficacy of antimicrobial metaphylaxis in finishing pigs: A randomized clinical trial. Preventive Veterinary Medicine, 121(1-2), 176-178. DOI: 10.1016/j.prevetmed.2015.06.002

Tidhar, A., Rushing, M. D., Kim, B., & Slauch, J. M. (2015). Periplasmic superoxide dismutase SodCI of Salmonella binds peptidoglycan to remain tethered within the periplasm. Molecular Microbiology, 97(5), 832-843. DOI: 10.1111/mmi.13067

Nobu, M. K., Narihiro, T., Rinke, C., Kamagata, Y., Tringe, S. G., Woyke, T., & Liu, W. T. (2015). Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME Journal, 9(8), 1710-1722. DOI: 10.1038/ismej.2014.256

Hoeflinger, J. L., Kashtanov, D. O., Cox, S. B., Dowd, S. E., Jouni, Z. E., Donovan, S. M., & Miller, M. J. (2015). Characterization of the intestinal lactobacilli community following galactooligosaccharides and polydextrose supplementation in the neonatal piglet. PLoS ONE, 10(8), [e0135494]. DOI: 10.1371/journal.pone.0135494

Fang, X., Nevo, E., Han, L., Levanon, E. Y., Zhao, J., Avivi, A., ... Krogh, A. (2015). Erratum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax (Nature Communications (2015) 5 (3966) DOI: 10.1038/ncomms4966). Nature Communications, 6, [8051]. DOI: 10.1038/ncomms9051

Lu, L., Ku, K. M., Palma-Salgado, S. P., Storm, A. P., Feng, H., Juvik, J. A., & Nguyen, T. H. (2015). Influence of epicuticular physicochemical properties on porcine rotavirus adsorption to 24 leafy green vegetables and tomatoes. PLoS ONE, 10(7), [e0132841]. DOI: 10.1371/journal.pone.0132841

Logue, M. W., Smith, A. K., Baldwin, C., Wolf, E. J., Guffanti, G., Ratanatharathorn, A., ... Miller, M. W. (2015). An analysis of gene expression in PTSD implicates genes involved in the glucocorticoid receptor pathway and neural responses to stress. Psychoneuroendocrinology, 57, 1-13. DOI: 10.1016/j.psyneuen.2015.03.016

Roch, S., & Warnow, T. (2015). On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods. Systematic Biology, 64(4), 663-676. DOI: 10.1093/sysbio/syv016

LaDeau, S. L., Allan, B. F., Leisnham, P. T., & Levy, M. Z. (2015). The ecological foundations of transmission potential and vector-borne disease in urban landscapes. Functional Ecology, 29(7), 889-901. DOI: 10.1111/1365-2435.12487

Meyers, J. L., Salling, M. C., Almli, L. M., Ratanatharathorn, A., Uddin, M., Galea, S., ... Koenen, K. C. (2015). Frequency of alcohol consumption in humans; the role of metabotropic glutamate receptors and downstream signaling pathways. Translational Psychiatry, 5(6), [A070]. DOI: 10.1038/tp.2015.70

Bayzid, M. S., Mirarab, S., Boussau, B., & Warnow, T. (2015). Weighted statistical binning: Enabling statistically consistent genome-scale phylogenetic analyses. PLoS ONE, 10(6), [e0129183]. DOI: 10.1371/journal.pone.0129183

Gardner, A. M., Allan, B. F., Frisbie, L. A., & Muturi, E. J. (2015). Asymmetric effects of native and exotic invasive shrubs on ecology of the West Nile virus vector Culex pipiens (Diptera: Culicidae). Parasites and Vectors, 8(1), [329]. DOI: 10.1186/s13071-015-0941-z

Nguyen, N. P. D., Mirarab, S., Kumar, K., & Warnow, T. (2015). Ultra-large alignments using phylogeny-aware profiles. Genome Biology, 16(1), [124]. DOI: 10.1186/s13059-015-0688-z

Mirarab, S., & Warnow, T. (2015). ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44-i52. DOI: 10.1093/bioinformatics/btv234

Searle, C. L., Ochs, J. H., Cáceres, C. E., Chiang, S. L., Gerardo, N. M., Hall, S. R., & Duffy, M. A. (2015). Plasticity, not genetic variation, drives infection success of a fungal parasite. Parasitology, 142(6), 839-848. DOI: 10.1017/S0031182015000013

Bara, J., Rapti, Z., Cáceres, C. E., & Muturi, E. J. (2015). Effect of larval competition on extrinsic incubation period and vectorial capacity of Aedes albopictus for dengue virus. PLoS ONE, 10(5), [e0126703]. DOI: 10.1371/journal.pone.0126703

Gomez, A., Petrzelkova, K., Yeoman, C. J., Vlckova, K., Mrázek, J., Koppova, I., ... Leigh, S. R. (2015). Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology. Molecular Ecology, 24(10), 2551-2565. DOI: 10.1111/mec.13181

Lewis, Z. T., Totten, S. M., Smilowitz, J. T., Popovic, M., Parker, E., Lemay, D. G., ... Mills, D. A. (2015). Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants. Microbiome, 3(1), [13]. DOI: 10.1186/s40168-015-0071-z

Tang, Y., Werth, C. J., Sanford, R. A., Singh, R., Michelson, K., Nobu, M., ... Valocchi, A. J. (2015). Immobilization of selenite via two parallel pathways during in situ bioremediation. Environmental Science and Technology, 49(7), 4543-4550. DOI: 10.1021/es506107r

GOBLET Consortium (2015). GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training. PLoS Computational Biology, 11(4), [e1004143]. DOI: 10.1371/journal.pcbi.1004143

Hoeflinger, J. L., Davis, S. R., Chow, J., & Miller, M. J. (2015). In vitro impact of human milk oligosaccharides on Enterobacteriaceae growth. Journal of Agricultural and Food Chemistry, 63(12), 3295-3302. DOI: 10.1021/jf505721p

Lowe, S. R., Meyers, J. L., Galea, S., Aiello, A. E., Uddin, M., Wildman, D. E., & Koenen, K. C. (2015). RORA and posttraumatic stress trajectories: Main effects and interactions with childhood physical abuse history. Brain and Behavior, 5(4), 1-11. DOI: 10.1002/brb3.323

Bautista, M. A., Zhang, C., & Whitaker, R. J. (2015). Virus-induced dormancy in the archaeon Sulfolobus islandicus. mBio, 6(2), [e02565-14]. DOI: 10.1128/mBio.02565-14

Narihiro, T., Kim, N. K., Mei, R., Nobu, M. K., & Liu, W. T. (2015). Microbial community analysis of anaerobic reactors treating soft drink wastewater. PLoS ONE, 10(3), [e0119131]. DOI: 10.1371/journal.pone.0119131

Gundling, W. E., & Wildman, D. E. (2015). A review of inter- and intraspecific variation in the eutherian placenta. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1663), 20140072. DOI: 10.1098/rstb.2014.0072

Schneider, S. C., Parker, C. M., Miller, J. R., Page Fredericks, L., & Allan, B. F. (2015). Assessing the Contribution of Songbirds to the Movement of Ticks and Borrelia burgdorferi in the Midwestern United States During Fall Migration. EcoHealth, 12(1), 164-173. DOI: 10.1007/s10393-014-0982-3

Bhatia, S., Prabhu, P. N., Benefiel, A. C., Miller, M. J., Chow, J., Davis, S. R., & Gaskins, H. R. (2015). Galacto-oligosaccharides may directly enhance intestinal barrier function through the modulation of goblet cells. Molecular Nutrition and Food Research, 59(3), 566-573. DOI: 10.1002/mnfr.201400639

The Avian Phylogenomics Consortium (2015). Phylogenomic analyses data of the avian phylogenomics project. GigaScience, 4(1), [4]. DOI: 10.1186/s13742-014-0038-1

Chou, J., Gupta, A., Yaduvanshi, S., Davidson, R., Nute, M., Mirarab, S., & Warnow, T. (2015). A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genomics, 16, 1-11. DOI: 10.1186/1471-2164-16-S10-S2

Vachaspati, P., & Warnow, T. (2015). ASTRID: Accurate species TRees from internode distances. BMC Genomics, 16, 1-13. DOI: 10.1186/1471-2164-16-S10-S3

Youngblut, N. D., Wirth, J. S., Henriksen, J. R., Smith, M., Simon, H., Metcalf, W. W., & Whitaker, R. J. (2015). Genomic and phenotypic differentiation among Methanosarcina mazei populations from Columbia River sediment. ISME Journal, 9(10), 2191-2205. DOI: 10.1038/ismej.2015.31

Liu, P., Kim, M., Schlesinger, D., Kranz, C., Ha, S., Ha, J., ... Moe, C. (2015). Immunomagnetic separation combined with RT-qPCR for determining the efficacy of disinfectants against human noroviruses. Journal of Infection and Public Health, 8(2), 145-154. DOI: 10.1016/j.jiph.2014.08.007

Baranovich, T., Bahl, J., Marathe, B. M., Culhane, M., Stigger-Rosser, E., Darnell, D., ... Govorkova, E. A. (2015). Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Antiviral Research, 117, 10-19. DOI: 10.1016/j.antiviral.2015.02.004

Smith, M. W., Davis, R. E., Youngblut, N. D., Kärnä, T., Herfort, L., Whitaker, R. J., ... Simon, H. M. (2015). Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River. Frontiers in Microbiology, 6(OCT), [1074]. DOI: 10.3389/fmicb.2015.01074

Mirarab, S., Nguyen, N., Guo, S., Wang, L. S., Kim, J., & Warnow, T. (2015). PASTA: Ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. Journal of Computational Biology, 22(5), 377-386. DOI: 10.1089/cmb.2014.0156

Davidson, R., Vachaspati, P., Mirarab, S., & Warnow, T. (2015). Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genomics, 16, 1-12. DOI: 10.1186/1471-2164-16-S10-S1

Shen, Y., Monroy, G. L., Derlon, N., Janjaroen, D., Huang, C., Morgenroth, E., ... Nguyen, T. H. (2015). Role of biofilm roughness and hydrodynamic conditions in legionella pneumophila adhesion to and detachment from simulated drinking water biofilms. Environmental Science and Technology, 49(7), 4274-4282. DOI: 10.1021/es505842v

Rushmore, J., Allison, A. B., Edwards, E. E., Bagal, U., Altizer, S., Cranfield, M. R., ... Yabsley, M. J. (2015). Screening wild and semi-free ranging great apes for putative sexually transmitted diseases: Evidence of Trichomonadidae infections. American Journal of Primatology, 77(10), 1075-1085. DOI: 10.1002/ajp.22442

Simonsen, A. K., Han, S., Rekret, P., Rentschler, C. S., Heath, K. D., & Stinchcombe, J. R. (2015). Short-termfertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria. PeerJ, 2015(10), [e1291]. DOI: 10.7717/peerj.1291

Romero-Maraccini, O. C., Shisler, J. L., & Nguyen, T. H. (2015). Solar and temperature treatments affect the ability of human rotavirus Wa to bind to host cells and synthesize viral RNA. Applied and Environmental Microbiology, 81(12), 4090-4097. DOI: 10.1128/AEM.00027-15

Narihiro, T., Nobu, M. K., Kim, N. K., Kamagata, Y., & Liu, W. T. (2015). The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey. Environmental Microbiology, 17(5), 1707-1720. DOI: 10.1111/1462-2920.12616

Sears, K. E., Maier, J. A., Rivas-Astroza, M., Poe, R., Zhong, S., Kosog, K., ... Rapti, Z. (2015). The Relationship between Gene Network Structure and Expression Variation among Individuals and Species. PLoS Genetics, 11(8), [e1005398]. DOI: 10.1371/journal.pgen.1005398

Jameson Kiesling, N. M., Yi, S. V., Xu, K., Gianluca Sperone, F., & Wildman, D. E. (2015). The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis. Molecular Phylogenetics and Evolution, 82(PB), 386-399. DOI: 10.1016/j.ympev.2014.03.027

Lu, N., Massoudieh, A., Liang, X., Kamai, T., Zilles, J. L., Nguyen, T. H., & Ginn, T. R. (2015). A kinetic model of gene transfer via natural transformation of Azotobacter vinelandii. Environmental Science: Water Research and Technology, 1(3), 363-374. DOI: 10.1039/c5ew00023h

Liu, Y., Dong, S., Kuhlenschmidt, M. S., Kuhlenschmidt, T. B., Drnevich, J., & Nguyen, T. H. (2015). Inactivation mechanisms of: Cryptosporidium parvum oocysts by solar ultraviolet irradiation. Environmental Science: Water Research and Technology, 1(2), 188-198. DOI: 10.1039/c4ew00079j

Zhang, Y., Hong, P. Y., LeChevallier, M. W., & Liu, W. T. (2015). Phenotypic and phylogenetic identification of coliform bacteria obtained using 12 coliform methods approved by the U.S. Environmental Protection Agency. Applied and Environmental Microbiology, 81(17), 6012-6023. DOI: 10.1128/AEM.01510-15

Rui, J., Li, J., Wang, S., An, J., Liu, W. T., Lin, Q., ... Li, X. (2015). Responses of bacterial communities to simulated climate changes in alpine meadow soil of the Qinghai-Tibet plateau. Applied and Environmental Microbiology, 81(17), 6070-6077. DOI: 10.1128/AEM.00557-15

Lu, N., Massoudieh, A., Liang, X., Hu, D., Kamai, T., Ginn, T. R., ... Nguyen, T. H. (2015). Swimming motility reduces Azotobacter vinelandii deposition to silica surfaces. Journal of Environmental Quality, 44(5), 1366-1375. DOI: 10.2134/jeq2015.03.0141

Nguyen, N. P., Mirarab, S., Kumar, K., & Warnow, T. (2015). Ultra-large alignments using ensembles of hidden Markov models. In Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings (Vol. 9029, pp. 259-260). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9029). Springer Verlag. DOI: 10.1007/978-3-319-16706-0_26