PMI Publications

Andrianaivoarimanana, V., D. M. Wagner, D. N. Birdsell, B. Nikolay, F. Rakotoarimanana, L. N. Randriantseheno, A. J. Vogler, J. W. Sahl, C. M. Hall, N. Somprasong, S. Cauchemez, H. P. Schweizer, H. Razafimandimby, C. Rogier, and M. Rajerison. 2021. Transmission of antimicrobial resistant Yersinia pestis during a pneumonic plague outbreak. Clinical Infectious Diseases.

Bagagli, E., D. R. Matute, H. G. Garces, B. G. Tenório, A. G. Garces, L. G. d. B. Alves, D. H. Yamauchi, M. F. Hrycyk, B. M. Barker, and M. d. M. Teixeira. 2021. Paracoccidioides brasiliensis isolated from nine-banded armadillos (Dasypus novemcinctus) reveal population structure and admixture in the Amazon Basin. Journal of Fungi 7:54.

Baker, S. M., E. W. Settles, C. Davitt, P. Gellings, N. Kikendall, J. Hoffmann, Y. Wang, J. Bitoun, K.-R. Lodrigue, J. W. Sahl, P. Keim, C. Roy, J. McLachlan, and L. A. Morici. 2021. Burkholderia pseudomallei OMVs derived from infection mimicking conditions elicit similar protection to a live-attenuated vaccine. NPJ Vaccines 6:18-18.

Barker, B. M., C. A. Cuomo, and N. P. Govender. 2021. Editorial: Genomic characterization of emerging human fungal pathogens. Frontiers in Genetics 12:674765-674765.

Bechtel, M. J., K. K. Drake, T. C. Esque, N. C. Nieto, J. T. Foster, and M. B. Teglas. 2021. Borreliosis transmission from ticks associated with desert tortoise burrows: examples of tick-borne relapsing fever in the Mojave Desert. Vector-Borne and Zoonotic Diseases 21:635-637.

Bycura, D., A. C. Santos, A. Shiffer, S. Kyman, K. Winfree, J. Sutliffe, T. Pearson, D. Sonderegger, E. Cope, and J. G. Caporaso. 2021. Impact of different exercise modalities on the human gut microbiome. Sports 9:14.

Cai, Y., H. M. Juszczak, E. K. Cope, and A. N. Goldberg. 2021. The microbiome in obstructive sleep apnea. Sleep 44.

Cassin-Sackett, L., M. G. Campana, N. R. McInerney, H. C. Lim, N. A. S. Przelomska, B. Masuda, R. T. Chesser, E. H. Paxton, J. T. Foster, L. H. Crampton, and R. C. Fleischer. 2021. Genetic structure and population history in two critically endangered Kaua‘i honeycreepers. Conservation Genetics 22:601-614.

Colman, R. E., R. J. Brinkerhoff, J. D. Busch, C. Ray, A. Doyle, J. W. Sahl, P. Keim, S. K. Collinge, and D. M. Wagner. 2021. No evidence for enzootic plague within black‐tailed prairie dog (Cynomys ludovicianus) populations. Integrative Zoology.

Dale, A. P., M. Kretschmer, I. Ruberto, D. M. Wagner, C. Solomon, K. Komatsu, and H. Venkat. 2021. Notes from the field: delays in identification and treatment of a case of septicemic plague – Navajo County, Arizona, 2020. MMWR Morbidity and mortality weekly report 70:1063-1064.

Dillon, M. R., E. Bolyen, A. Adamov, A. Belk, E. Borsom, Z. Burcham, J. W. Debelius, H. Deel, A. Emmons, M. Estaki, C. Herman, C. R. Keefe, J. T. Morton, R. R. M. Oliveira, A. Sanchez, A. Simard, Y. Vázquez-Baeza, M. Ziemski, H. E. Miwa, T. A. Kerere, C. Coote, R. Bonneau, R. Knight, G. Oliveira, P. Gopalasingam, B. D. Kaehler, E. K. Cope, J. L. Metcalf, M. S. Robeson Ii, N. A. Bokulich, and J. G. Caporaso. 2021. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Computational Biology 17:e1009056-e1009056.

Dong, W., H. Mead, S. Jaramillo, T. Barr, D. S. Kollath, V. K. Coyne, N. E. Stone, A. Jones, J. Zhang, A. Li, L.-S. Wang, M. Milanes-Yearsley, P. S. Keim, B. M. Barker, M. Caligiuri, and J. Yu. 2021a. The K18-hACE2 transgenic mouse model recapitulates non-severe and severe COVID-19 in response to infectious dose of SARS-CoV-2 Virus. bioRxiv.

Dong, W., J. Wang, L. Tian, J. Zhang, H. Mead, S. A. Jaramillo, A. Li, R. E. Zumwalt, S. P. J. Whelan, E. W. Settles, P. S. Keim, B. M. Barker, M. A. Caligiuri, and J. Yu. 2021b. FXa cleaves the SARS-CoV-2 spike protein and blocks cell entry to protect against infection with inferior effects in B.1.1.7 variant. bioRxiv:2021.2006.2007.447437.

Durben, R. M., F. M. Walker, L. Holeski, A. R. Keith, Z. Kovacs, S. R. Hurteau, R. L. Lindroth, S. M. Shuster, and T. G. Whitham. 2021. Beavers, bugs and chemistry: a mammalian herbivore changes chemistry composition and arthropod communities in foundation tree species. Forests 12:877.

Finn, D. R., J. Maldonado, F. de Martini, J. Yu, C. R. Penton, R. S. Fontenele, K. Schmidlin, S. Kraberger, A. Varsani, G. H. Gile, B. Barker, D. R. Kollath, R. L. Muenich, P. Herckes, M. Fraser, and F. Garcia-Pichel. 2021. Agricultural practices drive biological loads, seasonal patterns and potential pathogens in the aerobiome of a mixed-land-use dryland. Science of the Total Environment 798:149239.

Gaughwin, M., F. Walker, L. Woolford, J. Upton, C. Sobek, A. Johnson, and D. Taggart. 2021. Observations on the mortality of young southern hairy-nosed wombats (Lasiorhinus latifrons) in the Murraylands of South Australia. Australian Mammalogy 43:126.

Golovliov, I., S. Bäckman, M. Granberg, E. Salomonsson, E. Lundmark, J. Näslund, J. D. Busch, D. Birdsell, J. W. Sahl, D. M. Wagner, A. Johansson, M. Forsman, and J. Thelaus. 2021. Long-term survival of virulent tularemia pathogens outside a host in conditions that mimic natural aquatic environments. Applied and Environmental Microbiology 87:e02713-02720.

Heacock-Kang, Y., I. A. McMillan, M. H. Norris, Z. Sun, J. Zarzycki-Siek, A. P. Bluhm, D. Cabanas, R. E. Norton, N. Ketheesan, J. F. Miller, H. P. Schweizer, and T. T. Hoang. 2021. The Burkholderia pseudomallei intracellular ‘TRANSITome’. Nature Communications 12:1907-1907.

Higgins Keppler, E. A., H. L. Mead, B. M. Barker, and H. D. Bean. 2021. Life cycle dominates the volatilome character of dimorphic fungus Coccidioides spp. mSphere 6.

Keppler, E. A. H., H. L. Mead, B. M. Barker, and H. D. Bean. 2021. Lifecycle dominates the volatilome character of the dimorphic fungus Coccidioides spp. bioRxiv.

Knight, E. C., A. L. Harrison, A. L. Scarpignato, S. L. Van Wilgenburg, E. M. Bayne, J. W. Ng, E. Angell, R. Bowman, R. M. Brigham, B. Drolet, W. E. Easton, T. R. Forrester, J. T. Foster, S. Haché, K. C. Hannah, K. G. Hick, J. Ibarzabal, T. L. Imlay, S. A. Mackenzie, A. Marsh, L. P. McGuire, G. N. Newberry, D. Newstead, A. Sidler, P. H. Sinclair, J. L. Stephens, D. L. Swanson, J. A. Tremblay, and P. P. Marra. 2021. Comprehensive estimation of spatial and temporal migratory connectivity across the annual cycle to direct conservation efforts. Ecography 44:665-679.

Ladner, J. T., S. N. Henson, A. S. Boyle, A. L. Engelbrektson, Z. W. Fink, F. Rahee, J. D’Ambrozio, K. E. Schaecher, M. Stone, W. Dong, S. Dadwal, J. Yu, M. A. Caligiuri, P. Cieplak, M. Bjørås, M. H. Fenstad, S. A. Nordbø, D. E. Kainov, N. Muranaka, M. S. Chee, S. A. Shiryaev, and J. A. Altin. 2021. Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses. Cell Reports Medicine 2:100189-100189.

Lang, Y., N. R. Shah, X. Tao, S. M. Reeve, J. Zhou, B. Moya, A. R. M. Sayed, S. Dharuman, J. L. Oyer, A. J. Copik, B. A. Fleischer, E. Shin, C. Werkman, K. B. Basso, D. Deveson Lucas, D. S. Sutaria, M. Mégroz, T. H. Kim, V. Loudon‐Hossler, A. Wright, R. H. Jimenez‐Nieves, M. J. Wallace, K. C. Cadet, Y. Jiao, J. D. Boyce, E. D. LoVullo, H. P. Schweizer, R. A. Bonomo, N. Bharatham, B. T. Tsuji, C. B. Landersdorfer, M. H. Norris, B. Soo Shin, A. Louie, V. Balasubramanian, R. E. Lee, G. L. Drusano, and J. B. Bulitta. 2021. Combating multidrug‐resistant bacteria by integrating a novel target site penetration and receptor binding assay platform into translational modeling. Clinical Pharmacology & Therapeutics 109:1000-1020.

Langwig, K. E., J. P. White, K. L. Parise, H. M. Kaarakka, J. A. Redell, J. E. DePue, W. H. Scullon, J. T. Foster, A. M. Kilpatrick, and J. R. Hoyt. 2021. Mobility and infectiousness in the spatial spread of an emerging fungal pathogen. Journal of Animal Ecology 90:1134-1141.

Martínez Arbas, S., S. Narayanasamy, M. Herold, L. A. Lebrun, M. R. Hoopmann, S. Li, T. J. Lam, B. J. Kunath, N. D. Hicks, C. M. Liu, L. B. Price, C. C. Laczny, J. D. Gillece, J. M. Schupp, P. S. Keim, R. L. Moritz, K. Faust, H. Tang, Y. Ye, A. Skupin, P. May, E. E. L. Muller, and P. Wilmes. 2021. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nature Microbiology 6:123-135.

Mead, H. L., D. Kollath, M. de Melo Teixeira, C. C. Roe, P. K. Keim, C. Plude, J. Terriquez, N. Nandurkar, C. Donohoo, B. L. W. O’Connor, and B. M. Barker. 2021. Disease triangle dynamics of Coccidioidomycosis in Northern Arizona. medRxiv.

Miller, E., V. Barragan, J. Chiriboga, C. Weddell, L. Luna, D. J. Jiménez, J. Aleman, J. R. Mihaljevic, S. Olivas, J. Marks, R. Izurieta, N. Nieto, P. Keim, G. Trueba, J. G. Caporaso, and T. Pearson. 2021. Leptospira in river and soil in a highly endemic area of Ecuador. BMC Microbiology 21:17-17.

O’Rourke, D. R., M. T. Mangan, K. E. Mangan, N. A. Bokulich, M. D. MacManes, and J. T. Foster. 2021. Lord of the Diptera (and moths and a spider): molecular diet analyses and foraging ecology of Indiana bats in Illinois. Frontiers in Ecology and Evolution 9.

Öhrman, C., J. W. Sahl, A. Sjödin, I. Uneklint, R. Ballard, L. Karlsson, R. F. McDonough, D. Sundell, K. Soria, S. Bäckman, K. Chase, B. Brindefalk, S. Sozhamannan, A. Vallesi, E. Hägglund, J. G. Ramirez-Paredes, J. Thelaus, D. Colquhoun, K. Myrtennäs, D. Birdsell, A. Johansson, D. M. Wagner, and M. Forsman. 2021. Reorganized genomic taxonomy of Francisellaceae enables design of robust environmental pcr assays for detection of Francisella tularensis. Microorganisms 9:146.

Panisello Yagüe, D., J. Mihaljevic, M. Mbegbu, C. V. Wood, C. Hepp, S. Kyman, H. Hornstra, R. Trotter, E. Cope, and T. Pearson. 2021. Survival of Staphylococcus aureus on sampling swabs stored at different temperatures. Journal of Applied Microbiology:10.1111/jam.15023.

Porter, W. T., Z. A. Barrand, J. Wachara, K. DaVall, J. R. Mihaljevic, T. Pearson, D. J. Salkeld, and N. C. Nieto. 2021. Predicting the current and future distribution of the western black-legged tick, Ixodes pacificus, across the Western US using citizen science collections. PLoS One 16:e0244754-e0244754.

Ridenour, C. L., J. Cocking, S. Poidmore, D. Erickson, B. Brock, M. Valentine, C. C. Roe, S. J. Young, J. A. Henke, K. Y. Hung, J. Wittie, E. Stefanakos, C. Sumner, M. Ruedas, V. Raman, N. Seaton, W. Bendik, H. M. Hornstra O’Neill, K. Sheridan, H. Centner, D. Lemmer, V. Fofanov, K. Smith, J. Will, J. Townsend, J. T. Foster, P. S. Keim, D. M. Engelthaler, and C. M. Hepp. 2021. St. Louis Encephalitis Virus in the Southwestern United States: a phylogeographic case for a multi-variant introduction event. Frontiers in Genetics 12:667895-667895.

Sanchez, J. E., S. A. Jaramillo, E. Settles, J. J. Velazquez Salazar, A. Lehr, J. Gonzalez, C. Rodríguez Aranda, H. R. Navarro-Contreras, M. O. Raniere, M. Harvey, D. M. Wagner, A. Koppisch, R. Kellar, P. Keim, and M. Jose Yacaman. 2021. Detection of SARS-CoV-2 and its S and N proteins using surface enhanced Raman spectroscopy. RSC Advances 11:25788-25794.

Smith, T. J., C. H. D. Williamson, K. K. Hill, S. L. Johnson, G. Xie, F. Anniballi, B. Auricchio, R. A. Fernández, P. A. Caballero, P. Keim, and J. W. Sahl. 2021. The distinctive evolution of orfx Clostridium parabotulinum strains and their botulinum neurotoxin type A and F gene clusters is influenced by environmental factors and gene interactions via mobile genetic elements. Frontiers in Microbiology 12:566908-566908.

Sobek, C. J., and F. M. Walker. 2021. Square salads: exploring the diet of the southern hairy-nosed wombat (Lasiorhinus latifrons) via DNA metabarcoding. Australian Mammalogy 43:104-109.

Somprasong, N., C. M. Hall, J. R. Webb, J. W. Sahl, D. M. Wagner, P. Keim, B. J. Currie, and H. P. Schweizer. 2021a. Burkholderia ubonensis high-level tetracycline resistance is due to efflux pump synergy involving a novel TetA(64) resistance determinant. Antimicrobial Agents and Chemotherapy 65:e01767-01720.

Somprasong, N., J. Yi, C. M. Hall, J. R. Webb, J. W. Sahl, D. M. Wagner, P. Keim, B. J. Currie, and H. P. Schweizer. 2021b. Conservation of resistance-nodulation-cell division efflux pump-mediated antibiotic resistance in Burkholderia cepacia complex and Burkholderia pseudomallei complex species. Antimicrobial Agents and Chemotherapy 65:e0092021-e0092021.

Stone, N. E., S. A. Jaramillo, A. N. Jones, A. J. Vazquez, M. Martz, L. M. Versluis, M. O. Raniere, H. E. Nunnally, K. E. Zarn, R. Nottingham, K. R. Ng, J. W. Sahl, D. M. Wagner, S. Knudsen, E. W. Settles, P. Keim, and C. T. French. 2021a. Stenoparib, an inhibitor of cellular poly (Adp-ribose) polymerase, blocks replication of the SARS-COV-2 and HCOV-nl63 human coronaviruses in vitro. mBio 12.

Stone, N. E., A. E. Nunnally, C. C. Roe, H. M. Hornstra, D. M. Wagner, and J. W. Sahl. 2021b. Complete genome sequence of Peptacetobacter (Clostridium) hiranonis strain DGF055142, isolated from dog feces from Flagstaff, Arizona, USA, 2019. Microbiology Resource Announcements 10:e00067-00021.

Suárez-Esquivel, M., N. Ruiz-Villalobos, W. Hidalgo-Jara, C. Chacón-Díaz, A. M. Zúñiga-Pereira, M. Masís-Mora, E. Fernández-Fernández, G. Hernández-Mora, E. Barquero-Calvo, E. Chaves-Olarte, N. R. Thomson, J. T. Foster, E. Moreno, and C. Guzmán-Verri. 2021. Canine brucellosis in Costa Rica reveals widespread Brucella canis infection and the recent introduction of foreign strains. Veterinary Microbiology 257:109072.

Teixeira, M., B. F. Lang, D. R. Matute, J. E. Stajich, and B. M. Barker. 2021a. Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii. G3 Genes|Genomes|Genetics 11.

Teixeira, M., J. E. Stajich, J. W. Sahl, G. R. Thompson, A. V. Blackmon, H. L. Mead, P. Keim, and B. M. Barker. 2021b. A chromosomal-level reference genome of the widely utilized Coccidioides posadasii laboratory strain “Silveira”. bioRxiv.

van Dijk, J. G. B., S. A. Iverson, H. G. Gilchrist, N. J. Harms, H. L. Hennin, O. P. Love, E. I. Buttler, S. Lesceu, J. T. Foster, M. R. Forbes, and C. Soos. 2021. Herd immunity drives the epidemic fadeout of avian cholera in Arctic-nesting seabirds. Scientific Reports 11:1046-1046.

Van Dyke, M. C., H. L. Mead, M. Bryant, K. L. Laux, D. R. Kollath, V. K. Coyne, K. J. Miller, N. E. Stone, S. A. Jaramillo, P. Keim, C. Milikowski, V. K. Gupta, S. M. Vickers, A. K. Saluja, M. R. Velagapudi, and B. M. Barker. 2021. The effect of minnelide against SARS-CoV-2 in a murine model. bioRxiv.

Vizentin-Bugoni, J., J. H. Sperry, J. P. Kelley, J. M. Gleditsch, J. T. Foster, D. R. Drake, A. M. Hruska, R. C. Wilcox, S. B. Case, and C. E. Tarwater. 2021. Ecological correlates of species’ roles in highly invaded seed dispersal networks. Proceedings of the National Academy of Sciences USA 118:e2009532118.

Walker, F. M., R. Durben, S. M. Shuster, R. L. Lindroth, and T. G. Whitham. 2021a. Heterozygous trees rebound the fastest after felling by beavers to positively affect arthropod community diversity. Forests 12:694.

Walker, F. M., C. J. Sobek, C. E. Platts-McPharlin, and C. L. Chambers. 2021b. Relatedness and genetic structure of big brown bat (Eptesicus fuscus) maternity colonies in an urban-wildland interface with periodic rabies virus outbreaks. Journal of Wildlife Diseases 57:303–312.

Walker, F. M., J. R. Upton, C. J. Sobek, D. A. Taggart, and M. D. Gaughwin. 2021c. Genetic monitoring of southern hairy-nosed wombats over two decades reveals that individuals can live for at least 18 years in the same warrens. Australian Mammalogy 43:22-29.

Whatmore, A. M., and J. T. Foster. 2021. Emerging diversity and ongoing expansion of the genus Brucella. Infection, Genetics and Evolution 92:104865.

Whitmer, S. L., M. K. Lo, H. M. Sazzad, S. Zufan, E. S. Gurley, S. Sultana, B. Amman, J. T. Ladner, M. Z. Rahman, and S. Doan. 2021. Inference of Nipah virus evolution, 1999–2015. Virus Evolution 7:veaa062.

Wood, C., J. Sahl, S. Maltinsky, B. Coyne, B. Russakoff, D. P. Yagüe, J. Bowers, and T. Pearson. 2021. SaQuant: a real-time PCR assay for quantitative assessment of Staphylococcus aureus. BMC Microbiology 21:174-174.

Yang, Y., J. T. Foster, M. Yi, L. Zhan, Y. Zhang, B. Zhou, J. Jiang, and L. Mei. 2021. Phenotypic homogeneity of emetic Bacillus cereus isolates in China. Letters in Applied Microbiology.

Allen, A. R., G. Milne, K. Drees, E. Presho, J. Graham, P. McAdam, K. Jones, L. Wright, R. Skuce, A. M. Whatmore, J. Graham, and J. T. Foster. 2020. Genomic epizootiology of a Brucella abortus outbreak in Northern Ireland (1997–2012). Infection, Genetics and Evolution 81:104235.

Barger, S. D., M. R. Lininger, R. T. Trotter, 2nd, H. A. Wayment, M. Mbegbu, S. Kyman, and T. Pearson. 2020. Educational attainment and Staphylococcus aureus colonization in a Hispanic border community: testing fundamental cause theory. mSphere 5:e00623-00620.

Bassiouni, A., S. Paramasivan, A. Shiffer, M. R. Dillon, E. K. Cope, C. Cooksley, M. Ramezanpour, S. Moraitis, M. J. Ali, B. S. Bleier, C. Callejas, M. E. Cornet, R. G. Douglas, D. Dutra, C. Georgalas, R. J. Harvey, P. H. Hwang, A. U. Luong, R. J. Schlosser, P. Tantilipikorn, M. A. Tewfik, S. Vreugde, P.-J. Wormald, J. G. Caporaso, and A. J. Psaltis. 2020. Microbiotyping the sinonasal microbiome. Frontiers in Cellular and Infection Microbiology 10.

Biggs, T. D., M. A. Karavis, J. V. Harris, J. M. Hill, R. C. Bernhards, L. B. Price, P. Keim, B. G. Goodwin, and S. Sozhamannan. 2020. Draft whole-genome sequences of Ciprofloxacin-resistant derivatives of a Bacillus anthracis ΔANR strain lacking pXO1 and pXO2 plasmids. Microbiology Resource Announcements 9:e00056-00020.

Biot, F. V., B. A. Bachert, K. D. Mlynek, R. G. Toothman, G. I. Koroleva, S. P. Lovett, C. P. Klimko, G. F. Palacios, C. K. Cote, J. T. Ladner, and J. A. Bozue. 2020. Evolution of antibiotic resistance in surrogates of Francisella tularensis (LVS and Francisella novicida): effects on biofilm formation and fitness. Frontiers in Microbiology 11:593542-593542.

Bokulich, N. A., P. Łaniewski, D. M. Chase, J. G. Caporaso, and M. M. Herbst-Kralovetz. 2020. Integration of multi-omics data improves prediction of cervicovaginal microenvironment in cervical cancer. medRxiv.

Bolyen, E., M. R. Dillon, N. A. Bokulich, J. T. Ladner, B. B. Larsen, C. M. Hepp, D. Lemmer, J. W. Sahl, A. Sanchez, C. Holdgraf, C. Sewell, A. G. Choudhury, J. Stachurski, M. McKay, A. Simard, D. M. Engelthaler, M. Worobey, P. Keim, and J. G. Caporaso. 2020. Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity. F1000 Research 9:657-657.

Borsom, E. M., K. Lee, and E. K. Cope. 2020. Do the bugs in your gut eat your memories? relationship between gut microbiota and Alzheimer’s disease. Brain Sciences 10:814.

Brown, J. J., J. R. Mihaljevic, L. Des Marteaux, and J. Hrček. 2020. Metacommunity theory for transmission of heritable symbionts within insect communities. Ecology and Evolution 10:1703-1721.

Chandler, C. E., E. M. Harberts, M. R. Pelletier, I. Thaipisuttikul, J. W. Jones, A. M. Hajjar, J. W. Sahl, D. R. Goodlett, A. C. Pride, D. A. Rasko, M. S. Trent, R. E. Bishop, and R. K. Ernst. 2020. Early evolutionary loss of the lipid A modifying enzyme PagP resulting in innate immune evasion in Yersinia pestis. Proceedings of the National Academy of Sciences USA 117:22984-22991.

Cocking, J. H., M. Deberg, J. Schupp, J. Sahl, K. Wiggins, A. Porty, H. M. Hornstra, C. Hepp, C. Jardine, T. N. Furstenau, A. Schulte-Hostedde, V. Y. Fofanov, and T. Pearson. 2020. Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples. Genomics 112:1872-1878.

Estaki, M., L. Jiang, N. A. Bokulich, D. McDonald, A. González, T. Kosciolek, C. Martino, Q. Zhu, A. Birmingham, Y. Vázquez‐Baeza, M. R. Dillon, E. Bolyen, J. G. Caporaso, and R. Knight. 2020. QIIME 2 enables comprehensive end‐to‐end analysis of diverse microbiome data and comparative studies with publicly available data. Current Protocols in Bioinformatics 70.

Eudes Filho, J., I. B. D. Santos, C. M. S. Reis, J. S. L. Patané, V. Paredes, J. P. R. A. Bernardes, S. d. S. C. Poggiani, T. d. C. B. Castro, O. M. Gomez, and S. A. Pereira. 2020. A novel Sporothrix brasiliensis genomic variant in Midwestern Brazil: evidence for an older and wider sporotrichosis epidemic. Emerging Microbes & Infections 9:2515-2525.

Fink, Z. W., V. Martinez, J. Altin, and J. T. Ladner. 2020. PepSIRF: a flexible and comprehensive tool for the analysis of data from highly-multiplexed DNA-barcoded peptide assays. arXiv 2007.05050.

Foster, J. T., R. L. Bull, and P. Keim. 2020. Ricin Forensics: Comparisons to Microbial Forensics. Pages 241-250 in B. Budowle, S. A. Morse, and S. Schutzer, editors. Microbial Forensics, 3rd edition. Elsevier Press.

Gaughwin, M., A. Horsup, C. Dickman, R. Wells, F. Walker, and D. Taggart. 2020. Variation in the sex ratio of pouch young and adult hairy-nosed wombats (Lasiorhinus latifrons and Lasiorhinus krefftii). Behavioral Ecology and Sociobiology 74:90.

Herold, M., S. Martínez Arbas, S. Narayanasamy, A. R. Sheik, L. A. K. Kleine-Borgmann, L. A. Lebrun, B. J. Kunath, H. Roume, I. Bessarab, R. B. H. Williams, J. D. Gillece, J. M. Schupp, P. S. Keim, C. Jäger, M. R. Hoopmann, R. L. Moritz, Y. Ye, S. Li, H. Tang, A. Heintz-Buschart, P. May, E. E. L. Muller, C. C. Laczny, and P. Wilmes. 2020. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nature Communications 11:5281-5281.

Hoyt, J. R., K. E. Langwig, K. Sun, K. L. Parise, A. Li, Y. Wang, X. Huang, L. Worledge, H. Miller, J. P. White, H. M. Kaarakka, J. A. Redell, T. Görföl, S. A. Boldogh, D. Fukui, M. Sakuyama, S. Yachimori, A. Sato, M. Dalannast, A. Jargalsaikhan, N. Batbayar, Y. Yovel, E. Amichai, I. Natradze, W. F. Frick, J. T. Foster, J. Feng, and A. M. Kilpatrick. 2020. Environmental reservoir dynamics predict global infection patterns and population impacts for the fungal disease white-nose syndrome. Proceedings of the National Academy of Sciences USA 117:7255-7262.

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Mbala-Kingebeni, P., A. Aziza, N. Di Paola, M. R. Wiley, S. Makiala-Mandanda, K. Caviness, C. B. Pratt, J. T. Ladner, J. R. Kugelman, and K. Prieto. 2019. Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment. The Lancet Infectious Diseases 19:648-657.

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Taylor, J. W., and B. M. Barker. 2019. The endozoan, small-mammal reservoir hypothesis and the life cycle of Coccidioides species. Medical Mycology 57:S16-S20.

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Van Dyke, M. C. C., G. R. Thompson 3rd, J. N. Galgiani, and B. M. Barker. 2019b. The rise of coccidioides: forces against the dust devil unleashed. Frontiers in Immunology 10:2188.

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Walker, F. M., A. Tobin, N. B. Simmons, C. J. Sobek, D. E. Sanchez, C. L. Chambers, and V. Y. Fofanov. 2019. A fecal sequel: Testing the limits of a genetic assay for bat species identification. PLoS One 14:e0224969.

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Beck, L., S. Coates, J. Gee, T. Hadfield, P. Jackson, P. Keim, L. Lindler, V. Olson, E. Ostlund, and F. Roberto. 2018. Overview of Performance Standards for Biological Threat Agent Assays for Department of Defense Applications. Journal of AOAC International 101:1665.

Birdsell, D. N., Y. Özsürekci, A. Rawat, A. E. Aycan, C. L. Mitchell, J. W. Sahl, A. Johansson, R. E. Colman, J. M. Schupp, and M. Ceyhan. 2018. Coinfections identified from metagenomic analysis of cervical lymph nodes from tularemia patients. BMC Infectious Diseases 18:1-8.

Boehmer, T., A. J. Vogler, A. Thomas, S. Sauer, M. Hergenroether, R. K. Straubinger, D. Birdsell, P. Keim, J. W. Sahl, and C. H. D. Williamson. 2018. Phenotypic characterization and whole genome analysis of extended-spectrum beta-lactamase-producing bacteria isolated from dogs in Germany. PLoS One 13:e0206252.

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Cattana, M. E., M. D. M. Teixeira, M. F. Tracogna, A. Arechavala, R. Negroni, G. Santiso, N. Cech, J. M. Ortellado, Y. A. Chacon, and G. Nino-Vega. 2018. Whole genome sequencing of P. brasiliensis isolates of endemic areas in Argentina and Paraguay. Pages S25-S25  Medical Mycology. Oxford University Press, Oxford, UK.

Deatherage Kaiser, B. L., K. K. Hill, T. J. Smith, C. H. D. Williamson, P. Keim, J. W. Sahl, and K. L. Wahl. 2018. Proteomic analysis of four Clostridium botulinum strains identifies proteins that link biological responses to proteomic signatures. PLoS One 13:e0205586.

Dokubo, E. K., A. Wendland, S. E. Mate, J. T. Ladner, E. L. Hamblion, P. Raftery, D. J. Blackley, A. S. Laney, N. Mahmoud, and G. Wayne-Davies. 2018. Persistence of Ebola virus after the end of widespread transmission in Liberia: an outbreak report. The Lancet Infectious Diseases 18:1015-1024.

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Enger, K. S., J. Mitchell, B. Murali, D. N. Birdsell, P. Keim, P. L. Gurian, and D. M. Wagner. 2018. Evaluating the long‐term persistence of Bacillus spores on common surfaces. Microbial Biotechnology 11:1048-1059.

Fleshman, A., K. Mullins, J. Sahl, C. Hepp, N. Nieto, K. Wiggins, H. Hornstra, D. Kelly, T.-C. Chan, and R. Phetsouvanh. 2018a. Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity. Microbial Genomics 4.

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Foster, J. T., F. M. Walker, B. D. Rannals, M. H. Hussain, K. P. Drees, R. V. Tiller, A. R. Hoffmaster, A. Al-Rawahi, P. Keim, and M. Saqib. 2018. African lineage Brucella melitensis isolates from Omani livestock. Frontiers in Microbiology 8.

Furstenau, T. N., J. H. Cocking, J. W. Sahl, and V. Y. Fofanov. 2018. Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites. BMC Bioinformatics 19:1-13.

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Hoyt, J. R., K. E. Langwig, J. P. White, H. M. Kaarakka, J. A. Redell, A. Kurta, J. E. DePue, W. H. Scullon, K. L. Parise, J. T. Foster, W. F. Frick, and A. M. Kilpatrick. 2018. Cryptic connections illuminate pathogen transmission within community networks. Nature 563:710-713.

Jimenez, V., Jr., R. Moreno, E. Settles, B. J. Currie, P. Keim, and F. P. Monroy. 2018. A mouse model of binge alcohol consumption and Burkholderia infection. PLoS One 13:e0208061.

Kaufman, E. L., N. E. Stone, G. A. Scoles, C. M. Hepp, J. D. Busch, and D. M. Wagner. 2018. Range-wide genetic analysis of Dermacentor variabilis and its Francisella-like endosymbionts demonstrates phylogeographic concordance between both taxa. Parasites & Vectors 11:1-11.

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Koster, K. J., A. Largen, J. T. Foster, K. P. Drees, L. Qian, E. Desmond, X. Wan, S. Hou, and J. T. Douglas. 2018b. Genomic sequencing is required for identification of tuberculosis transmission in Hawaii. BMC Infectious Diseases 18:608.

Liu, C. M., M. Stegger, M. Aziz, T. J. Johnson, K. Waits, L. Nordstrom, L. Gauld, B. Weaver, D. Rolland, S. Statham, J. Horwinski, S. Sariya, G. S. Davis, E. Sokurenko, P. Keim, J. R. Johnson, and L. B. Price. 2018. Escherichia coli ST131-H22 as a foodborne uropathogen. mBio 9.

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Smith, T., C. H. D. Williamson, K. Hill, J. Sahl, and P. Keim. 2018. Botulinum neurotoxin-producing bacteria. Isn’t it time that we called a species a species? mBio 9.

Teixeira, M. M., and B. M. Barker. 2018. Phylogenetic genome-level trees, population genetics and species delineation in dimorphic fungi: Does it help us understand infection? Pages S29-S29  Medical Mycology. Oxford University Press, Oxford, UK.

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Woolbright, S. A., B. J. Rehill, R. L. Lindroth, S. P. DiFazio, G. D. Martinsen, M. S. Zinkgraf, G. J. Allan, P. Keim, and T. G. Whitham. 2018. Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery. Ecology and Evolution 8:3726-3737.

Al Dahouk, S., S. Kohler, A. Occhialini, M. P. Jimenez de Bagues, J. A. Hammerl, T. Eisenberg, G. Vergnaud, A. Cloeckaert, M. S. Zygmunt, A. M. Whatmore, F. Melzer, K. P. Drees, J. T. Foster, A. R. Wattam, and H. C. Scholz. 2017. Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts. Scientific Reports 7:44420.

Antwerpen, M. H., J. W. Sahl, D. Birdsell, T. Pearson, M. J. Pearce, C. Redmond, H. Meyer, and P. S. Keim. 2017. Unexpected relations of historical anthrax strain. mBio 8.

Barker, B. M. 2017. The changing epidemiology and diagnosis of Valley Fever. Clinical Microbiology Newsletter 39:159-164.

Barragan, V., N. Nieto, P. Keim, and T. Pearson. 2017a. Meta-analysis to estimate the load of Leptospira excreted in urine: beyond rats as important sources of transmission in low-income rural communities. BMC Research Notes 10:71.

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Bernard, R. F., E. V. Willcox, K. L. Parise, J. T. Foster, and G. F. McCracken. 2017. White-nose syndrome fungus, Pseudogymnoascus destructans, on bats captured emerging from caves during winter in the southeastern United States. BMC Zoology 2:12.

Campana, M. G., N. P. Kurata, J. T. Foster, L. E. Helgen, D. M. Reeder, R. C. Fleischer, and K. M. Helgen. 2017. White-nose syndrome fungus in a 1918 bat specimen from France. Emerging Infectious Diseases 23:1611-1612.

Cheng, T. L., H. Mayberry, L. P. McGuire, J. R. Hoyt, K. E. Langwig, H. Nguyen, K. L. Parise, J. T. Foster, C. K. R. Willis, A. M. Kilpatrick, and W. F. Frick. 2017. Efficacy of a probiotic bacterium to treat bats affected by the disease white-nose syndrome. Journal of Applied Ecology 54:701-708.

Chewapreecha, C., M. T. Holden, M. Vehkala, N. Valimaki, Z. Yang, S. R. Harris, A. E. Mather, A. Tuanyok, B. De Smet, S. Le Hello, C. Bizet, M. Mayo, V. Wuthiekanun, D. Limmathurotsakul, R. Phetsouvanh, B. G. Spratt, J. Corander, P. Keim, G. Dougan, D. A. Dance, B. J. Currie, J. Parkhill, and S. J. Peacock. 2017. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nature Microbiology 2:16263.

Drees, K. P., J. M. Lorch, S. J. Puechmaille, K. L. Parise, G. Wibbelt, J. R. Hoyt, K. Sun, A. Jargalsaikhan, M. Dalannast, J. M. Palmer, D. L. Lindner, A. Marm Kilpatrick, T. Pearson, P. S. Keim, D. S. Blehert, and J. T. Foster. 2017a. Phylogenetics of a fungal invasion: origins and widespread dispersal of white-nose syndrome. mBio 8:e01941-01917.

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Ertz-Archambault, N., P. Keim, and D. Von Hoff. 2017. Microbiome and pancreatic cancer: A comprehensive topic review of literature. World Journal of Gastroenterology 23:1899-1908.

Frick, W. F., T. L. Cheng, K. E. Langwig, J. R. Hoyt, A. F. Janicki, K. L. Parise, J. T. Foster, and A. M. Kilpatrick. 2017. Pathogen dynamics during invasion and establishment of white-nose syndrome explain mechanisms of host persistence. Ecology 98:624-631.

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Gee, J., J. Arce, L. C. Beck, T. R. Blank, L. Blyn, R. Cahall, A. J. Clark, B. Currie, K. Damer, and M. Davenport. 2017. AOAC SMPR 2016.010: Standard Method Performance Requirements (SMPRs) for DNA-Based Methods of Detecting Burkholderia pseudomallei in Field-Deployable, Department of Defense Aerosol Collection Devices. Journal of AOAC International 100:261-265.

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Jimenez, V., Jr., R. Moreno, E. Kaufman, H. Hornstra, E. Settles, B. J. Currie, P. Keim, and F. P. Monroy. 2017. Effects of binge alcohol exposure on Burkholderia thailandensis-alveolar macrophage interaction. Alcohol 64:55-63.

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Lal, D., P. Keim, J. Delisle, B. Barker, M. A. Rank, N. Chia, J. M. Schupp, J. D. Gillece, and E. K. Cope. 2017. Mapping and comparing bacterial microbiota in the sinonasal cavity of healthy, allergic rhinitis, and chronic rhinosinusitis subjects. Pages 561-569 in International Forum of Allergy & Rhinology.

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Merkley, E. D., L. H. Sego, A. Lin, O. P. Leiser, B. L. D. Kaiser, J. N. Adkins, P. S. Keim, D. M. Wagner, and H. W. Kreuzer. 2017. Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague. PLoS One 12:e0183478.

Mitchell, C. L., V. Andrianaivoarimanana, R. E. Colman, J. Busch, H. Hornstra-O’Neill, P. S. Keim, D. M. Wagner, M. Rajerison, and D. N. Birdsell. 2017. Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model. PLoS Neglected Tropical Diseases 11:e0006077.

Mueller, L. O., L. C. Breza, M. A. Genung, C. P. Giardina, N. E. Stone, L. C. Sidak‐Loftis, J. D. Busch, D. M. Wagner, J. K. Bailey, and J. A. Schweitzer. 2017. Ecosystem consequences of plant genetic divergence with colonization of new habitat. Ecosphere 8:e01743.

Muller, E. E. L., S. Narayanasamy, M. Zeimes, C. C. Laczny, L. A. Lebrun, M. Herold, N. D. Hicks, J. D. Gillece, J. M. Schupp, P. Keim, and P. Wilmes. 2017. First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ. Standards in Genomic Sciences 12:64.

Niño-Vega, G. A., E. Camacho, Á. Restrepo, Á. Tobón, B. Gómez, M. Teixeira, and B. M. Barker. 2017. Paracoccidioides spp and paracoccidioidomycosis. Pages 281-308  Current Progress in Medical Mycology. Springer.

Nualnoi, T., M. H. Norris, A. Tuanyok, P. J. Brett, M. N. Burtnick, P. S. Keim, E. W. Settles, C. J. Allender, and D. P. AuCoin. 2017. Development of Immunoassays for Burkholderia pseudomallei Typical and Atypical Lipopolysaccharide Strain Typing. American Journal of Tropical Medical and Hygiene 96:358-367.

Podnecky, N. L., K. A. Rhodes, T. Mima, H. R. Drew, S. Chirakul, V. Wuthiekanun, J. M. Schupp, D. S. Sarovich, B. J. Currie, P. Keim, and H. P. Schweizer. 2017. Mechanisms of Resistance to Folate Pathway Inhibitors in Burkholderia pseudomallei: Deviation from the Norm. mBio 8.

Price, E. P., D. S. Sarovich, J. R. Webb, C. M. Hall, S. A. Jaramillo, J. W. Sahl, M. Kaestli, M. Mayo, G. Harrington, and A. L. Baker. 2017. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis. PLoS Neglected Tropical Diseases 11:e0005928.

Sahl, J. W., J. R. Sistrunk, N. I. Baby, Y. Begum, Q. Luo, A. Sheikh, F. Qadri, J. M. Fleckenstein, and D. A. Rasko. 2017. Insights into enterotoxigenic Escherichia coli diversity in Bangladesh utilizing genomic epidemiology. Scientific Reports 7:1-12.

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Teixeira, M. M., L. F. Moreno, B. J. Stielow, A. Muszewska, M. Hainaut, L. Gonzaga, A. Abouelleil, J. S. Patané, M. Priest, R. Souza, S. Young, K. S. Ferreira, Q. Zeng, M. M. da Cunha, A. Gladki, B. Barker, V. A. Vicente, E. M. de Souza, S. Almeida, B. Henrissat, A. T. Vasconcelos, S. Deng, H. Voglmayr, T. A. Moussa, A. Gorbushina, M. S. Felipe, C. A. Cuomo, and G. S. de Hoog. 2017. Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota). Studies in Mycology 86:1-28.

Thompson, G. R., B. M. Barker, and N. P. Wiederhold. 2017. Large-scale evaluation of in vitro amphotericin B, triazole, and echinocandin activity against Coccidioides species from US institutions. Antimicrobial Agents and Chemotherapy 61.

Tuanyok, A., M. Mayo, H. Scholz, C. M. Hall, C. J. Allender, M. Kaestli, J. Ginther, S. Spring-Pearson, M. C. Bollig, J. K. Stone, E. W. Settles, J. D. Busch, L. Sidak-Loftis, J. W. Sahl, A. Thomas, L. Kreutzer, E. Georgi, J. E. Gee, R. A. Bowen, J. T. Ladner, S. Lovett, G. Koroleva, G. Palacios, D. M. Wagner, B. J. Currie, and P. Keim. 2017. Burkholderia humptydooensis sp. nov., a new species related to Burkholderia thailandensis and the fifth member of the Burkholderia pseudomallei complex. Applied and Environmental Microbiology 83.

Venkateswaran, K., N. K. Singh, A. Checinska Sielaff, R. K. Pope, N. H. Bergman, S. P. van Tongeren, N. B. Patel, P. A. Lawson, M. Satomi, C. H. D. Williamson, J. W. Sahl, P. Keim, D. Pierson, and J. Perry. 2017. Non-toxin-producing Bacillus cereus strains belonging to the B. anthracis clade isolated from the International Space Station. mSystems 2.

Vogler, A. J., V. Andrianaivoarimanana, S. Telfer, C. M. Hall, J. W. Sahl, C. M. Hepp, H. Centner, G. Andersen, D. N. Birdsell, L. Rahalison, R. Nottingham, P. Keim, D. M. Wagner, and M. Rajerison. 2017. Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague. PLoS Neglected Tropical Diseases 11:e0005887.

Williamson, C. H. D., T. J. Smith, B. T. Foley, K. Hill, P. Keim, and J. W. Sahl. 2017a. Botulinum-neurotoxin-like sequences identified from an Enterococcus sp. genome assembly. bioRxiv:228098.

Williamson, C. H. D., A. J. Vazquez, K. Hill, T. J. Smith, R. Nottingham, N. E. Stone, C. J. Sobek, J. H. Cocking, R. A. Fernández, and P. A. Caballero. 2017b. Differentiating botulinum neurotoxin-producing Clostridia with a simple, multiplex PCR assay. Applied and Environmental Microbiology 83.

Yaglom, H., E. Rodriguez, M. Gaither, M. Schumacher, N. Kwit, C. Nelson, J. Terriquez, J. Vinocur, D. Birdsell, and D. M. Wagner. 2017. Notes from the field: fatal pneumonic tularemia associated with dog exposure—Arizona, June 2016. MMWR Morbidity and mortality weekly report 66:891-891.

Zhang, I., S. D. Pletcher, A. N. Goldberg, B. M. Barker, and E. K. Cope. 2017. Fungal microbiota in chronic airway inflammatory disease and emerging relationships with the host immune response. Frontiers in Microbiology 8:2477.

Avena, C. V., L. W. Parfrey, J. W. Leff, H. M. Archer, W. F. Frick, K. E. Langwig, A. M. Kilpatrick, K. E. Powers, J. T. Foster, and V. J. McKenzie. 2016. Deconstructing the bat skin microbiome: influences of the host and the environment. Frontiers in Microbiology 7.

Barragan, V., J. Chiriboga, E. Miller, S. Olivas, D. Birdsell, C. Hepp, H. Hornstra, J. M. Schupp, M. Morales, M. Gonzalez, S. Reyes, C. de la Cruz, P. Keim, R. Hartskeerl, G. Trueba, and T. Pearson. 2016a. High Leptospira diversity in animals and humans complicates the search for common reservoirs of human disease in rural Ecuador. PLoS Neglected Tropical Diseases 10:e0004990.

Barragan, V., J. W. Sahl, K. Wiggins, J. Chiriboga, A. Salinas, N. E. Cantos, M. N. Loor, B. I. Intriago, M. Morales, and G. Trueba. 2016b. Draft genome sequence of the first pathogenic Leptospira isolates from ecuador. Genome Announcements 4.

Blanchong, J. A., S. J. Robinson, M. D. Samuel, and J. T. Foster. 2016. Application of genetics and genomics to wildlife epidemiology. Journal of Wildlife Management 80:593-608.

Bos, K. I., A. Herbig, J. Sahl, N. Waglechner, M. Fourment, S. A. Forrest, J. Klunk, V. J. Schuenemann, D. Poinar, M. Kuch, G. B. Golding, O. Dutour, P. Keim, D. M. Wagner, E. C. Holmes, J. Krause, and H. N. Poinar. 2016. Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus. Elife 5:e12994.

Bowers, J. R., D. Lemmer, J. W. Sahl, T. Pearson, E. M. Driebe, D. M. Engelthaler, and P. Keim. 2016a. KlebSeq: a diagnostic tool for healthcare surveillance and antimicrobial resistance monitoring of Klebsiella pneumoniae. bioRxiv:043471.

Bowers, J. R., D. Lemmer, J. W. Sahl, T. Pearson, E. M. Driebe, B. Wojack, M. A. Saubolle, D. M. Engelthaler, and P. Keim. 2016b. KlebSeq, a diagnostic tool for surveillance, detection, and monitoring of Klebsiella pneumoniae. Journal of Clinical Microbiology 54:2582-2596.

Chow, N. A., D. W. Griffin, B. M. Barker, V. N. Loparev, and A. P. Litvintseva. 2016. Molecular detection of airborne Coccidioides in Tucson, Arizona. Medical Mycology 54:584-592.

Cobble, K. R., K. J. Califf, N. E. Stone, M. M. Shuey, D. N. Birdsell, R. E. Colman, J. M. Schupp, M. Aziz, R. Van Andel, and T. E. Rocke. 2016. Genetic variation at the MHC DRB1 locus is similar across Gunnison’s prairie dog (Cynomys gunnisoni) colonies regardless of plague history. Ecology and Evolution 6:2624-2651.

Drees, K. P., J. M. Palmer, R. Sebra, J. M. Lorch, C. Chen, C. C. Wu, J. W. Bok, N. P. Keller, D. S. Blehert, C. A. Cuomo, D. L. Lindner, and J. T. Foster. 2016. Use of multiple sequencing technologies to produce a high-quality genome of the fungus Pseudogymnoascus destructans, the causative agent of bat white-nose syndrome. Genome Announcements 4.

Duggan, A. T., M. F. Perdomo, D. Piombino-Mascali, S. Marciniak, D. Poinar, M. V. Emery, J. P. Buchmann, S. Duchêne, R. Jankauskas, and M. Humphreys. 2016. 17th century variola virus reveals the recent history of smallpox. Current Biology 26:3407-3412.

Dwibedi, C., D. Birdsell, A. Larkeryd, K. Myrtennas, C. Ohrman, E. Nilsson, E. Karlsson, C. Hochhalter, A. Rivera, S. Maltinsky, B. Bayer, P. Keim, H. C. Scholz, H. Tomaso, M. Wittwer, C. Beuret, N. Schuerch, P. Pilo, M. Hernandez Perez, D. Rodriguez-Lazaro, R. Escudero, P. Anda, M. Forsman, D. M. Wagner, P. Larsson, and A. Johansson. 2016. Long-range dispersal moved Francisella tularensis into Western Europe from the East. Microbial Genomics 2:e000100.

Engelthaler, D. M., C. C. Roe, C. M. Hepp, M. Teixeira, E. M. Driebe, J. M. Schupp, L. Gade, V. Waddell, K. Komatsu, and E. Arathoon. 2016a. Local population structure and patterns of Western Hemisphere dispersal for Coccidioides spp., the fungal cause of Valley Fever. mBio 7.

Engelthaler, D. M., M. Valentine, J. Bowers, J. Pistole, E. M. Driebe, J. Terriquez, L. Nienstadt, M. Carroll, M. Schumacher, M. E. Ormsby, S. Brady, E. Livar, D. Yazzie, V. Waddell, M. Peoples, K. Komatsu, and P. Keim. 2016b. Hypervirulent emm59 Clone in Invasive Group A Streptococcus Outbreak, Southwestern United States. Emerging Infectious Diseases 22:734-738.

Garner, B. A., B. K. Hand, S. J. Amish, L. Bernatchez, J. T. Foster, K. M. Miller, P. A. Morin, S. R. Narum, S. J. O’Brien, G. Roffler, W. D. Templin, P. Sunnucks, J. Strait, K. I. Warheit, T. R. Seamons, J. Wenburg, J. Olsen, and G. Luikart. 2016. Genomics in conservation: case studies and bridging the gap between data and application. Trends in Ecology & Evolution 31:81-83.

Hammond, R. L., L. H. Crampton, and J. T. Foster. 2016. Nesting success of native and introduced forest birds on the island of Kaua’i. Journal of Avian Biology 47:252-262.

Hoyt, J. R., K. E. Langwig, K. Sun, G. Lu, K. L. Parise, T. Jiang, W. F. Frick, J. T. Foster, J. Feng, and A. M. Kilpatrick. 2016a. Host persistence or extinction from emerging infectious disease: insights from white-nose syndrome in endemic and invading regions. Proceedings of the Royal Society of London B: Biological Sciences 283:20152861.

Hoyt, J. R., K. P. Sun, K. L. Parise, G. J. Lu, K. E. Langwig, T. L. Jiang, S. B. Yang, W. F. Frick, A. M. Kilpatrick, J. T. Foster, and J. Feng. 2016b. Widespread bat white-nose syndrome fungus, northeastern China. Emerging Infectious Diseases 22:140-142.

Johnson, S. L., K. A. Bishop-Lilly, J. T. Ladner, H. E. Daligault, K. W. Davenport, J. Jaissle, K. G. Frey, G. I. Koroleva, D. C. Bruce, and S. R. Coyne. 2016a. Correction: Johnson et al., Complete genome sequences for 59 Burkholderia isolates, both pathogenic and near neighbor [Genome Announcements, 3, 2, e00159-15,(2015. Genome Announcements 4:e00313-00316.

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Kamath, P. L., J. T. Foster, K. P. Drees, G. Luikart, C. Quance, N. J. Anderson, P. R. Clarke, E. K. Cole, M. L. Drew, W. H. Edwards, J. C. Rhyan, J. J. Treanor, R. L. Wallen, P. J. White, S. Robbe-Austerman, and P. C. Cross. 2016. Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock. Nature Communications 7:11448.

Karlsson, E., I. Golovliov, A. Lärkeryd, M. Granberg, E. Larsson, C. Öhrman, M. Niemcewicz, D. Birdsell, D. M. Wagner, and M. Forsman. 2016. Clonality of erythromycin resistance in Francisella tularensis. Journal of Antimicrobial Chemotherapy 71:2815-2823.

Keim, P. 2016. A novel botulinum neurotoxin and how it tested our scientific institutions. Journal of Infectious Diseases 213:332-334.

Keim, P. S., D. Wagner, J. Appler, T. Bauer, L. Beck, J. Boylan, R. Cahall, K. Damer, M. Davenport, M. Forsman, S. H. Hinrichs, K. Kiss, L. Maple, S. A. Morse, P. Naraghi-Arani, J. Petersen, D. Pettit, M. Retford, M. Scheckelhoff, S. Shah, S. Sozhamannan, and S. G. Coates. 2016. AOAC SMPR(R) 2016.007. Journal of AOAC International 99:1090-1094.

Kersh, G. J., R. A. Priestley, H. M. Hornstra, J. S. Self, K. A. Fitzpatrick, B. J. Biggerstaff, P. Keim, T. Pearson, and R. F. Massung. 2016. Genotyping and axenic growth of Coxiella burnetii isolates found in the United States environment. Vector-Borne and Zoonotic Diseases 16:588-594.

Langwig, K. E., W. F. Frick, J. R. Hoyt, K. L. Parise, K. P. Drees, T. H. Kunz, J. T. Foster, and A. M. Kilpatrick. 2016. Drivers of variation in species impacts for a multi-host fungal disease of bats. Philosophical Transactions of the Royal Society of London Series B 371.

Leal, N. C., M. Sobreira, A. F. Q. Araújo, J. L. O. Magalhães, A. J. Vogler, M. C. Bollig, R. Nottingham, P. Keim, D. M. Wagner, and A. M. P. Almeida. 2016. Viability of Yersinia pestis subcultures in agar stabs. Letters in Applied Microbiology 62:91-95.

Lorch, J. M., J. M. Palmer, D. L. Lindner, A. E. Ballmann, K. G. George, K. Griffin, S. Knowles, J. R. Huckabee, K. H. Haman, C. D. Anderson, P. A. Becker, J. B. Buchanan, J. T. Foster, and D. S. Blehert. 2016. First detection of bat white-nose syndrome in Western North America. mSphere 1.

McGuire, L. P., J. M. Turner, L. Warnecke, G. McGregor, T. K. Bollinger, V. Misra, J. T. Foster, W. F. Frick, A. M. Kilpatrick, and C. K. Willis. 2016. White-nose syndrome disease severity and a comparison of diagnostic methods. EcoHealth 13:60-71.

Okinaka, R. T., and P. Keim. 2016. The Phylogeny of Bacillus cereus sensu lato. Microbiology Spectrum 4.

Olivas, S., H. Hornstra, R. A. Priestley, E. Kaufman, C. Hepp, D. L. Sonderegger, K. Handady, R. F. Massung, P. Keim, G. J. Kersh, and T. Pearson. 2016. Massive dispersal of Coxiella burnetii among cattle across the United States. Microbial Genomics 2:e000068.

Pearson, T., J. H. Cocking, H. M. Hornstra, and P. Keim. 2016. False detection of Coxiella burnetii-what is the risk? FEMS Microbiology Letters 363.

Price, E. P., B. MacHunter, B. G. Spratt, D. M. Wagner, B. J. Currie, and D. S. Sarovich. 2016a. Improved multilocus sequence typing of Burkholderia pseudomallei and closely related species. Journal of Medical Microbiology 65:992-997.

Price, E. P., D. S. Sarovich, E. J. Smith, B. MacHunter, G. Harrington, V. Theobald, C. M. Hall, H. M. Hornstra, E. McRobb, and Y. Podin. 2016b. Unprecedented melioidosis cases in northern Australia caused by an Asian Burkholderia pseudomallei strain identified by using large-scale comparative genomics. Applied and Environmental Microbiology 82:954-963.

Roe, C. C., K. S. Horn, E. M. Driebe, J. Bowers, J. A. Terriquez, P. Keim, and D. M. Engelthaler. 2016. Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections. Hereditas 153:11.

Sahl, J. W., D. Lemmer, J. Travis, J. M. Schupp, J. D. Gillece, M. Aziz, E. M. Driebe, K. Drees, N. Hicks, and C. H. D. Williamson. 2016a. The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets. bioRxiv:037267.

Sahl, J. W., D. Lemmer, J. Travis, J. M. Schupp, J. D. Gillece, M. Aziz, E. M. Driebe, K. P. Drees, N. D. Hicks, C. H. D. Williamson, C. M. Hepp, D. E. Smith, C. Roe, D. M. Engelthaler, D. M. Wagner, and P. Keim. 2016b. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microbial Genomics 2:e000074.

Sahl, J. W., T. Pearson, R. Okinaka, J. M. Schupp, J. D. Gillece, H. Heaton, D. Birdsell, C. Hepp, V. Fofanov, R. Noseda, A. Fasanella, A. Hoffmaster, D. M. Wagner, and P. Keim. 2016c. A Bacillus anthracis genome sequence from the Sverdlovsk 1979 autopsy specimens. mBio 7.

Sahl, J. W., A. J. Vazquez, C. M. Hall, J. D. Busch, A. Tuanyok, M. Mayo, J. M. Schupp, M. Lummis, T. Pearson, and K. Shippy. 2016d. The effects of signal erosion and core genome reduction on the identification of diagnostic markers. mBio 7.

Shabbir, M., M. Aleem, S. Javed, D. M. Wagner, P. S. Keim, S. A. Eqani, and H. Bokhari. 2016. Spatial analysis and identification of high risk plague regions in Pakistan based on associated rodent species distribution. Journal of Infection in Developing Countries 10:687-693.

Stone, N. E., L. C. Sidak-Loftis, J. W. Sahl, A. J. Vazquez, K. B. Wiggins, J. D. Gillece, N. D. Hicks, J. M. Schupp, J. D. Busch, and P. Keim. 2016. More than 50% of Clostridium difficile isolates from pet dogs in Flagstaff, USA, carry toxigenic genotypes. PLoS One 11:e0164504.

Teixeira, M. d. M., J. S. L. Patané, M. L. Taylor, B. L. Gómez, R. C. Theodoro, S. de Hoog, D. M. Engelthaler, R. M. Zancopé-Oliveira, M. S. S. Felipe, and B. M. Barker. 2016. Worldwide phylogenetic distributions and population dynamics of the genus Histoplasma. PLoS Neglected Tropical Diseases 10:e0004732.

Teixeira, M. M., and B. M. Barker. 2016. Use of population genetics to assess the ecology, evolution, and population structure of Coccidioides. Emerging Infectious Diseases 22:1022.

Vogler, A. J., P. Keim, and D. M. Wagner. 2016a. A review of methods for subtyping Yersinia pestis: from phenotypes to whole genome sequencing. Infection, Genetics and Evolution 37:21-36.

Vogler, A. J., R. Nottingham, J. D. Busch, J. W. Sahl, M. M. Shuey, J. T. Foster, J. M. Schupp, S. R. Smith, T. E. Rocke, P. Keim, and D. M. Wagner. 2016b. VNTR diversity in Yersinia pestis isolates from an animal challenge study reveals the potential for in vitro mutations during laboratory cultivation. Infection Genetics and Evolution 45:297-302.

Walker, F. M., C. H. D. Williamson, D. E. Sanchez, C. J. Sobek, and C. L. Chambers. 2016. Species from feces: order-wide identification of chiroptera from guano and other non-invasive genetic samples. PLoS One 11:e0162342.

Williamson, C. H. D., J. W. Sahl, T. J. Smith, G. Xie, B. T. Foley, L. A. Smith, R. A. Fernández, M. Lindström, H. Korkeala, P. Keim, J. Foster, and K. Hill. 2016a. Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia. BMC Genomics 17:1-20.

Williamson, C. H. D., A. Sanchez, A. Vazquez, J. Gutman, and J. W. Sahl. 2016b. Bacterial genome reduction as a result of short read sequence assembly. bioRxiv:091314.

Araya-Anchetta, A., J. D. Busch, G. A. Scoles, and D. M. Wagner. 2015. Thirty years of tick population genetics: a comprehensive review. Infection, Genetics and Evolution 29:164-179.

Austin, C. R., A. W. Goodyear, I. L. Bartek, A. Stewart, M. D. Sutherland, E. B. Silva, A. Zweifel, N. P. Vitko, A. Tuanyok, G. Highnam, D. Mittelman, P. Keim, H. P. Schweizer, A. Vazquez-Torres, S. W. Dow, and M. I. Voskuil. 2015. A Burkholderia pseudomallei colony variant necessary for gastric colonization. mBio 6.

Barlow, A. M., L. Worledge, H. Miller, K. P. Drees, P. Wright, J. T. Foster, C. Sobek, A. M. Borman, and M. Fraser. 2015. First confirmation of Pseudogymnoascus destructans in British bats and hibernacula. Veterinary Record 177.

Bauer, A. E., S. Olivas, M. Cooper, H. Hornstra, P. Keim, T. Pearson, and A. J. Johnson. 2015. Estimated herd prevalence and sequence types of Coxiella burnetii in bulk tank milk samples from commercial dairies in Indiana. BMC Veterinary Research 11:186.

Bernard, R. F., J. T. Foster, E. V. Willcox, K. L. Parise, and G. F. McCracken. 2015. Molecular detection of the causative agent of white-nose syndrome on Rafinesque’s big-eared bats (Corynorhinus rafinesquii) and two species of migratory bats in the southeastern USA. Journal of Wildlife Diseases 51:519-522.

Bowers, J. R., B. Kitchel, E. M. Driebe, D. R. MacCannell, C. Roe, D. Lemmer, T. de Man, J. K. Rasheed, D. M. Engelthaler, P. Keim, and B. M. Limbago. 2015. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic. PLoS One 10:e0133727.

Caffrey, A. K., M. M. Lehmann, J. M. Zickovich, V. Espinosa, K. M. Shepardson, C. P. Watschke, K. M. Hilmer, A. Thammahong, B. M. Barker, and A. Rivera. 2015. IL-1α signaling is critical for leukocyte recruitment after pulmonary Aspergillus fumigatus challenge. PLoS Pathogens 11:e1004625.

Califf, K. J., P. S. Keim, D. W. Wagner, and J. W. Sahl. 2015. Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics. Microbial Genomics 1.

Chiriboga, J., V. Barragan, G. Arroyo, A. Sosa, D. N. Birdsell, K. Espana, A. Mora, E. Espin, M. E. Mejia, M. Morales, C. Pinargote, M. Gonzalez, R. Hartskeerl, P. Keim, G. Bretas, J. N. Eisenberg, and G. Trueba. 2015. High Prevalence of Intermediate Leptospira spp. DNA in Febrile Humans from Urban and Rural Ecuador. Emerging Infectious Diseases 21:2141-2147.

Colman, R. E., J. M. Schupp, N. D. Hicks, D. E. Smith, J. L. Buchhagen, F. Valafar, V. Crudu, E. Romancenco, E. Noroc, L. Jackson, D. G. Catanzaro, T. C. Rodwell, A. Catanzaro, P. Keim, and D. M. Engelthaler. 2015. Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing. PLoS One 10:e0126626.

De Smet, B., M. Mayo, C. Peeters, J. E. A. Zlosnik, T. Spilker, T. J. Hird, J. J. LiPuma, T. J. Kidd, M. Kaestli, J. L. Ginther, D. M. Wagner, P. Keim, S. C. Bell, J. A. Jacobs, B. J. Currie, and P. Vandamme. 2015. Burkholderia stagnalis sp. nov. and Burkholderia territorii sp. nov., two novel Burkholderia cepacia complex species from environmental and human sources. International Journal of Systematic and Evolutionary Microbiology 65:2265-2271.

Deng, X., N. Shariat, E. M. Driebe, C. C. Roe, B. Tolar, E. Trees, P. Keim, W. Zhang, E. G. Dudley, P. I. Fields, and D. M. Engelthaler. 2015. Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis. Journal of Clinical Microbiology 53:212-218.

Driebe, E. M., J. W. Sahl, C. Roe, J. R. Bowers, J. M. Schupp, J. D. Gillece, E. Kelley, L. B. Price, T. R. Pearson, and C. M. Hepp. 2015. Using whole genome analysis to examine recombination across diverse sequence types of Staphylococcus aureus. PLoS One 10:e0130955.

Foster, J. T., T. Pearson, and P. Keim. 2015. Genomic microbiology as applied to animal forensics. Microbiologist 16:14-17.

Frick, W. F., S. J. Puechmaille, J. R. Hoyt, B. A. Nickel, K. E. Langwig, J. T. Foster, K. E. Barlow, T. Bartonicka, D. Feller, A. J. Haarsma, C. Herzog, I. Horacek, J. van der Kooij, B. Mulkens, B. Petrov, R. Reynolds, L. Rodrigues, C. W. Stihler, G. G. Turner, and A. M. Kilpatrick. 2015. Disease alters macroecological patterns of North American bats. Global Ecology and Biogeography 24:741-749.

Garofolo, G., J. T. Foster, K. Drees, K. Zilli, I. Platone, M. Ancora, C. Camma, F. De Massis, P. Calistri, and E. Di Giannatale. 2015. Genome sequences of 11 Brucella abortus isolates from persistently infected Italian regions. Genome Announcements 3.

Ginther, J. L., M. Mayo, S. D. Warrington, M. Kaestli, T. Mullins, D. M. Wagner, B. J. Currie, A. Tuanyok, and P. Keim. 2015. Identification of Burkholderia pseudomallei near-neighbor species in the Northern Territory of Australia. PLoS Neglected Tropical Diseases 9:e0003892.

Hall, C. M., J. D. Busch, K. Shippy, C. J. Allender, M. Kaestli, M. Mayo, J. W. Sahl, J. M. Schupp, R. E. Colman, P. Keim, B. J. Currie, and D. M. Wagner. 2015. Diverse Burkholderia species isolated from soils in the southern United States with no evidence of B. pseudomallei. PLoS One 10:e0143254.

Hammond, R. L., L. H. Crampton, and J. T. Foster. 2015. Breeding biology of two endangered forest birds on the island of Kauai, Hawaii. Condor 117:31-40.

Janicki, A. F., W. F. Frick, A. M. Kilpatrick, K. L. Parise, J. T. Foster, and G. F. McCracken. 2015. Efficacy of visual surveys for white-nose syndrome at bat hibernacula. PLoS One 10.

Jung, W., M. Barrett, C. Brooks, A. Rivera, D. N. Birdsell, D. M. Wagner, and F. Zenhausern. 2015. An air-pressure-free elastomeric valve for integrated nucleic acid analysis by capillary electrophoresis. Journal of Micromechanics and Microengineering 25:125004.

Karah, N., Ø. Samuelsen, R. Zarrilli, J. W. Sahl, S. N. Wai, and B. E. Uhlin. 2015. CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping. PLoS One 10:e0118205.

Keim, P., R. Grunow, R. Vipond, G. Grass, A. Hoffmaster, D. N. Birdsell, S. R. Klee, S. Pullan, M. Antwerpen, and B. N. Bayer. 2015. Whole genome analysis of injectional anthrax identifies two disease clusters spanning more than 13 years. EBioMedicine 2:1613-1618.

Kilic, S., D. N. Birdsell, A. Karagöz, B. Çelebi, Z. Bakkaloglu, M. Arikan, J. W. Sahl, C. Mitchell, A. Rivera, and S. Maltinsky. 2015. Water as source of Francisella tularensis infection in humans, Turkey. Emerging Infectious Diseases 21:2213.

Langwig, K. E., W. F. Frick, R. Reynolds, K. L. Parise, K. P. Drees, J. R. Hoyt, T. L. Cheng, T. H. Kunz, J. T. Foster, and A. M. Kilpatrick. 2015a. Host and pathogen ecology drive the seasonal dynamics of a fungal disease, white-nose syndrome. Proceedings of the Royal Society of London B: Biological Sciences 282.

Langwig, K. E., J. R. Hoyt, K. L. Parise, J. Kath, D. Kirk, W. F. Frick, J. T. Foster, and A. M. Kilpatrick. 2015b. Invasion dynamics of white-nose syndrome fungus, Midwestern United States, 2012-2014. Emerging Infectious Diseases 21:1023-1026.

Lee, M. J., H. Liu, B. M. Barker, B. D. Snarr, F. N. Gravelat, Q. Al Abdallah, C. Gavino, S. R. Baistrocchi, H. Ostapska, and T. Xiao. 2015. The fungal exopolysaccharide galactosaminogalactan mediates virulence by enhancing resistance to neutrophil extracellular traps. PLoS Pathogens 11:e1005187.

Leiser, O. P., E. D. Merkley, B. H. Clowers, B. L. Deatherage Kaiser, A. Lin, J. R. Hutchison, A. M. Melville, D. M. Wagner, P. S. Keim, and J. T. Foster. 2015. Investigation of Yersinia pestis laboratory adaptation through a combined genomics and proteomics approach. PLoS One 10:e0142997.

Lewis, E. R. G., J. R. Bowers, and B. M. Barker. 2015a. Dust devil: the life and times of the fungus that causes valley fever. PLoS Pathogens 11:e1004762.

Lewis, E. R. G., V. R. David, A. L. Doyle, K. Rajabi, J. A. Kiefer, P. Pirrotte, and B. M. Barker. 2015b. Differences in host innate response among isolates of Coccidioides in a murine model of pulmonary coccidioidomycosis. Eukaryotic Cell.

Litvintseva, A. P., N. Marsden-Haug, S. Hurst, H. Hill, L. Gade, E. M. Driebe, C. Ralston, C. Roe, B. M. Barker, and M. Goldoft. 2015. Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington State soil associated with recent human infection. Clinical Infectious Diseases 60:e1-e3.

Liu, C. M., B. A. Hungate, A. A. Tobian, J. Ravel, J. L. Prodger, D. Serwadda, G. Kigozi, R. M. Galiwango, F. Nalugoda, P. Keim, M. J. Wawer, L. B. Price, and R. H. Gray. 2015. Penile microbiota and female partner bacterial vaginosis in Rakai, Uganda. mBio 6:e00589.

Mau, R. L., C. M. Liu, M. Aziz, E. Schwartz, P. Dijkstra, J. C. Marks, L. B. Price, P. Keim, and B. A. Hungate. 2015. Linking soil bacterial biodiversity and soil carbon stability. ISME Journal 9:1477-1480.

McRobb, E., D. S. Sarovich, E. P. Price, M. Kaestli, M. Mayo, P. Keim, and B. J. Currie. 2015. Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply. Journal of Clinical Microbiology 53:1144-1148.

Momany, M., A. Di Pietro, W. G. Alexander, B. M. Barker, O. S. Harb, S. Kamoun, F. Martin, J. C. Pires, J. E. Stajich, and B. P. H. J. Thomma. 2015. Meeting report: fungal genomics meets social media: highlights of the 28th fungal genetics conference at asilomar. G3: Genes, Genomes, Genetics.

Olson, N. D., S. P. Lund, R. E. Colman, J. T. Foster, J. W. Sahl, J. M. Schupp, P. Keim, J. B. Morrow, M. L. Salit, and J. M. Zook. 2015. Best practices for evaluating single nucleotide variant calling methods for microbial genomics. Frontiers in Genetics 6:235.

Özsürekci, Y., D. N. Birdsell, M. Çelik, E. Karadağ-Öncel, A. Johansson, M. Forsman, A. J. Vogler, P. Keim, M. Ceyhan, and D. M. Wagner. 2015. Diverse Francisella tularensis strains and oropharyngeal tularemia, Turkey. Emerging Infectious Diseases 21:173.

Price, E. P., D. S. Sarovich, E. J. Smith, B. MacHunter, G. Harrington, V. Theobald, C. M. Hall, H. M. Hornstra, E. McRobb, and Y. Podin. 2015a. Large-scale comparative genomics identifies unprecedented melioidosis cases in northern Australia caused by an Asian Burkholderia pseudomallei strain. Applied and Environmental Microbiology.

Price, E. P., D. S. Sarovich, L. Viberg, M. Mayo, M. Kaestli, A. Tuanyok, J. T. Foster, P. Keim, T. Pearson, and B. J. Currie. 2015b. Whole-genome sequencing of Burkholderia pseudomallei isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type. Journal of Clinical Microbiology 53:282-286.

Pullan, S. T., T. R. Pearson, J. Latham, J. Mason, B. Atkinson, N. J. Silman, C. K. Marston, J. W. Sahl, D. Birdsell, and A. R. Hoffmaster. 2015. Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case. Microbial Genomics 1.

Riehm, J. M., M. Projahn, A. J. Vogler, M. Rajerison, G. Andersen, C. M. Hall, T. Zimmermann, R. Soanandrasana, V. Andrianaivoarimanana, R. K. Straubinger, R. Nottingham, P. Keim, D. M. Wagner, and H. C. Scholz. 2015. Diverse genotypes of Yersinia pestis caused plague in Madagascar in 2007. PLoS Neglected Tropical Diseases 9:e0003844.

Ronai, Z., Z. Kreizinger, A. Dan, K. Drees, J. T. Foster, K. Banyai, S. Marton, L. Szeredi, S. Janosi, and M. Gyuranecz. 2015. First isolation and characterization of Brucella microti from wild boar. BMC Veterinary Research 11.

Roume, H., A. Heintz-Buschart, E. E. L. Muller, P. May, V. P. Satagopam, C. C. Laczny, S. Narayanasamy, L. A. Lebrun, M. R. Hoopmann, J. M. Schupp, J. D. Gillece, N. D. Hicks, D. M. Engelthaler, T. Sauter, P. S. Keim, R. L. Moritz, and P. Wilmes. 2015. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. NPJ Biofilms Microbiomes 1:15007.

Sahl, J. W., C. J. Allender, R. E. Colman, K. J. Califf, J. M. Schupp, B. J. Currie, K. E. Van Zandt, H. C. Gelhaus, P. Keim, and A. Tuanyok. 2015a. Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence. PLoS One 10:e0121052.

Sahl, J. W., S. M. Beckstrom-Sternberg, J. S. Babic-Sternberg, J. D. Gillece, C. M. Hepp, R. K. Auerbach, W. Tembe, D. M. Wagner, P. S. Keim, and T. Pearson. 2015b. The in silico genotyper (ISG): an open-source pipeline to rapidly identify and annotate nucleotide variants for comparative genomics applications. bioRxiv:015578.

Sahl, J. W., M. Del Franco, S. Pournaras, R. E. Colman, N. Karah, L. Dijkshoorn, and R. Zarrilli. 2015c. Phylogenetic and genomic diversity in isolates from the globally distributed Acinetobacter baumannii ST25 lineage. Scientific Reports 5:1-12.

Sahl, J. W., C. R. Morris, J. Emberger, C. M. Fraser, J. B. Ochieng, J. Juma, B. Fields, R. F. Breiman, M. Gilmour, and J. P. Nataro. 2015d. Defining the phylogenomics of Shigella species: a pathway to diagnostics. Journal of Clinical Microbiology 53:951-960.

Sahl, J. W., J. M. Schupp, D. A. Rasko, R. E. Colman, J. T. Foster, and P. Keim. 2015e. Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data. Genome Medicine 7:52.

Sahl, J. W., J. R. Sistrunk, C. M. Fraser, E. Hine, N. Baby, Y. Begum, Q. Luo, A. Sheikh, F. Qadri, and J. M. Fleckenstein. 2015f. Examination of the enterotoxigenic Escherichia coli population structure during human infection. mBio 6.

Shubitz, L. F., H. T. Trinh, J. N. Galgiani, M. L. Lewis, A. W. Fothergill, N. P. Wiederhold, B. M. Barker, E. R. G. Lewis, A. L. Doyle, and W. J. Hoekstra. 2015. Evaluation of VT-1161 for treatment of coccidioidomycosis in murine infection models. Antimicrobial Agents and Chemotherapy 59:7249-7254.

Smith, T. J., K. K. Hill, G. Xie, B. T. Foley, C. H. D. Williamson, J. T. Foster, S. L. Johnson, O. Chertkov, H. Teshima, H. S. Gibbons, L. A. Johnsky, M. A. Karavis, and L. A. Smith. 2015. Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes. Infection Genetics and Evolution 30:102-113.

Spring-Pearson, S. M., J. K. Stone, A. Doyle, C. J. Allender, R. T. Okinaka, M. Mayo, S. M. Broomall, J. M. Hill, M. A. Karavis, K. S. Hubbard, J. M. Insalaco, L. A. McNew, C. N. Rosenzweig, H. S. Gibbons, B. J. Currie, D. M. Wagner, P. Keim, and A. Tuanyok. 2015. Pangenome analysis of Burkholderia pseudomallei: genome evolution preserves gene order despite high recombination rates. PLoS One 10:e0140274.

Struve, C., C. C. Roe, M. Stegger, S. G. Stahlhut, D. S. Hansen, D. M. Engelthaler, P. S. Andersen, E. M. Driebe, P. Keim, and K. A. Krogfelt. 2015. Mapping the Evolution of Hypervirulent Klebsiella pneumoniae. mBio 6:e00630.

Vogler, A. J., R. Nottingham, K. L. Parise, P. Keim, and B. M. Barker. 2015. Effective disinfectants for Coccidioides immitis and C. posadasii. Applied Biosafety 20:154-158.

Zancope-Oliveira, R., M. Teixeira, J. Patane, M. Taylor, D. Engelthaler, B. Barker, and M. Felipe. 2015. Reevaluating the worldwide phylogenetic distribution and population structure of Histoplasma capsulatum based on four genetic markers: S04. 4*. Mycoses 58:24-25.

Atkinson, C. T., R. B. Utzurrum, D. A. Lapointe, R. J. Camp, L. H. Crampton, J. T. Foster, and T. W. Giambelluca. 2014. Changing climate and the altitudinal range of avian malaria in the Hawaiian Islands – an ongoing conservation crisis on the island of Kaua’i. Global Change Biology 20:2426-2436.

Baltrus, D. A., K. Dougherty, S. M. Beckstrom-Sternberg, J. S. Beckstrom-Sternberg, and J. T. Foster. 2014. Incongruence between multi-locus sequence analysis ( MLSA) and whole-genome-based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale. Molecular Plant Pathology 15:461-465.

Birdsell, D. N., A. Johansson, C. Ohrman, E. Kaufman, C. Molins, T. Pearson, M. Gyuranecz, A. Naumann, A. J. Vogler, K. Myrtennas, P. Larsson, M. Forsman, A. Sjodin, J. D. Gillece, J. Schupp, J. M. Petersen, P. Keim, and D. M. Wagner. 2014a. Francisella tularensis subsp. tularensis group A.I, United States. Emerging Infectious Diseases 20:861-865.

Birdsell, D. N., A. J. Vogler, J. Buchhagen, A. Clare, E. Kaufman, A. Naumann, E. Driebe, D. M. Wagner, and P. S. Keim. 2014b. TaqMan real-time PCR assays for single-nucleotide polymorphisms which identify Francisella tularensis and its subspecies and subpopulations. PLoS One 9:e107964.

Busch, J. D., N. E. Stone, R. Nottingham, A. Araya-Anchetta, J. Lewis, C. Hochhalter, J. R. Giles, J. Gruendike, J. Freeman, and G. Buckmeier. 2014. Widespread movement of invasive cattle fever ticks (Rhipicephalus microplus) in southern Texas leads to shared local infestations on cattle and deer. Parasites & Vectors 7:1-16.

Chung, D., B. M. Barker, C. C. Carey, B. Merriman, E. R. Werner, B. E. Lechner, S. Dhingra, C. Cheng, W. Xu, and S. J. Blosser. 2014. ChIP-seq and in vivo transcriptome analyses of the Aspergillus fumigatus SREBP SrbA reveals a new regulator of the fungal hypoxia response and virulence. PLoS Pathogens 10:e1004487.

Engelthaler, D. M., N. D. Hicks, J. D. Gillece, C. C. Roe, J. M. Schupp, E. M. Driebe, F. Gilgado, F. Carriconde, L. Trilles, C. Firacative, P. Ngamskulrungroj, E. Castaneda, S. Lazera Mdos, M. S. Melhem, A. Perez-Bercoff, G. Huttley, T. C. Sorrell, K. Voelz, R. C. May, M. C. Fisher, G. R. Thompson, 3rd, S. R. Lockhart, P. Keim, and W. Meyer. 2014. Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. mBio 5:e01464-01414.

Eppinger, M., T. Pearson, S. S. Koenig, O. Pearson, N. Hicks, S. Agrawal, F. Sanjar, K. Galens, S. Daugherty, J. Crabtree, R. S. Hendriksen, L. B. Price, B. P. Upadhyay, G. Shakya, C. M. Fraser, J. Ravel, and P. S. Keim. 2014. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. mBio 5:e01721.

Giles, J. R., A. T. Peterson, J. D. Busch, P. U. Olafson, G. A. Scoles, R. B. Davey, J. M. Pound, D. M. Kammlah, K. H. Lohmeyer, and D. M. Wagner. 2014. Invasive potential of cattle fever ticks in the southern United States. Parasites & Vectors 7:1-11.

Gopaul, K. K., J. Sells, R. Lee, S. M. Beckstrom- Sternberg, J. T. Foster, and A. M. Whatmore. 2014. Development and assessment of multiplex high resolution melting assay as a tool for rapid single-tube identification of five Brucella species. BMC Research Notes 7:903.

Gyuranecz, M., K. Sulyok, E. Balla, T. Mag, A. Balazs, Z. Simor, B. Denes, S. Hornok, P. Bajnoczi, H. Hornstra, T. Pearson, P. Keim, and A. Dan. 2014. Q fever epidemic in Hungary, April to July 2013. Euro Surveill 19.

Hanczaruk, M., U. Reischl, T. Holzmann, D. Frangoulidis, D. M. Wagner, P. S. Keim, M. H. Antwerpen, H. Meyer, and G. Grass. 2014a. Injectional anthrax in heroin users, Europe, 2000-2012. Emerging Infectious Diseases 20:322-323.

Hanczaruk, M., U. Reischl, T. Holzmann, D. Frangoulidis, D. M. Wagner, P. S. Keim, M. H. Antwerpen, H. Meyer, and G. Grass. 2014b. Injectional anthrax in heroin users, Europe, 2000–2012. Emerging Infectious Diseases 20:322.

Hazen, T. H., L. Zhao, J. W. Sahl, G. Robinson, A. D. Harris, D. A. Rasko, and J. K. Johnson. 2014. Characterization of Klebsiella sp. strain 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates. Antimicrobial Agents and Chemotherapy 58:1879-1888.

Heitkamp, R., J. Sahl, A. Summers, A. L. Roth, and B. C. Kirkup. 2014. Resolving antagonistic interactions among clinical isolates of Acinetobacter baumannii with phylogenetic analysis. PeerJ.

Johansson, A., A. Larkeryd, M. Widerstrom, S. Mortberg, K. Myrtannas, C. Ohrman, D. Birdsell, P. Keim, D. M. Wagner, M. Forsman, and P. Larsson. 2014. An outbreak of respiratory tularemia caused by diverse clones of Francisella tularensis. Clinical Infectious Diseases 59:1546-1553.

Kelley, E. J., E. M. Driebe, K. Etienne, M. E. Brandt, J. M. Schupp, J. D. Gillece, J. S. Trujillo, S. R. Lockhart, E. Deak, P. S. Keim, and D. M. Engelthaler. 2014. Real-time PCR assays for genotyping of Cryptococcus gattii in North America. BMC Microbiology 14:125.

Khmaladze, E., D. N. Birdsell, A. A. Naumann, C. B. Hochhalter, M. L. Seymour, R. Nottingham, S. M. Beckstrom-Sternberg, J. Beckstrom-Sternberg, M. P. Nikolich, G. Chanturia, E. Zhgenti, M. Zakalashvili, L. Malania, G. Babuadze, N. Tsertsvadze, N. Abazashvili, M. Kekelidze, S. Tsanava, P. Imnadze, H. H. Ganz, W. M. Getz, O. Pearson, P. Gajer, M. Eppinger, J. Ravel, D. M. Wagner, R. T. Okinaka, J. M. Schupp, P. Keim, and T. Pearson. 2014. Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes. PLoS One 9:e102651.

Kreizinger, Z., J. T. Foster, Z. Ronai, K. M. Sulyok, E. Wehmann, S. Janosi, and M. Gyuranecz. 2014. Genetic relatedness of Brucella suis biovar 2 isolates from hares, wild boars and domestic pigs. Veterinary Microbiology 172:492-498.

Legagneux, P., L. L. Berzins, M. Forbes, N. J. Harms, H. L. Hennin, S. Bourgeon, H. G. Gilchrist, J. Bety, C. Soos, O. P. Love, J. T. Foster, S. Descamps, and G. Burness. 2014. No selection on immunological markers in response to a highly virulent pathogen in an Arctic breeding bird. Evolutionary Applications 7:765-773.

Litvintseva, A. P., S. Hurst, L. Gade, M. A. Frace, R. Hilsabeck, J. M. Schupp, J. D. Gillece, C. Roe, D. Smith, P. Keim, S. R. Lockhart, S. Changayil, M. R. Weil, D. R. MacCannell, M. E. Brandt, and D. M. Engelthaler. 2014. Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections. Journal of Clinical Microbiology 52:3216-3222.

Losada, L., B. M. Barker, S. Pakala, S. Pakala, V. Joardar, N. Zafar, S. Mounaud, N. Fedorova, W. C. Nierman, and R. A. Cramer. 2014. Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA. Mycopathologia 178:331-339.

Mohawk, K. L., F. Poly, J. W. Sahl, D. A. Rasko, and P. Guerry. 2014. High frequency, spontaneous motA mutations in Campylobacter jejuni strain 81-176. PLoS One 9:e88043.

Muller, E. E., N. Pinel, C. C. Laczny, M. R. Hoopmann, S. Narayanasamy, L. A. Lebrun, H. Roume, J. Lin, P. May, N. D. Hicks, A. Heintz-Buschart, L. Wampach, C. M. Liu, L. B. Price, J. D. Gillece, C. Guignard, J. M. Schupp, N. Vlassis, N. S. Baliga, R. L. Moritz, P. S. Keim, and P. Wilmes. 2014. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature Communications 5:5603.

Okinaka, R. T., J. Challacombe, K. Drees, D. N. Birdsell, N. Janke, A. Naumann, M. Seymour, H. Hornstra, J. Schupp, and J. Sahl. 2014. Genome sequence of Bacillus anthracis STI, a Sterne-like Georgian/Soviet vaccine strain. Genome Announcements 2.

Orata, F. D., P. S. Keim, and Y. Boucher. 2014. The 2010 cholera outbreak in Haiti: how science solved a controversy. PLoS Pathogens 10:e1003967.

Pearson, T., H. M. Hornstra, R. Hilsabeck, L. T. Gates, S. M. Olivas, D. M. Birdsell, C. M. Hall, S. German, J. M. Cook, M. L. Seymour, R. A. Priestley, A. V. Kondas, C. L. Clark Friedman, E. P. Price, J. M. Schupp, C. M. Liu, L. B. Price, R. F. Massung, G. J. Kersh, and P. Keim. 2014. High prevalence and two dominant host-specific genotypes of Coxiella burnetii in U.S. milk. BMC Microbiology 14:41.

Podin, Y., D. S. Sarovich, E. P. Price, M. Kaestli, M. Mayo, K. Hii, H. Ngian, S. Wong, I. Wong, J. Wong, A. Mohan, M. Ooi, T. Fam, J. Wong, A. Tuanyok, P. Keim, P. M. Giffard, and B. J. Currie. 2014. Burkholderia pseudomallei isolates from Sarawak, Malaysian Borneo, are predominantly susceptible to aminoglycosides and macrolides. Antimicrobial Agents and Chemotherapy 58:162-166.

Rawat, A., D. M. Engelthaler, E. M. Driebe, P. Keim, and J. T. Foster. 2014. MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing. PLoS One 9:e110915.

Sackett, L. C., A. Seglund, R. P. Guralnick, M. N. Mazzella, D. M. Wagner, J. D. Busch, and A. P. Martin. 2014. Evidence for two subspecies of Gunnison’s prairie dogs (Cynomys gunnisoni), and the general importance of the subspecies concept. Biological Conservation 174:1-11.

Sahl, J. W., J. G. Caporaso, D. A. Rasko, and P. Keim. 2014. The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ 2:e332.

Scholz, H. C., T. Pearson, H. Hornstra, M. Projahn, R. Terzioglu, R. Wernery, E. Georgi, J. M. Riehm, D. M. Wagner, P. S. Keim, M. Joseph, B. Johnson, J. Kinne, S. Jose, C. M. Hepp, A. Witte, and U. Wernery. 2014. Genotyping of Burkholderia mallei from an outbreak of glanders in Bahrain suggests multiple introduction events. PLoS Neglected Tropical Diseases 8:e3195.

Shuey, M. M., K. P. Drees, D. L. Lindner, P. Keim, and J. T. Foster. 2014. Highly sensitive quantitative pcr for the detection and differentiation of Pseudogymnoascus destructans and other Pseudogymnoascus species. Applied and Environmental Microbiology 80:1726-1731.

Stone, J. K., C. Heiss, Z. Wang, I. Black, S. A. Grasso, A. T. Koppisch, P. Azadi, P. Keim, and A. Tuanyok. 2014a. Structural characterization of polysaccharides expressed by Burkholderia oklahomensis E0147. Carbohydrate Research 386:68-72.

Stone, N. E., P. U. Olafson, R. B. Davey, G. Buckmeier, D. Bodine, L. C. Sidak-Loftis, J. R. Giles, R. Duhaime, R. J. Miller, and J. Mosqueda. 2014b. Multiple mutations in the para-sodium channel gene are associated with pyrethroid resistance in Rhipicephalus microplus from the United States and Mexico. Parasites & Vectors 7:1-14.

Sulyok, K. M., Z. Kreizinger, H. M. Hornstra, T. Pearson, A. Szigeti, A. Dan, E. Balla, P. S. Keim, and M. Gyuranecz. 2014. Genotyping of Coxiella burnetii from domestic ruminants and human in Hungary: indication of various genotypes. BMC Veterinary Research 10:107.

Vogler, A. J., S. Jones, and P. Keim. 2014. Incident reporting and biosafety training in a BSL-3 select agent facility. Applied Biosafety 19:192-200.

Wagner, D. M., J. Klunk, M. Harbeck, A. Devault, N. Waglechner, J. W. Sahl, J. Enk, D. N. Birdsell, M. Kuch, and C. Lumibao. 2014. Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis. Lancet Infectious Diseases 14:319-326.

Wahab, T., D. N. Birdsell, M. Hjertqvist, C. L. Mitchell, D. M. Wagner, P. S. Keim, I. Hedenström, and S. Löfdahl. 2014. Insights to genetic characterization tools for epidemiological tracking of Francisella tularensis in Sweden. PLoS One 9:e112167.

Walker, F. M., J. T. Foster, K. P. Drees, and C. L. Chambers. 2014. Spotted bat (Euderma maculatum) microsatellite discovery using illumina sequencing. Conservation Genetics Resources 6:457-459.

Wan, X., L. Qian, S. Hou, K. P. Drees, J. T. Foster, and J. T. Douglas. 2014. Complete genome sequences of Beijing and Manila family strains of Mycobacterium tuberculosis. Genome Announcements 2.

Wang, Y., Y. Peng, R. Hai, L. Xia, H. Li, Z. Zhang, H. Cai, Y. Liang, X. Shen, D. Yu, D. Birdsell, D. M. Wagner, and P. Keim. 2014. Diversity of Francisella tularensis subsp. holarctica lineages, China. Emerging Infectious Diseases 20:1191-1194.

Wattam, A. R., J. T. Foster, S. P. Mane, S. M. Beckstrom-Sternberg, J. M. Beckstrom-Sternberg, A. W. Dickerman, P. Keim, T. Pearson, M. Shukla, D. V. Ward, K. P. Williams, B. W. Sobral, R. M. Tsolis, A. M. Whatmore, and D. O’Callaghan. 2014. Comparative phylogenomics and evolution of the brucellae reveal a path to virulence. Journal of Bacteriology 196:920-930.

Wendt, J. M., D. Kaul, B. M. Limbago, M. Ramesh, S. Cohle, A. M. Denison, E. M. Driebe, J. K. Rasheed, S. R. Zaki, D. M. Blau, C. D. Paddock, L. K. McDougal, D. M. Engelthaler, P. S. Keim, C. C. Roe, H. Akselrod, M. J. Kuehnert, and S. V. Basavaraju. 2014. Transmission of methicillin-resistant Staphylococcus aureus infection through solid organ transplantation: confirmation via whole genome sequencing. American Journal of Transplantation 14:2633-2639.

Andersen, P. S., M. Stegger, M. Aziz, T. Contente-Cuomo, H. S. Gibbons, P. Keim, E. V. Sokurenko, J. R. Johnson, and L. B. Price. 2013. Complete genome sequence of the epidemic and highly virulent CTX-M-15-producing H30-Rx subclone of Escherichia coli ST131. Genome Announcements 1.

Araya‐Anchetta, A., G. A. Scoles, J. Giles, J. D. Busch, and D. M. Wagner. 2013. Hybridization in natural sympatric populations of Dermacentor ticks in northwestern North America. Ecology and Evolution 3:714-724.

Birdsell, D. N., M. Antwerpen, P. Keim, M. Hanczaruk, J. T. Foster, J. W. Sahl, D. M. Wagner, and G. Grass. 2013. Draft genome sequences of two Bulgarian Bacillus anthracis strains. Genome Announcements 1:e0015213.

Busch, J. D., R. Van Andel, N. E. Stone, K. R. Cobble, R. Nottingham, J. Lee, M. VerSteeg, J. Corcoran, J. Cordova, W. Van Pelt, M. M. Shuey, J. T. Foster, J. M. Schupp, S. Beckstrom-Sternberg, J. Beckstrom-Sternberg, P. Keim, S. Smith, J. Rodriguez-Ramos, J. L. Williamson, T. E. Rocke, and D. M. Wagner. 2013. The innate immune response may be important for surviving plague in wild Gunnison’s prairie dogs. Journal of Wildlife Diseases 49:920-931.

Casadevall, A., L. Enquist, M. J. Imperiale, P. Keim, M. T. Osterholm, and D. A. Relman. 2013. Redaction of sensitive data in the publication of dual use research of concern. mBio 5:e00991-00913.

Duncan, D. D., A. J. Vogler, M. J. Wolcott, F. Li, D. S. Sarovich, D. N. Birdsell, L. M. Watson, T. A. Hall, R. Sampath, R. Housley, L. B. Blyn, S. A. Hofstadler, D. J. Ecker, P. Keim, D. M. Wagner, and M. W. Eshoo. 2013. Identification and typing of Francisella tularensis with a highly automated genotyping assay. Letters in Applied Microbiology 56:128-134.

Engelthaler, D. M., E. Kelley, E. M. Driebe, J. Bowers, C. F. Eberhard, J. Trujillo, F. Decruyenaere, J. M. Schupp, J. Mossong, P. Keim, and J. Even. 2013. Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries. BMC Infectious Diseases 13:339.

Garofolo, G., E. Di Giannatale, F. De Massis, K. Zilli, M. Ancora, C. Camma, P. Calistri, and J. T. Foster. 2013. Investigating genetic diversity of Brucella abortus and Brucella melitensis in Italy with MLVA-16. Infection Genetics and Evolution 19:59-70.

Gyuranecz, M., J. T. Foster, A. Dan, H. S. Ip, K. F. Egstad, P. G. Parker, J. M. Higashiguchi, M. A. Skinner, U. Hofle, Z. Kreizinger, G. M. Dorrestein, S. Solt, E. Sos, Y. J. Kim, M. Uhart, A. Pereda, G. Gonzalez-Hein, H. Hidalgo, J. M. Blanco, and K. Erdelyi. 2013a. Worldwide phylogenetic relationship of avian poxviruses. Journal of Virology 87:4938-4951.

Gyuranecz, M., B. D. Rannals, C. A. Allen, S. Janosi, P. S. Keim, and J. T. Foster. 2013b. Within-host evolution of Brucella canis during a canine brucellosis outbreak in a kennel. BMC Veterinary Research 9:76.

Hall, C. M., J. D. Busch, G. A. Scoles, K. A. Palma-Cagle, M. W. Ueti, L. S. Kappmeyer, and D. M. Wagner. 2013. Genetic characterization of Theileria equi infecting horses in North America: evidence for a limited source of US introductions. Parasites & Vectors 6:1-12.

Harbeck, M., L. Seifert, S. Hansch, D. M. Wagner, D. Birdsell, K. L. Parise, I. Wiechmann, G. Grupe, A. Thomas, P. Keim, L. Zoller, B. Bramanti, J. M. Riehm, and H. C. Scholz. 2013. Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague. PLoS Pathogens 9:e1003349.

Leiser, O. P., J. L. Corn, B. S. Schmit, P. S. Keim, and J. T. Foster. 2013. Feral swine brucellosis in the United States and prospective genomic techniques for disease epidemiology. Veterinary Microbiology 166:1-10.

Limmathurotsakul, D., D. A. B. Dance, V. Wuthiekanun, M. Kaestli, M. Mayo, J. Warner, D. M. Wagner, A. Tuanyok, H. Wertheim, and T. Y. Cheng. 2013. Systematic review and consensus guidelines for environmental sampling of Burkholderia pseudomallei. PLoS Neglected Tropical Diseases 7:e2105.

Liu, C. M., B. A. Hungate, A. A. Tobian, D. Serwadda, J. Ravel, R. Lester, G. Kigozi, M. Aziz, R. M. Galiwango, F. Nalugoda, T. L. Contente-Cuomo, M. J. Wawer, P. Keim, R. H. Gray, and L. B. Price. 2013a. Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria. mBio 4:e00076.

Liu, C. M., K. Soldanova, L. Nordstrom, M. G. Dwan, O. L. Moss, T. L. Contente-Cuomo, P. Keim, L. B. Price, and A. P. Lane. 2013b. Medical therapy reduces microbiota diversity and evenness in surgically recalcitrant chronic rhinosinusitis. International Forum of Allergy & Rhinology 3:775-781.

Morris, C. R., C. L. Grassel, J. C. Redman, J. W. Sahl, E. M. Barry, and D. A. Rasko. 2013. Characterization of intracellular growth regulator icgR by utilizing transcriptomics to identify mediators of pathogenesis in Shigella flexneri. Infection and immunity 81:3068-3076.

Nguyen, C., B. M. Barker, S. Hoover, D. E. Nix, N. M. Ampel, J. A. Frelinger, M. J. Orbach, and J. N. Galgiani. 2013. Recent advances in our understanding of the environmental, epidemiological, immunological, and clinical dimensions of coccidioidomycosis. Clinical Microbiology Reviews 26:505-525.

Pearson, T., H. M. Hornstra, J. W. Sahl, S. Schaack, J. M. Schupp, S. M. Beckstrom-Sternberg, M. W. O’Neill, R. A. Priestley, M. D. Champion, J. S. Beckstrom-Sternberg, G. J. Kersh, J. E. Samuel, R. F. Massung, and P. Keim. 2013. When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii. Systematic Biology 62:752-762.

Perego, U. A., A. Achilli, J. E. Ekins, L. Milani, M. Lari, E. Pilli, A. Brown, E. P. Price, S. R. Wolken, M. Matthews, C. A. Allen, T. R. Pearson, N. Angerhofer, D. Caramelli, T. Kupferschmid, P. S. Keim, and S. R. Woodward. 2013. The Mountain Meadows Massacre and “poisoned springs”: scientific testing of the more recent, anthrax theory. International Journal of Legal Medicine 127:77-83.

Price, E. P., D. S. Sarovich, M. Mayo, A. Tuanyok, K. P. Drees, M. Kaestli, S. M. Beckstrom-Sternberg, J. S. Babic-Sternberg, T. J. Kidd, S. C. Bell, P. Keim, T. Pearson, and B. J. Currie. 2013a. Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection. mBio 4.

Price, E. P., D. S. Sarovich, J. R. Webb, J. L. Ginther, M. Mayo, J. M. Cook, M. L. Seymour, M. Kaestli, V. Theobald, C. M. Hall, J. D. Busch, J. T. Foster, P. Keim, D. M. Wagner, A. Tuanyok, T. Pearson, and B. J. Currie. 2013b. Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR. PLoS One 8:e71647.

Price, L. B., J. R. Johnson, M. Aziz, C. Clabots, B. Johnston, V. Tchesnokova, L. Nordstrom, M. Billig, S. Chattopadhyay, M. Stegger, P. S. Andersen, T. Pearson, K. Riddell, P. Rogers, D. Scholes, B. Kahl, P. Keim, and E. V. Sokurenko. 2013c. The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. mBio 4:e00377-00313.

Qu, P. H., S. Y. Chen, H. C. Scholz, H. J. Busse, Q. Gu, P. Kampfer, J. T. Foster, S. P. Glaeser, C. Chen, and Z. C. Yang. 2013. Francisella guangzhouensis sp nov., isolated from air-conditioning systems. International Journal of Systematic and Evolutionary Microbiology 63:3628-3635.

Sahl, J. W., J. D. Gillece, J. M. Schupp, V. G. Waddell, E. M. Driebe, D. M. Engelthaler, and P. Keim. 2013a. Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in Acinetobacter. PLoS One 8:e54287.

Sahl, J. W., J. K. Stone, H. C. Gelhaus, R. L. Warren, C. J. Cruttwell, S. G. Funnell, P. Keim, and A. Tuanyok. 2013b. Genome Sequence of Burkholderia pseudomallei NCTC 13392. Genome Announcements 1.

Sarovich, D. S., R. E. Colman, E. P. Price, C. Massire, A. T. Von Schulze, V. Waddell, S. M. Anderson, D. J. Ecker, A. P. Liguori, D. M. Engelthaler, R. Sampath, P. Keim, M. W. Eshoo, and D. M. Wagner. 2013. Molecular genotyping of Acinetobacter spp. isolated in Arizona, USA, using multilocus PCR and mass spectrometry. Journal of Medical Microbiology 62:1295-1300.

Shepardson, K. M., L. Y. Ngo, V. Aimanianda, J.-P. Latge, B. M. Barker, S. J. Blosser, Y. Iwakura, T. M. Hohl, and R. A. Cramer. 2013. Hypoxia enhances innate immune activation to Aspergillus fumigatus through cell wall modulation. Microbes and Infection 15:259-269.

Stegger, M., E. M. Driebe, C. Roe, D. Lemmer, J. R. Bowers, D. M. Engelthaler, P. Keim, and P. S. Andersen. 2013. Genome Sequence of Staphylococcus aureus Strain CA-347, a USA600 Methicillin-Resistant Isolate. Genome Announcements 1.

Stone, J. K., S. L. Johnson, D. C. Bruce, J. C. Detter, M. Mayo, B. J. Currie, H. C. Gelhaus, P. Keim, and A. Tuanyok. 2013. Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305. Genome Announcements 1.

Trueba, G., V. Garces, V. B. V, R. E. Colman, M. Seymour, A. J. Vogler, and P. Keim. 2013. Escherichia coli O157:H7 in Ecuador: animal reservoirs, yet no human disease. Vector-Borne and Zoonotic Diseases 13:295-298.

Vogler, A. J., F. Chan, R. Nottingham, G. Andersen, K. Drees, S. M. Beckstrom-Sternberg, D. M. Wagner, S. Chanteau, and P. Keim. 2013. A decade of plague in Mahajanga, Madagascar: insights into the global maritime spread of pandemic plague. mBio 4:e00623-00612.

Aarestrup, F. M., E. W. Brown, C. Detter, P. Gerner-Smidt, M. W. Gilmour, D. Harmsen, R. S. Hendriksen, R. Hewson, D. L. Heymann, K. Johansson, K. Ijaz, P. S. Keim, M. Koopmans, A. Kroneman, D. Lo Fo Wong, O. Lund, D. Palm, P. Sawanpanyalert, J. Sobel, and J. Schlundt. 2012. Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response. Emerging Infectious Diseases 18:e1.

Barker, B. M., K. Kroll, M. Vödisch, A. Mazurie, O. Kniemeyer, and R. A. Cramer. 2012a. Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter. BMC Genomics 13:1-25.

Barker, B. M., J. A. Tabor, L. F. Shubitz, R. Perrill, and M. J. Orbach. 2012b. Detection and phylogenetic analysis of Coccidioides posadasii in Arizona soil samples. Fungal Ecology 5:163-176.

Berns, K. I., A. Casadevall, M. L. Cohen, S. A. Ehrlich, L. W. Enquist, J. P. Fitch, D. R. Franz, C. M. Fraser-Liggett, C. M. Grant, M. J. Imperiale, J. Kanabrocki, P. S. Keim, S. M. Lemon, S. B. Levy, J. R. Lumpkin, J. F. Miller, R. Murch, M. E. Nance, M. T. Osterholm, D. A. Relman, J. A. Roth, and A. K. Vidaver. 2012a. Policy: Adaptations of avian flu virus are a cause for concern. Nature 482:153-154.

Berns, K. I., A. Casadevall, M. L. Cohen, S. A. Ehrlich, L. W. Enquist, J. P. Fitch, D. R. Franz, C. M. Fraser-Liggett, C. M. Grant, M. J. Imperiale, J. Kanabrocki, P. S. Keim, S. M. Lemon, S. B. Levy, J. R. Lumpkin, J. F. Miller, R. Murch, M. E. Nance, M. T. Osterholm, D. A. Relman, J. A. Roth, and A. K. Vidaver. 2012b. Public health and biosecurity. Adaptations of avian flu virus are a cause for concern. Science 335:660-661.

Birdsell, D. N., T. Pearson, E. P. Price, H. M. Hornstra, R. D. Nera, N. Stone, J. Gruendike, E. L. Kaufman, A. H. Pettus, A. N. Hurbon, J. L. Buchhagen, N. J. Harms, G. Chanturia, M. Gyuranecz, D. M. Wagner, and P. S. Keim. 2012. Melt analysis of mismatch amplification mutation assays (Melt-MAMA): a functional study of a cost-effective SNP genotyping assay in bacterial models. PLoS One 7:e32866.

Bowers, J. R., E. M. Driebe, J. L. Nibecker, B. R. Wojack, D. S. Sarovich, A. H. Wong, P. M. Brzoska, N. Hubert, A. Knadler, L. M. Watson, D. M. Wagner, M. R. Furtado, M. Saubolle, D. M. Engelthaler, and P. S. Keim. 2012. Dominance of multidrug resistant CC271 clones in macrolide-resistant Streptococcus pneumoniae in Arizona. BMC Microbiology 12:12.

Etienne, K. A., J. Gillece, R. Hilsabeck, J. M. Schupp, R. Colman, S. R. Lockhart, L. Gade, E. H. Thompson, D. A. Sutton, R. Neblett-Fanfair, B. J. Park, G. Turabelidze, P. Keim, M. E. Brandt, E. Deak, and D. M. Engelthaler. 2012. Whole genome sequence typing to investigate the Apophysomyces outbreak following a tornado in Joplin, Missouri, 2011. PLoS One 7:e49989.

Foster, J. T., L. B. Price, S. M. Beckstrom-Sternberg, T. Pearson, W. D. Brown, D. M. Kiesling, C. A. Allen, C. M. Liu, J. Beckstrom-Sternberg, and F. F. Roberto. 2012. Genotyping of Brucella species using clade specific SNPs. BMC Microbiology 12:110.

Frerichs, R. R., J. Boncy, R. Barrais, P. S. Keim, and R. Piarroux. 2012a. Source attribution of 2010 cholera epidemic in Haiti. Proceedings of the National Academy of Sciences USA 109:E3208; author reply E3209.

Frerichs, R. R., P. S. Keim, R. Barrais, and R. Piarroux. 2012b. Nepalese origin of cholera epidemic in Haiti. Clinical Microbiology and Infection 18:E158-163.

Gyuranecz, M., D. N. Birdsell, W. Splettstoesser, E. Seibold, S. M. Beckstrom-Sternberg, L. Makrai, L. Fodor, M. Fabbi, N. Vicari, A. Johansson, J. D. Busch, A. J. Vogler, P. Keim, and D. M. Wagner. 2012. Phylogeography of Francisella tularensis subsp. holarctica, Europe. Emerging Infectious Diseases 18:290-293.

Kaestli, M., L. J. Richardson, R. E. Colman, A. Tuanyok, E. P. Price, J. R. Bowers, M. Mayo, E. Kelley, M. L. Seymour, D. S. Sarovich, T. Pearson, D. M. Engelthaler, D. M. Wagner, P. S. Keim, J. M. Schupp, and B. J. Currie. 2012a. Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens. Journal of Clinical Microbiology 50:2059-2062.

Kaestli, M., M. Schmid, M. Mayo, M. Rothballer, G. Harrington, L. Richardson, A. Hill, J. Hill, A. Tuanyok, P. Keim, A. Hartmann, and B. J. Currie. 2012b. Out of the ground: aerial and exotic habitats of the melioidosis bacterium Burkholderia pseudomallei in grasses in Australia. Environmental Microbiology 14:2058-2070.

Keim, P. S. 2012a. Q&A: Reasons for proposed redaction of flu paper. Nature 482:156-157.

Keim, P. S. 2012b. The NSABB recommendations: rationale, impact, and implications. mBio 3.

Liu, C. M., M. Aziz, S. Kachur, P. R. Hsueh, Y. T. Huang, P. Keim, and L. B. Price. 2012a. BactQuant: an enhanced broad-coverage bacterial quantitative real-time PCR assay. BMC Microbiology 12:56.

Liu, C. M., S. Kachur, M. G. Dwan, A. G. Abraham, M. Aziz, P. R. Hsueh, Y. T. Huang, J. D. Busch, L. J. Lamit, C. A. Gehring, P. Keim, and L. B. Price. 2012b. FungiQuant: a broad-coverage fungal quantitative real-time PCR assay. BMC Microbiology 12:255.

Muller, E. E., N. Pinel, J. D. Gillece, J. M. Schupp, L. B. Price, D. M. Engelthaler, C. Levantesi, V. Tandoi, K. Luong, N. S. Baliga, J. Korlach, P. S. Keim, and P. Wilmes. 2012. Genome sequence of “Candidatus Microthrix parvicella” Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant. Journal of Bacteriology 194:6670-6671.

Nikolakakis, K., S. Amber, J. S. Wilbur, E. J. Diner, S. K. Aoki, S. J. Poole, A. Tuanyok, P. S. Keim, S. Peacock, C. S. Hayes, and D. A. Low. 2012. The toxin/immunity network of Burkholderia pseudomallei contact-dependent growth inhibition (CDI) systems. Molecular Microbiology 84:516-529.

Price, E. P., J. L. Dale, J. M. Cook, D. S. Sarovich, M. L. Seymour, J. L. Ginther, E. L. Kaufman, S. M. Beckstrom-Sternberg, M. Mayo, M. Kaestli, M. B. Glass, J. E. Gee, V. Wuthiekanun, J. M. Warner, A. Baker, J. T. Foster, P. Tan, A. Tuanyok, D. Limmathurotsakul, S. J. Peacock, B. J. Currie, D. M. Wagner, P. Keim, and T. Pearson. 2012a. Development and validation of Burkholderia pseudomallei-specific real-time PCR assays for clinical, environmental or forensic detection applications. PLoS One 7.

Price, E. P., M. L. Seymour, D. S. Sarovich, J. Latham, S. R. Wolken, J. Mason, G. Vincent, K. P. Drees, S. M. Beckstrom-Sternberg, A. M. Phillippy, S. Koren, R. T. Okinaka, W. K. Chung, J. M. Schupp, D. M. Wagner, R. Vipond, J. T. Foster, N. H. Bergman, J. Burans, T. Pearson, T. Brooks, and P. Keim. 2012b. Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe. Emerging Infectious Diseases 18:1307-1313.

Price, L. B., M. Stegger, H. Hasman, M. Aziz, J. Larsen, P. S. Andersen, T. Pearson, A. E. Waters, J. T. Foster, J. Schupp, J. Gillece, E. Driebe, C. M. Liu, B. Springer, I. Zdovc, A. Battisti, A. Franco, J. Zmudzki, S. Schwarz, P. Butaye, E. Jouy, C. Pomba, M. C. Porrero, R. Ruimy, T. C. Smith, D. A. Robinson, J. S. Weese, C. S. Arriola, F. Yu, F. Laurent, P. Keim, R. Skov, and F. M. Aarestrup. 2012c. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. mBio 3.

Qiu, S., X. Xu, Y. Wang, G. Yang, Z. Wang, H. Wang, L. Zhang, N. Liu, C. Chen, W. Liu, J. Li, W. Su, L. Jia, L. Wang, H. Jin, P. Keim, Z. Yuan, L. Huang, and H. Song. 2012. Emergence of resistance to fluoroquinolones and third-generation cephalosporins in Shigella flexneri subserotype 1c isolates from China. Clinical Microbiology and Infection 18:E95-98.

Richardson, L. J., M. Kaestli, M. Mayo, J. R. Bowers, A. Tuanyok, J. Schupp, D. Engelthaler, D. M. Wagner, P. S. Keim, and B. J. Currie. 2012. Towards a rapid molecular diagnostic for melioidosis: Comparison of DNA extraction methods from clinical specimens. Journal of Microbiological Methods 88:179-181.

Rocke, T. E., J. Williamson, K. R. Cobble, J. D. Busch, M. F. Antolin, and D. M. Wagner. 2012. Resistance to plague among black-tailed prairie dog populations. Vector-Borne and Zoonotic Diseases 12:111-116.

Sarovich, D. S., E. P. Price, D. Limmathurotsakul, J. M. Cook, A. T. Von Schulze, S. R. Wolken, P. Keim, S. J. Peacock, and T. Pearson. 2012a. Development of ceftazidime resistance in an acute Burkholderia pseudomallei infection. Infection and Drug Resistance 5:129-132.

Sarovich, D. S., E. P. Price, A. T. Von Schulze, J. M. Cook, M. Mayo, L. M. Watson, L. Richardson, M. L. Seymour, A. Tuanyok, D. M. Engelthaler, T. Pearson, S. J. Peacock, B. J. Currie, P. Keim, and D. M. Wagner. 2012b. Characterization of ceftazidime resistance mechanisms in clinical isolates of Burkholderia pseudomallei from Australia. PLoS One 7:e30789.

Stone, J. K., M. Mayo, S. A. Grasso, J. L. Ginther, S. D. Warrington, C. J. Allender, A. Doyle, S. Georgia, M. Kaestli, S. M. Broomall, M. A. Karavis, J. M. Insalaco, K. S. Hubbard, L. A. McNew, H. S. Gibbons, B. J. Currie, P. Keim, and A. Tuanyok. 2012. Detection of Burkholderia pseudomallei O-antigen serotypes in near-neighbor species. BMC Microbiology 12:250.

Tuanyok, A., J. K. Stone, M. Mayo, M. Kaestli, J. Gruendike, S. Georgia, S. Warrington, T. Mullins, C. J. Allender, D. M. Wagner, N. Chantratita, S. J. Peacock, B. J. Currie, and P. Keim. 2012. The genetic and molecular basis of O-antigenic diversity in Burkholderia pseudomallei lipopolysaccharide. PLoS Neglected Tropical Diseases 6:e1453.

Van Zandt, K. E., A. Tuanyok, P. S. Keim, R. L. Warren, and H. C. Gelhaus. 2012. An objective approach for Burkholderia pseudomallei strain selection as challenge material for medical countermeasures efficacy testing. Frontiers in Cellular and Infection Microbiology 2:120.

Baker, A., T. Pearson, E. P. Price, J. Dale, P. Keim, H. Hornstra, A. Greenhill, G. Padilla, and J. Warner. 2011. Molecular phylogeny of Burkholderia pseudomallei from a remote region of Papua New Guinea. PLoS One 6:e18343.

Blatzer, M., B. M. Barker, S. D. Willger, N. Beckmann, S. J. Blosser, E. J. Cornish, A. Mazurie, N. Grahl, H. Haas, and R. A. Cramer. 2011. SREBP coordinates iron and ergosterol homeostasis to mediate triazole drug and hypoxia responses in the human fungal pathogen Aspergillus fumigatus. PLoS Genetics 7:e1002374.

Busch, J. D., R. Van Andel, J. Cordova, R. E. Colman, P. Keim, T. E. Rocke, J. G. Leid, W. E. Van Pelt, and D. M. Wagner. 2011. Population differences in host immune factors may influence survival of Gunnison’s prairie dogs (Cynomys gunnisoni) during plague outbreaks. Journal of Wildlife Diseases 47:968-973.

Chanturia, G., D. N. Birdsell, M. Kekelidze, E. Zhgenti, G. Babuadze, N. Tsertsvadze, S. Tsanava, P. Imnadze, S. M. Beckstrom-Sternberg, J. S. Beckstrom-Sternberg, M. D. Champion, S. Sinari, M. Gyuranecz, J. Farlow, A. H. Pettus, E. L. Kaufman, J. D. Busch, T. Pearson, J. T. Foster, A. J. Vogler, D. M. Wagner, and P. Keim. 2011. Phylogeography of Francisella tularensis subspecies holarctica from the country of Georgia. BMC Microbiology 11:139.

Dale, J., E. P. Price, H. Hornstra, J. D. Busch, M. Mayo, D. Godoy, V. Wuthiekanun, A. Baker, J. T. Foster, D. M. Wagner, A. Tuanyok, J. Warner, B. G. Spratt, S. J. Peacock, B. J. Currie, P. Keim, and T. Pearson. 2011. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei. PLoS Neglected Tropical Diseases 5.

Davis, T. S., R. W. Hofstetter, J. T. Foster, N. E. Foote, and P. Keim. 2011. Interactions between the yeast Ogataea pini and filamentous fungi associated with the western pine beetle. Microbial Ecology 61:626-634.

Engelthaler, D. M., J. Bowers, J. A. Schupp, T. Pearson, J. Ginther, H. M. Hornstra, J. Dale, T. Stewart, R. Sunenshine, V. Waddell, C. Levy, J. Gillece, L. B. Price, T. Contente, S. M. Beckstrom-Sternberg, D. D. Blaney, D. M. Wagner, M. Mayo, B. J. Currie, P. Keim, and A. Tuanyok. 2011a. Molecular investigations of a locally acquired case of melioidosis in Southern AZ, USA. PLoS Neglected Tropical Diseases 5:e1347.

Engelthaler, D. M., T. Chiller, J. A. Schupp, J. Colvin, S. M. Beckstrom-Sternberg, E. M. Driebe, T. Moses, W. Tembe, S. Sinari, J. S. Beckstrom-Sternberg, A. Christoforides, J. V. Pearson, J. Carpten, P. Keim, A. Peterson, D. Terashita, and S. A. Balajee. 2011b. Next-generation sequencing of Coccidioides immitis isolated during cluster investigation. Emerging Infectious Diseases 17:227-232.

Foster, J. T., R.L. Bull, and P. Keim. 2011. Ricin Forensics, Chapter 19. Pages 315-326 in B. Budowle, S.E. Schutzer, R.G. Breeze, P.S. Keim, and S. A. Morse, editors. Microbial Forensics. Elsevier Press 

Gillece, J. D., J. M. Schupp, S. A. Balajee, J. Harris, T. Pearson, Y. Yan, P. Keim, E. DeBess, N. Marsden-Haug, R. Wohrle, D. M. Engelthaler, and S. R. Lockhart. 2011. Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity. PLoS One 6:e28550.

Hansen, C. M., A. J. Vogler, P. Keim, D. M. Wagner, and K. Hueffer. 2011. Tularemia in Alaska, 1938-2010. Acta Veterinaria Scandinavica 53:1-7.

Hendriksen, R. S., L. B. Price, J. M. Schupp, J. D. Gillece, R. S. Kaas, D. M. Engelthaler, V. Bortolaia, T. Pearson, A. E. Waters, B. P. Upadhyay, S. D. Shrestha, S. Adhikari, G. Shakya, P. S. Keim, and F. M. Aarestrup. 2011. Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. mBio 2:e00157-00111.

Hoopes, J. D., E. M. Driebe, E. Kelley, D. M. Engelthaler, P. S. Keim, A. S. Perelson, L. Rong, G. T. Went, and J. T. Nguyen. 2011. Triple combination antiviral drug (TCAD) composed of amantadine, oseltamivir, and ribavirin impedes the selection of drug-resistant influenza A virus. PLoS One 6:e29778.

Hornstra, H. M., R. A. Priestley, S. M. Georgia, S. Kachur, D. N. Birdsell, R. Hilsabeck, L. T. Gates, J. E. Samuel, R. A. Heinzen, G. J. Kersh, P. Keim, R. F. Massung, and T. Pearson. 2011. Rapid typing of Coxiella burnetii. PLoS One 6:e26201.

James, S. H., C. B. Hartline, E. A. Harden, E. M. Driebe, J. M. Schupp, D. M. Engelthaler, P. S. Keim, T. L. Bowlin, E. R. Kern, and M. N. Prichard. 2011. Cyclopropavir inhibits the normal function of the human cytomegalovirus UL97 kinase. Antimicrobial Agents and Chemotherapy 55:4682-4691.

Kang, Y., M. H. Norris, B. A. Wilcox, A. Tuanyok, P. S. Keim, and T. T. Hoang. 2011. Knockout and pullout recombineering for naturally transformable Burkholderia thailandensis and Burkholderia pseudomallei. Nature Protocols 6:1085-1104.

Keim, P. S., F. M. Aarestrup, G. Shakya, L. B. Price, R. S. Hendriksen, D. M. Engelthaler, and T. Pearson. 2011. Reply to “South Asia instead of Nepal may be the origin of the Haitian cholera outbreak strain”. mBio 2:e00245-00211.

Kunz, T. H., J.T. Foster, W.F. Frick, A.M. Kilpatrick, G.F. McCracken, M.S. Moore, J.D. Reichard, D. Reeder, and A. H. Robbins. 2011. White-nose syndrome: An overview of ongoing and future research needs. Pages 189-203 in Proceedings of Protection of Threatened Bats at Coal Mines. Office of Surface Mining and Coal Research Center, Southern Illinois University, Carbondale, IL.

Li, H., B. M. Barker, N. Grahl, S. Puttikamonkul, J. D. Bell, K. D. Craven, and R. A. Cramer. 2011. The small GTPase RacA mediates intracellular reactive oxygen species production, polarized growth, and virulence in the human fungal pathogen Aspergillus fumigatus. Eukaryotic Cell 10:174-186.

Liguori, A. P., S. D. Warrington, J. L. Ginther, T. Pearson, J. Bowers, M. B. Glass, M. Mayo, V. Wuthiekanun, D. Engelthaler, S. J. Peacock, B. J. Currie, D. M. Wagner, P. Keim, and A. Tuanyok. 2011. Diversity of 16S-23S rDNA internal transcribed spacer (ITS) reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors. PLoS One 6:e29323.

Liu, C. M., M. K. Cosetti, M. Aziz, J. L. Buchhagen, T. L. Contente-Cuomo, L. B. Price, P. S. Keim, and A. K. Lalwani. 2011. The otologic microbiome: a study of the bacterial microbiota in a pediatric patient with chronic serous otitis media using 16SrRNA gene-based pyrosequencing. Archives of Otolaryngology-Head & Neck Surgery 137:664-668.

Marston, C. K., C. A. Allen, J. Beaudry, E. P. Price, S. R. Wolken, T. Pearson, P. Keim, and A. R. Hoffmaster. 2011. Molecular epidemiology of anthrax cases associated with recreational use of animal hides and yarn in the United States. PLoS One 6:e28274.

Mukhopadhyay, C., M. Kaestli, K. E. Vandana, K. Sushma, M. Mayo, L. Richardson, A. Tuanyok, P. Keim, D. Godoy, B. G. Spratt, and B. J. Currie. 2011. Molecular characterization of clinical Burkholderia pseudomallei isolates from India. American Journal of Tropical Medical and Hygiene 85:121-123.

Okinaka, R. T., K.K. Hill, T. Pearson, J.T. Foster, A. J. Vogler, A. Tuanyok, D. M. Wagner, and P. Keim. 2011a. Forensic Analysis in Bacterial Pathogens, Chapter 16. Pages 259-276 in B. Budowle, S.E. Schutzer, R.G. Breeze, P.S. Keim, and S. A. Morse, editors. Microbial Forensics. Elsevier Press.

Okinaka, R. T., E. P. Price, S. R. Wolken, J. M. Gruendike, W. K. Chung, T. Pearson, G. Xie, C. Munk, K. K. Hill, J. Challacombe, B. E. Ivins, J. M. Schupp, S. M. Beckstrom-Sternberg, A. Friedlander, and P. Keim. 2011b. An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics. BMC Genomics 12:477.

Price, L. B., C. M. Liu, Y. M. Frankel, J. H. Melendez, M. Aziz, J. Buchhagen, T. Contente-Cuomo, D. M. Engelthaler, P. S. Keim, J. Ravel, G. S. Lazarus, and J. M. Zenilman. 2011. Macroscale spatial variation in chronic wound microbiota: a cross-sectional study. Wound Repair Regen 19:80-88.

Rasko, D. A., P. L. Worsham, T. G. Abshire, S. T. Stanley, J. D. Bannan, M. R. Wilson, R. J. Langham, R. S. Decker, L. Jiang, T. D. Read, A. M. Phillippy, S. L. Salzberg, M. Pop, M. N. Van Ert, L. J. Kenefic, P. S. Keim, C. M. Fraser-Liggett, and J. Ravel. 2011. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of Sciences USA 108:5027-5032.

Rivarola, M., J. T. Foster, A. P. Chan, A. L. Williams, D. W. Rice, X. Liu, A. Melake-Berhan, H. Huot Creasy, D. Puiu, M. J. Rosovitz, H. M. Khouri, S. M. Beckstrom-Sternberg, G. J. Allan, P. Keim, J. Ravel, and P. D. Rabinowicz. 2011. Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One 6:e21743.

Stewart, T., D. M. Engelthaler, D. D. Blaney, A. Tuanyok, E. Wangsness, T. L. Smith, T. Pearson, K. K. Komatsu, P. Keim, B. J. Currie, C. Levy, and R. Sunenshine. 2011. Epidemiology and investigation of melioidosis, Southern Arizona. Emerging Infectious Diseases 17:1286-1288.

Vogler, A. J., D. N. Birdsell, J. Lee, J. Vaissaire, C. L. Doujet, M. Lapalus, D. M. Wagner, and P. Keim. 2011a. Phylogeography of Francisella tularensis ssp. holarctica in France. Letters in Applied Microbiology 52:177-180.

Vogler, A. J., F. Chan, D. M. Wagner, P. Roumagnac, J. Lee, R. Nera, M. Eppinger, J. Ravel, L. Rahalison, B. W. Rasoamanana, S. M. Beckstrom-Sternberg, M. Achtman, S. Chanteau, and P. Keim. 2011b. Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS Neglected Tropical Diseases 5:e1319.

Waters, A. E., T. Contente-Cuomo, J. Buchhagen, C. M. Liu, L. Watson, K. Pearce, J. T. Foster, J. Bowers, E. M. Driebe, D. M. Engelthaler, P. S. Keim, and L. B. Price. 2011. Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry. Clinical Infectious Diseases 52:1227-1230.

Aikembayev, A. M., L. Lukhnova, G. Temiraliyeva, T. Meka-Mechenko, Y. Pazylov, S. Zakaryan, G. Denissov, W. R. Easterday, M. N. Van Ert, P. Keim, S. C. Francesconi, J. K. Blackburn, M. Hugh-Jones, and T. Hadfield. 2010. Historical distribution and molecular diversity of Bacillus anthracis, Kazakhstan. Emerging Infectious Diseases 16:789-796.

Auerbach, R., B. J. Currie, A. Tuanyok, D. Wagner, and P. Keim. 2010. Burkholderia pseudomallei Diagnostic Genetic Elements that Predict Mortality in Melioidosis. US Patent App. 12/598,315.

Bowers, J. R., D. M. Engelthaler, J. L. Ginther, T. Pearson, S. J. Peacock, A. Tuanyok, D. M. Wagner, B. J. Currie, and P. S. Keim. 2010. BurkDiff: a real-time PCR allelic discrimination assay for Burkholderia pseudomallei and B. mallei. PLoS One 5:e15413.

Brown, A. N., J. J. McSharry, Q. Weng, E. M. Driebe, D. M. Engelthaler, K. Sheff, P. S. Keim, J. Nguyen, and G. L. Drusano. 2010. In vitro system for modeling influenza A virus resistance under drug pressure. Antimicrobial Agents and Chemotherapy 54:3442-3450.

Chen, P. E., K. M. Willner, A. Butani, S. Dorsey, M. George, A. Stewart, S. M. Lentz, C. E. Cook, A. Akmal, L. B. Price, P. S. Keim, A. Mateczun, T. N. Brahmbhatt, K. A. Bishop-Lilly, M. E. Zwick, T. D. Read, and S. Sozhamannan. 2010. Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing. PLoS One 5:e12397.

Cummings, C. A., C. A. Bormann Chung, R. Fang, M. Barker, P. Brzoska, P. C. Williamson, J. Beaudry, M. Matthews, J. Schupp, D. M. Wagner, D. Birdsell, A. J. Vogler, M. R. Furtado, P. Keim, and B. Budowle. 2010. Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investigative Genetics 1:1-14.

Davis, T. S., R. W. Hofstetter, K. D. Klepzig, J. T. Foster, and P. Keim. 2010. Interactions between multiple fungi isolated from two bark beetles, Dendroctonus brevicomis and Dendroctonus frontalis (Coleoptera: Curculionidae). Journal of Yeast and Fungal Research 1:118-126.

Foster, J. T., G. J. Allan, A. P. Chan, P. D. Rabinowicz, J. Ravel, P. J. Jackson, and P. Keim. 2010. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC Plant Biology 10:13.

Friggens, M. M., R. R. Parmenter, M. Boyden, P. L. Ford, K. Gage, and P. Keim. 2010. Flea abundance, diversity, and plague in Gunnison’s prairie dogs (Cynomys gunnisoni) and their burrows in montane grasslands in northern New Mexico. Journal of Wildlife Diseases 46:356-367.

Gasser, U., C. Eisenmann, G. Maret, and P. Keim. 2010. Melting of crystals in two dimensions. ChemPhysChem 11:963-970.

Greenberg, D. L., J. D. Busch, P. Keim, and D. M. Wagner. 2010. Identifying experimental surrogates for Bacillus anthracis spores: a review. Investigative Genetics 1:1-12.

Johansson, A., J. Celli, W. Conlan, K. L. Elkins, M. Forsman, P. S. Keim, P. Larsson, C. Manoil, F. E. Nano, J. M. Petersen, and A. Sjostedt. 2010. Objections to the transfer of Francisella novicida to the subspecies rank of Francisella tularensis. International Journal of Systematic and Evolutionary Microbiology 60:1717-1718.

Liu, C. M., E. M. Driebe, J. Schupp, E. Kelley, J. T. Nguyen, J. J. McSharry, Q. Weng, D. M. Engelthaler, and P. S. Keim. 2010. Rapid quantification of single-nucleotide mutations in mixed influenza A viral populations using allele-specific mixture analysis. Journal of Virological Methods 163:109-115.

Losada, L., C. M. Ronning, D. DeShazer, D. Woods, N. Fedorova, H. S. Kim, S. A. Shabalina, T. R. Pearson, L. Brinkac, P. Tan, T. Nandi, J. Crabtree, J. Badger, S. Beckstrom-Sternberg, M. Saqib, S. E. Schutzer, P. Keim, and W. C. Nierman. 2010. Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biology and Evolution 2:102-116.

Morelli, G., Y. Song, C. J. Mazzoni, M. Eppinger, P. Roumagnac, D. M. Wagner, M. Feldkamp, B. Kusecek, A. J. Vogler, Y. Li, Y. Cui, N. R. Thomson, T. Jombart, R. Leblois, P. Lichtner, L. Rahalison, J. M. Petersen, F. Balloux, P. Keim, T. Wirth, J. Ravel, R. Yang, E. Carniel, and M. Achtman. 2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics 42:1140-1143.

Nandi, T., C. Ong, A. P. Singh, J. Boddey, T. Atkins, M. Sarkar-Tyson, A. E. Essex-Lopresti, H. H. Chua, T. Pearson, J. F. Kreisberg, C. Nilsson, P. Ariyaratne, C. Ronning, L. Losada, Y. Ruan, W. K. Sung, D. Woods, R. W. Titball, I. Beacham, I. Peak, P. Keim, W. C. Nierman, and P. Tan. 2010. A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathogens 6:e1000845.

Neafsey, D. E., B. M. Barker, T. J. Sharpton, J. E. Stajich, D. J. Park, E. Whiston, C.-Y. Hung, C. McMahan, J. White, and S. Sykes. 2010. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research 20:938-946.

Price, E. P., H. M. Hornstra, D. Limmathurotsakul, T. L. Max, D. S. Sarovich, A. J. Vogler, J. L. Dale, J. L. Ginther, B. Leadem, R. E. Colman, J. T. Foster, A. Tuanyok, D. M. Wagner, S. J. Peacock, T. Pearson, and P. Keim. 2010a. Within-host evolution of Burkholderia pseudomallei in four cases of acute melioidosis. PLoS Pathogens 6:e1000725.

Price, E. P., M. A. Matthews, J. A. Beaudry, J. L. Allred, J. M. Schupp, D. N. Birdsell, T. Pearson, and P. Keim. 2010b. Cost-effective interrogation of single nucleotide polymorphisms using the mismatch amplification mutation assay and capillary electrophoresis. Electrophoresis 31:3881-3888.

Price, L. B., C. M. Liu, K. E. Johnson, M. Aziz, M. K. Lau, J. Bowers, J. Ravel, P. S. Keim, D. Serwadda, M. J. Wawer, and R. H. Gray. 2010c. The effects of circumcision on the penis microbiome. PLoS One 5:e8422.

Reutter, D., S. E. Schutzer, C. M. Craft, J. Fletcher, F. L. Fricke, S. A. Holowachuk, R. C. Johnson, P. S. Keim, J. L. Pearson, R. W. Sibert, and S. Velsko. 2010. Planning for exercises of chemical, biological, radiological, and nuclear (CBRN) forensic capabilities. Biosecurity and Bioterrorism 8:343-355.

Sarovich, D. S., R. E. Colman, E. P. Price, W. K. Chung, J. Lee, J. M. Schupp, K. R. Cobble, J. D. Busch, J. Alexander, and P. Keim. 2010. Selective isolation of Yersinia pestis from plague-infected fleas. Journal of Microbiological Methods 82:95-97.

Sheff, K. W., E. R. York, E. M. Driebe, B. M. Barker, S. D. Rounsley, V. G. Waddell, S. M. Beckstrom-Sternberg, J. S. Beckstrom-Sternberg, P. S. Keim, and D. M. Engelthaler. 2010. Development of a rapid, cost-effective TaqMan Real-Time PCR Assay for identification and differentiation of Coccidioides immitis and Coccidioides posadasii. Medical Mycology 48:466-469.

Wagner, D. M., J. Runberg, A. J. Vogler, J. Lee, E. Driebe, L. B. Price, D. M. Engelthaler, W. F. Fricke, J. Ravel, and P. Keim. 2010. No resistance plasmid in Yersinia pestis, North America. Emerging Infectious Diseases 16:885-887.

Birdsell, D. N., T. Stewart, A. J. Vogler, E. Lawaczeck, A. Diggs, T. L. Sylvester, J. L. Buchhagen, R. K. Auerbach, P. Keim, and D. M. Wagner. 2009. Francisella tularensis subsp. novicida isolated from a human in Arizona. BMC Research Notes 2:1-6.

Champion, M. D., Q. Zeng, E. B. Nix, F. E. Nano, P. Keim, C. D. Kodira, M. Borowsky, S. Young, M. Koehrsen, R. Engels, M. Pearson, C. Howarth, L. Larson, J. White, L. Alvarado, M. Forsman, S. W. Bearden, A. Sjostedt, R. Titball, S. L. Michell, B. Birren, and J. Galagan. 2009. Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies. PLoS Pathogens 5:e1000459.

Coleman, J. J., S. D. Rounsley, M. Rodriguez-Carres, A. Kuo, C. C. Wasmann, J. Grimwood, J. Schmutz, M. Taga, G. J. White, and S. Zhou. 2009. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics 5:e1000618.

Colman, R. E., A. J. Vogler, J. L. Lowell, K. L. Gage, C. Morway, P. J. Reynolds, P. Ettestad, P. Keim, M. Y. Kosoy, and D. M. Wagner. 2009. Fine-scale identification of the most likely source of a human plague infection. Emerging Infectious Diseases 15:1623.

Cummings, C. A., C. A. B. Chung, R. Fang, M. Barker, P. M. Brzoska, P. Williamson, J. A. Beaudry, M. Matthews, J. M. Schupp, and D. M. Wagner. 2009. Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms. Forensic Science International: Genetics Supplement Series 2:300-301.

Currie, B. J., A. Haslem, T. Pearson, H. Hornstra, B. Leadem, M. Mayo, D. Gal, L. Ward, D. Godoy, B. G. Spratt, and P. Keim. 2009. Identification of melioidosis outbreak by multilocus variable number tandem repeat analysis. Emerging Infectious Diseases 15:169-174.

Ebert, F., P. Dillmann, G. Maret, and P. Keim. 2009. The experimental realization of a two-dimensional colloidal model system. Review of Scientific Instruments 80:083902.

Foster, J. T. 2009. The history and impacts of exotic birds in the Hawaiian Islands, Chapter 13.in T.K. Pratt, C.T. Atkinson, P.C. Banko, J.D. Jacobi, and B. L. Woodworth, editors. Conservation Biology of Hawaiian Forest Birds. Yale University Press, New Haven, CT.

Foster, J. T., S. M. Beckstrom-Sternberg, T. Pearson, J. S. Beckstrom-Sternberg, P. S. G. Chain, F. F. Roberto, J. Hnath, T. Brettin, and P. Keim. 2009. Whole-genome-based phylogeny and divergence of the genus Brucella. Journal of Bacteriology 191:2864-2870.

Franz, D. R., S. A. Ehrlich, A. Casadevall, M. J. Imperiale, and P. S. Keim. 2009. The “nuclearization” of biology is a threat to health and security. Biosecurity and Bioterrorism 7:243-244.

Hornstra, H., T. Pearson, S. Georgia, A. Liguori, J. Dale, E. Price, M. O’Neill, D. Deshazer, G. Muhammad, M. Saqib, A. Naureen, and P. Keim. 2009. Molecular epidemiology of glanders, Pakistan. Emerging Infectious Diseases 15:2036-2039.

Keim, P. 2009. Biosecurity. Paul Keim on his life with the FBI during the anthrax investigation. Interview by Yudhijit Bhattacharjee. Science 323:1416.

Keim, P., J. M. Gruendike, A. M. Klevytska, J. M. Schupp, J. Challacombe, and R. Okinaka. 2009. The genome and variation of Bacillus anthracis. Molecular Aspects of Medicine 30:397-405.

Keim, P. S., and D. M. Wagner. 2009. Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases. Nature Reviews Microbiology 7:813-821.

Kenefic, L. J., T. Pearson, R. T. Okinaka, J. M. Schupp, D. M. Wagner, A. R. Hoffmaster, C. B. Trim, W. K. Chung, J. A. Beaudry, L. Jiang, P. Gajer, J. T. Foster, J. I. Mead, J. Ravel, and P. Keim. 2009. Pre-Columbian origins for North American anthrax. PLoS One 4:e4813.

Larsson, P., D. Elfsmark, K. Svensson, P. Wikstrom, M. Forsman, T. Brettin, P. Keim, and A. Johansson. 2009. Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen. PLoS Pathogens 5:e1000472.

Nguyen, J. T., J. D. Hoopes, D. F. Smee, M. N. Prichard, E. M. Driebe, D. M. Engelthaler, M. H. Le, P. S. Keim, R. P. Spence, and G. T. Went. 2009. Triple combination of oseltamivir, amantadine, and ribavirin displays synergistic activity against multiple influenza virus strains in vitro. Antimicrobial Agents and Chemotherapy 53:4115-4126.

Pearson, T., P. Giffard, S. Beckstrom-Sternberg, R. Auerbach, H. Hornstra, A. Tuanyok, E. P. Price, M. B. Glass, B. Leadem, J. S. Beckstrom-Sternberg, G. J. Allan, J. T. Foster, D. M. Wagner, R. T. Okinaka, S. H. Sim, O. Pearson, Z. Wu, J. Chang, R. Kaul, A. R. Hoffmaster, T. S. Brettin, R. A. Robison, M. Mayo, J. E. Gee, P. Tan, B. J. Currie, and P. Keim. 2009a. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biology 7:78.

Pearson, T., R. T. Okinaka, J. T. Foster, and P. Keim. 2009b. Phylogenetic understanding of clonal populations in an era of whole genome sequencing. Infection Genetics and Evolution 9:1010-1019.

Price, L. B., C. M. Liu, J. H. Melendez, Y. M. Frankel, D. Engelthaler, M. Aziz, J. Bowers, R. Rattray, J. Ravel, C. Kingsley, P. S. Keim, G. S. Lazarus, and J. M. Zenilman. 2009. Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota. PLoS One 4:e6462.

Ravel, J., L. Jiang, S. T. Stanley, M. R. Wilson, R. S. Decker, T. D. Read, P. Worsham, P. S. Keim, S. L. Salzberg, C. M. Fraser-Liggett, and D. A. Rasko. 2009. The complete genome sequence of Bacillus anthracis Ames “Ancestor”. Journal of Bacteriology 191:445-446.

Reding, D. M., J. T. Foster, H. F. James, H. D. Pratt, and R. C. Fleischer. 2009. Convergent evolution of ‘creepers’ in the Hawaiian honeycreeper radiation. Biology Letters 5:221-224.

Schutzer, S. E., P. Keim, K. Czerwinski, and B. Budowle. 2009. Use of forensic methods under exigent circumstances without full validation. Science Translational Medicine 1:8cm7.

Sharpton, T. J., J. E. Stajich, S. D. Rounsley, M. J. Gardner, J. R. Wortman, V. S. Jordar, R. Maiti, C. D. Kodira, D. E. Neafsey, and Q. Zeng. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research 19:1722-1731.

Simonson, T. S., R. T. Okinaka, B. Wang, W. R. Easterday, L. Huynh, J. M. U’Ren, M. Dukerich, S. R. Zanecki, L. J. Kenefic, J. Beaudry, J. M. Schupp, T. Pearson, D. M. Wagner, A. Hoffmaster, J. Ravel, and P. Keim. 2009. Bacillus anthracis in China and its relationship to worldwide lineages. BMC Microbiology 9:71.

Tiller, R. V., B. K. De, M. Boshra, L. Y. Huynh, M. N. Van Ert, D. M. Wagner, J. Klena, T. S. Mohsen, S. S. El-Shafie, P. Keim, A. R. Hoffmaster, P. P. Wilkins, and G. Pimentel. 2009. Comparison of two multiple-locus variable-number tandem-repeat analysis methods for molecular strain typing of human Brucella melitensis isolates from the Middle East. Journal of Clinical Microbiology 47:2226-2231.

Trunck, L. A., K. L. Propst, V. Wuthiekanun, A. Tuanyok, S. M. Beckstrom-Sternberg, J. S. Beckstrom-Sternberg, S. J. Peacock, P. Keim, S. W. Dow, and H. P. Schweizer. 2009. Molecular basis of rare aminoglycoside susceptibility and pathogenesis of Burkholderia pseudomallei clinical isolates from Thailand. PLoS Neglected Tropical Diseases 3:e519.

Truong, A. P., D. L. Aubele, G. D. Probst, M. L. Neitzel, C. M. Semko, S. Bowers, D. Dressen, R. K. Hom, A. W. Konradi, H. L. Sham, A. W. Garofalo, P. S. Keim, J. Wu, M. S. Dappen, K. Wong, E. Goldbach, K. P. Quinn, J. M. Sauer, E. F. Brigham, W. Wallace, L. Nguyen, S. S. Hemphill, M. P. Bova, F. Bard, T. A. Yednock, and G. Basi. 2009. Design, synthesis, and structure-activity relationship of novel orally efficacious pyrazole/sulfonamide based dihydroquinoline gamma-secretase inhibitors. Bioorganic & Medicinal Chemistry Letters 19:4920-4923.

Vogler, A. J., D. Birdsell, L. B. Price, J. R. Bowers, S. M. Beckstrom-Sternberg, R. K. Auerbach, J. S. Beckstrom-Sternberg, A. Johansson, A. Clare, J. L. Buchhagen, J. M. Petersen, T. Pearson, J. Vaissaire, M. P. Dempsey, P. Foxall, D. M. Engelthaler, D. M. Wagner, and P. Keim. 2009a. Phylogeography of Francisella tularensis: global expansion of a highly fit clone. Journal of Bacteriology 191:2474-2484.

Vogler, A. J., D. Birdsell, D. M. Wagner, and P. Keim. 2009b. An optimized, multiplexed multi‐locus variable‐number tandem repeat analysis system for genotyping Francisella tularensis. Letters in Applied Microbiology 48:140-144.

Allender, C. J., K. M. Clancy, T. E. Degomez, J. D. McMillin, S. A. Woolbright, P. Keim, and D. M. Wagner. 2008. Lack of genetic differentiation in aggressive and secondary bark beetles (Coleoptera: Curculionidae, Scolytinae) from Arizona. Environmental Entomology 37:817-824.

Casadevall, A., S. A. Ehrlich, D. R. Franz, M. J. Imperiale, and P. S. Keim. 2008. Biodefense research: a win-win challenge. Biosecurity and Bioterrorism 6:291-292.

Foster, J. T., R. T. Okinaka, R. Svensson, K. Shaw, B. K. De, R. A. Robison, W. S. Probert, L. J. Kenefic, W. D. Brown, and P. Keim. 2008. Real-time PCR assays of single-nucleotide polymorphisms defining the major Brucella clades. Journal of Clinical Microbiology 46:296-301.

Huynh, L. Y., M. N. Van Ert, T. Hadfield, W. S. Probert, B. H. Bellaire, M. Dobson, R. J. Burgess, R. S. Weyant, T. Popovic, and S. Zanecki. 2008. Multiple locus variable number tandem repeat (VNTR) analysis (MLVA) of Brucella spp. identifies species-specific markers and insights into phylogenetic relationships. Pages 47-54  National Institute of Allergy and Infectious Diseases, NIH. Humana Press.

Keim, P., T. Pearson, and R. Okinaka. 2008. Microbial forensics: DNA fingerprinting of Bacillus anthracis (anthrax). Analytical Chemistry 80:4791-4799.

Kenefic, L. J., J. Beaudry, C. Trim, R. Daly, R. Parmar, S. Zanecki, L. Huynh, M. N. Van Ert, D. M. Wagner, T. Graham, and P. Keim. 2008a. High resolution genotyping of Bacillus anthracis outbreak strains using four highly mutable single nucleotide repeat markers. Letters in Applied Microbiology 46:600-603.

Kenefic, L. J., J. Beaudry, C. Trim, L. Huynh, S. Zanecki, M. Matthews, J. Schupp, M. Van Ert, and P. Keim. 2008b. A high resolution four-locus multiplex single nucleotide repeat (SNR) genotyping system in Bacillus anthracis. Journal of Microbiological Methods 73:269-272.

Kenefic, L. J., T. Pearson, R. T. Okinaka, W. K. Chung, T. Max, C. P. Trim, J. A. Beaudry, J. M. Schupp, M. N. Van Ert, C. K. Marston, K. Gutierrez, A. K. Swinford, A. R. Hoffmaster, and P. Keim. 2008c. Texas isolates closely related to Bacillus anthracis Ames. Emerging Infectious Diseases 14:1494-1496.

Malcolm, T. R., K. J. Swinnerton, J. J. Groombridge, B. D. Sparklin, C. N. Brosius, J. P. Vetter, and J. T. Foster. 2008. Ground-based rodent control in a remote Hawaiian rainforest on Maui. Pacific Conservation Biology 14:206-214.

Okinaka, R. T., M. Henrie, K. K. Hill, K. S. Lowery, M. Van Ert, T. Pearson, J. Schupp, L. Kenefic, J. Beaudry, S. A. Hofstadler, P. J. Jackson, and P. Keim. 2008. Single nucleotide polymorphism typing of Bacillus anthracis from Sverdlovsk tissue. Emerging Infectious Diseases 14:653-656.

Schmidt, B. K., J. T. Foster, G. R. Angehr, K. L. Durrant, and R. C. Fleischer. 2008. A new species of African forest robin from Gabon (Passeriformes : Muscicapidae : Stiphrornis). Zootaxa:27-42.

Sinclair, R., S. A. Boone, D. Greenberg, P. Keim, and C. P. Gerba. 2008. Persistence of category A select agents in the environment. Applied and Environmental Microbiology 74:555-563.

Tuanyok, A., B. R. Leadem, R. K. Auerbach, S. M. Beckstrom-Sternberg, J. S. Beckstrom-Sternberg, M. Mayo, V. Wuthiekanun, T. S. Brettin, W. C. Nierman, S. J. Peacock, B. J. Currie, D. M. Wagner, and P. Keim. 2008. Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics 9:566.

Vogler, A. J., E. M. Driebe, J. Lee, R. K. Auerbach, C. J. Allender, M. Stanley, K. Kubota, G. L. Andersen, L. Radnedge, P. L. Worsham, P. Keim, and D. M. Wagner. 2008. Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92. Biotechniques 44:201, 203-204, 207.

Woolbright, S. A., S. P. Difazio, T. Yin, G. D. Martinsen, X. Zhang, G. J. Allan, T. G. Whitham, and P. Keim. 2008. A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree. Heredity 100:59-70.

Auerbach, R. K., A. Tuanyok, W. S. Probert, L. Kenefic, A. J. Vogler, D. C. Bruce, C. Munk, T. S. Brettin, M. Eppinger, J. Ravel, D. M. Wagner, and P. Keim. 2007. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS One 2:e770.

Barker, B. M., K. A. Jewell, S. Kroken, and M. J. Orbach. 2007. The population biology of Coccidioides: epidemiologic implications for disease outbreaks. Annals of the New York Academy of Sciences 1111:147-163.

Beckstrom-Sternberg, S. M., R. K. Auerbach, S. Godbole, J. V. Pearson, J. S. Beckstrom-Sternberg, Z. Deng, C. Munk, K. Kubota, Y. Zhou, D. Bruce, J. Noronha, R. H. Scheuermann, A. Wang, X. Wei, J. Wang, J. Hao, D. M. Wagner, T. S. Brettin, N. Brown, P. Gilna, and P. S. Keim. 2007. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One 2:e947.

Budowle, B., J. A. Beaudry, N. G. Barnaby, A. M. Giusti, J. D. Bannan, and P. Keim. 2007. Role of law enforcement response and microbial forensics in investigation of bioterrorism. Croatian Medical Journal 48:437-449.

Challacombe, J. F., M. R. Altherr, G. Xie, S. S. Bhotika, N. Brown, D. Bruce, C. S. Campbell, M. L. Campbell, J. Chen, O. Chertkov, C. Cleland, M. Dimitrijevic, N. A. Doggett, J. J. Fawcett, T. Glavina, L. A. Goodwin, L. D. Green, C. S. Han, K. K. Hill, P. Hitchcock, P. J. Jackson, P. Keim, A. R. Kewalramani, J. Longmire, S. Lucas, S. Malfatti, D. Martinez, K. McMurry, L. J. Meincke, M. Misra, B. L. Moseman, M. Mundt, A. C. Munk, R. T. Okinaka, B. Parson-Quintana, L. P. Reilly, P. Richardson, D. L. Robinson, E. Saunders, R. Tapia, J. G. Tesmer, N. Thayer, L. S. Thompson, H. Tice, L. O. Ticknor, P. L. Wills, P. Gilna, and T. S. Brettin. 2007. The complete genome sequence of Bacillus thuringiensis Al Hakam. Journal of Bacteriology 189:3680-3681.

Dempsey, M. P., M. Dobson, C. Zhang, M. Zhang, C. Lion, C. B. Gutierrez-Martin, P. C. Iwen, P. D. Fey, M. E. Olson, D. Niemeyer, S. Francesconi, R. Crawford, M. Stanley, J. Rhodes, D. M. Wagner, A. J. Vogler, D. Birdsell, P. Keim, A. Johansson, S. H. Hinrichs, and A. K. Benson. 2007. Genomic deletion marking an emerging subclone of Francisella tularensis subsp. holarctica in France and the Iberian Peninsula. Applied and Environmental Microbiology 73:7465-7470.

Keim, P., A. Johansson, and D. M. Wagner. 2007. Molecular epidemiology, evolution, and ecology of Francisella. Annals of the New York Academy of Sciences 1105:30-66.

Lee, K., J. W. Costerton, J. Ravel, R. K. Auerbach, D. M. Wagner, P. Keim, and J. G. Leid. 2007. Phenotypic and functional characterization of Bacillus anthracis biofilms. Microbiology 153:1693-1701.

Mandel, M. A., B. M. Barker, S. Kroken, S. D. Rounsley, and M. J. Orbach. 2007. Genomic and population analyses of the mating type loci in Coccidioides species reveal evidence for sexual reproduction and gene acquisition. Eukaryotic Cell 6:1189-1199.

Pearson, T., J. M. U’Ren, J. M. Schupp, G. J. Allan, P. G. Foster, M. J. Mayo, D. Gal, J. L. Choy, R. L. Daugherty, S. Kachur, C. L. Friedman, B. Leadem, S. Georgia, H. Hornstra, A. J. Vogler, D. M. Wagner, P. Keim, and B. J. Currie. 2007. VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia. Infection, Genetics and Evolution 7:416-423.

Touchman, J. W., D. M. Wagner, J. Hao, S. D. Mastrian, M. K. Shah, A. J. Vogler, C. J. Allender, E. A. Clark, D. S. Benitez, D. J. Youngkin, J. M. Girard, R. K. Auerbach, S. M. Beckstrom-Sternberg, and P. Keim. 2007. A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS One 2:e220.

Tuanyok, A., R. K. Auerbach, T. S. Brettin, D. C. Bruce, A. C. Munk, J. C. Detter, T. Pearson, H. Hornstra, R. W. Sermswan, V. Wuthiekanun, S. J. Peacock, B. J. Currie, P. Keim, and D. M. Wagner. 2007. A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. Journal of Bacteriology 189:9044-9049.

U’Ren, J. M., H. Hornstra, T. Pearson, J. M. Schupp, B. Leadem, S. Georgia, R. W. Sermswan, and P. Keim. 2007a. Fine-scale genetic diversity among Burkholderia pseudomallei soil isolates in northeast Thailand. Applied and Environmental Microbiology 73:6678-6681.

U’Ren, J. M., J. M. Schupp, T. Pearson, H. Hornstra, C. L. Friedman, K. L. Smith, R. R. Daugherty, S. D. Rhoton, B. Leadem, S. Georgia, M. Cardon, L. Y. Huynh, D. DeShazer, S. P. Harvey, R. Robison, D. Gal, M. J. Mayo, D. Wagner, B. J. Currie, and P. Keim. 2007b. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping. BMC Microbiology 7:23.

Van Ert, M. N., W. R. Easterday, L. Y. Huynh, R. T. Okinaka, M. E. Hugh-Jones, J. Ravel, S. R. Zanecki, T. Pearson, T. S. Simonson, J. M. U’Ren, S. M. Kachur, R. R. Leadem-Dougherty, S. D. Rhoton, G. Zinser, J. Farlow, P. R. Coker, K. L. Smith, B. Wang, L. J. Kenefic, C. M. Fraser-Liggett, D. M. Wagner, and P. Keim. 2007a. Global genetic population structure of Bacillus anthracis. PLoS One 2:e461.

Van Ert, M. N., W. R. Easterday, T. S. Simonson, J. M. U’Ren, T. Pearson, L. J. Kenefic, J. D. Busch, L. Y. Huynh, M. Dukerich, C. B. Trim, J. Beaudry, A. Welty-Bernard, T. Read, C. M. Fraser, J. Ravel, and P. Keim. 2007b. Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. Journal of Clinical Microbiology 45:47-53.

Vogler, A. J., C. E. Keys, C. Allender, I. Bailey, J. Girard, T. Pearson, K. L. Smith, D. M. Wagner, and P. Keim. 2007. Mutations, mutation rates, and evolution at the hypervariable VNTR loci of Yersinia pestis. Mutation Research 616:145-158.

Welch, T. J., W. F. Fricke, P. F. McDermott, D. G. White, M.-L. Rosso, D. A. Rasko, M. K. Mammel, M. Eppinger, M. J. Rosovitz, and D. Wagner. 2007. Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS One 2:e309.

Wimp, G. M., S. Wooley, R. K. Bangert, W. P. Young, G. D. Martinsen, P. Keim, B. Rehill, R. L. Lindroth, and T. G. Whitham. 2007. Plant genetics predicts intra-annual variation in phytochemistry and arthropod community structure. Molecular Ecology 16:5057-5069.

Anderson, J. P., D. E. Walker, J. M. Goldstein, R. de Laat, K. Banducci, R. J. Caccavello, R. Barbour, J. Huang, K. Kling, M. Lee, L. Diep, P. S. Keim, X. Shen, T. Chataway, M. G. Schlossmacher, P. Seubert, D. Schenk, S. Sinha, W. P. Gai, and T. J. Chilcote. 2006. Phosphorylation of Ser-129 is the dominant pathological modification of alpha-synuclein in familial and sporadic Lewy body disease. Journal of Biological Chemistry 281:29739-29752.

Bangert, R. K., G. J. Allan, R. J. Turek, G. M. Wimp, N. Meneses, G. D. Martinsen, P. Keim, and T. G. Whitham. 2006a. From genes to geography: a genetic similarity rule for arthropod community structure at multiple geographic scales. Molecular Ecology 15:4215-4228.

Bangert, R. K., R. J. Turek, B. Rehill, G. M. Wimp, J. A. Schweitzer, G. J. Allan, J. K. Bailey, G. D. Martinsen, P. Keim, R. L. Lindroth, and T. G. Whitham. 2006b. A genetic similarity rule determines arthropod community structure. Molecular Ecology 15:1379-1391.

Fischer, D. G., S. C. Hart, B. J. Rehill, R. L. Lindroth, P. Keim, and T. G. Whitham. 2006. Do high-tannin leaves require more roots? Oecologia 149:668-675.

Han, C. S., G. Xie, J. F. Challacombe, M. R. Altherr, S. S. Bhotika, N. Brown, D. Bruce, C. S. Campbell, M. L. Campbell, J. Chen, O. Chertkov, C. Cleland, M. Dimitrijevic, N. A. Doggett, J. J. Fawcett, T. Glavina, L. A. Goodwin, L. D. Green, K. K. Hill, P. Hitchcock, P. J. Jackson, P. Keim, A. R. Kewalramani, J. Longmire, S. Lucas, S. Malfatti, K. McMurry, L. J. Meincke, M. Misra, B. L. Moseman, M. Mundt, A. C. Munk, R. T. Okinaka, B. Parson-Quintana, L. P. Reilly, P. Richardson, D. L. Robinson, E. Rubin, E. Saunders, R. Tapia, J. G. Tesmer, N. Thayer, L. S. Thompson, H. Tice, L. O. Ticknor, P. L. Wills, T. S. Brettin, and P. Gilna. 2006. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. Journal of Bacteriology 188:3382-3390.

Keim, P., M. Mock, J. Young, and T. M. Koehler. 2006. The International Bacillus anthracis, B. cereus, and B. thuringiensis Conference, “Bacillus-ACT05”. Journal of Bacteriology 188:3433-3441.

LeRoy, C. J., T. G. Whitham, P. Keim, and J. C. Marks. 2006. Plant genes link forests and streams. Ecology 87:255-261.

Maho, A., A. Rossano, H. Hachler, A. Holzer, E. Schelling, J. Zinsstag, M. H. Hassane, B. S. Toguebaye, A. J. Akakpo, M. Van Ert, P. Keim, L. Kenefic, J. Frey, and V. Perreten. 2006. Antibiotic susceptibility and molecular diversity of Bacillus anthracis strains in Chad: detection of a new phylogenetic subgroup. Journal of Clinical Microbiology 44:3422-3425.

Okinaka, R., T. Pearson, and P. Keim. 2006. Anthrax, but not Bacillus anthracis? PLoS Pathogens 2:e122.

Vogler, A. J., C. Keys, Y. Nemoto, R. E. Colman, Z. Jay, and P. Keim. 2006. Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7. Journal of Bacteriology 188:4253-4263.

Wagner, D. M., L. C. Drickamer, D. M. Krpata, C. J. Allender, W. E. Van Pelt, and P. Keim. 2006. Persistence of Gunnison’s prairie dog colonies in Arizona, USA. Biological Conservation 130:331-339.

Barns, S. M., C. C. Grow, R. T. Okinaka, P. Keim, and C. R. Kuske. 2005. Detection of diverse new Francisella-like bacteria in environmental samples. Applied and Environmental Microbiology 71:5494-5500.

Cheung, D. T., K. M. Kam, K. L. Hau, T. K. Au, C. K. Marston, J. E. Gee, T. Popovic, M. N. Van Ert, L. Kenefic, P. Keim, and A. R. Hoffmaster. 2005. Characterization of a Bacillus anthracis isolate causing a rare case of fatal anthrax in a 2-year-old boy from Hong Kong. Journal of Clinical Microbiology 43:1992-1994.

Easterday, W. R., M. N. Van Ert, T. S. Simonson, D. M. Wagner, L. J. Kenefic, C. J. Allender, and P. Keim. 2005a. Use of single nucleotide polymorphisms in the plcR gene for specific identification of Bacillus anthracis. Journal of Clinical Microbiology 43:1995-1997.

Easterday, W. R., M. N. Van Ert, S. Zanecki, and P. Keim. 2005b. Specific detection of Bacillus anthracis using a TaqMan mismatch amplification mutation assay. Biotechniques 38:731-735.

Farlow, J., D. M. Wagner, M. Dukerich, M. Stanley, M. Chu, K. Kubota, J. Petersen, and P. Keim. 2005. Francisella tularensis in the United States. Emerging Infectious Diseases 11:1835.

Fasanella, A., M. Van Ert, S. A. Altamura, G. Garofolo, C. Buonavoglia, G. Leori, L. Huynh, S. Zanecki, and P. Keim. 2005. Molecular diversity of Bacillus anthracis in Italy. Journal of Clinical Microbiology 43:3398-3401.

Keys, C., S. Kemper, and P. Keim. 2005. Highly diverse variable number tandem repeat loci in the E. coli O157:H7 and O55:H7 genomes for high-resolution molecular typing. Journal of Applied Microbiology 98:928-940.

Lowell, J. L., D. M. Wagner, B. Atshabar, M. F. Antolin, A. J. Vogler, P. Keim, M. C. Chu, and K. L. Gage. 2005. Identifying sources of human exposure to plague. Journal of Clinical Microbiology 43:650-656.

McRae, B. H., P. Beier, L. E. Dewald, L. Y. Huynh, and P. Keim. 2005. Habitat barriers limit gene flow and illuminate historical events in a wide-ranging carnivore, the American puma. Molecular Ecology 14:1965-1977.

U’Ren, J. M., M. N. Van Ert, J. M. Schupp, W. R. Easterday, T. S. Simonson, R. T. Okinaka, T. Pearson, and P. Keim. 2005. Use of a real-time PCR TaqMan assay for rapid identification and differentiation of Burkholderia pseudomallei and Burkholderia mallei. Journal of Clinical Microbiology 43:5771-5774.

Achtman, M., G. Morelli, P. Zhu, T. Wirth, I. Diehl, B. Kusecek, A. J. Vogler, D. M. Wagner, C. J. Allender, W. R. Easterday, V. Chenal-Francisque, P. Worsham, N. R. Thomson, J. Parkhill, L. E. Lindler, E. Carniel, and P. Keim. 2004. Microevolution and history of the plague bacillus, Yersinia pestis. Proceedings of the National Academy of Sciences USA 101:17837-17842.

Allender, C. J., W. R. Easterday, M. N. Van Ert, D. M. Wagner, and P. Keim. 2004. High-throughput extraction of arthropod vector and pathogen DNA using bead milling. Biotechniques 37:730, 732, 734.

DeWoody, J. A., J. Schupp, L. Kenefic, J. Busch, L. Murfitt, and P. Keim. 2004. Universal method for producing ROX-labeled size standards suitable for automated genotyping. Biotechniques 37:348, 350, 352.

Fischer, D. G., S. C. Hart, T. G. Whitham, G. D. Martinsen, and P. Keim. 2004. Ecosystem implications of genetic variation in water-use of a dominant riparian tree. Oecologia 139:288-297.

Forbes, S. N., R. K. Valenzuela, P. Keim, and P. M. Service. 2004. Quantitative trait loci affecting life span in replicated populations of Drosophila melanogaster. I. Composite interval mapping. Genetics 168:301-311.

Girard, J. M., D. M. Wagner, A. J. Vogler, C. Keys, C. J. Allender, L. C. Drickamer, and P. Keim. 2004. Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales. Proceedings of the National Academy of Sciences USA 101:8408-8413.

Hill, K. K., L. O. Ticknor, R. T. Okinaka, M. Asay, H. Blair, K. A. Bliss, M. Laker, P. E. Pardington, A. P. Richardson, M. Tonks, D. J. Beecher, J. D. Kemp, A. B. Kolsto, A. C. Wong, P. Keim, and P. J. Jackson. 2004. Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates. Applied and Environmental Microbiology 70:1068-1080.

Johansson, A., J. Farlow, P. Larsson, M. Dukerich, E. Chambers, M. Bystrom, J. Fox, M. Chu, M. Forsman, A. Sjostedt, and P. Keim. 2004. Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. Journal of Bacteriology 186:5808-5818.

Keim, P., M. N. Van Ert, T. Pearson, A. J. Vogler, L. Y. Huynh, and D. M. Wagner. 2004. Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infection, Genetics and Evolution 4:205-213.

Pearson, T., J. D. Busch, J. Ravel, T. D. Read, S. D. Rhoton, J. M. U’Ren, T. S. Simonson, S. M. Kachur, R. R. Leadem, M. L. Cardon, M. N. Van Ert, L. Y. Huynh, C. M. Fraser, and P. Keim. 2004. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proceedings of the National Academy of Sciences USA 101:13536-13541.

Takahashi, H., P. Keim, A. F. Kaufmann, C. Keys, K. L. Smith, K. Taniguchi, S. Inouye, and T. Kurata. 2004. Bacillus anthracis incident, Kameido, Tokyo, 1993. Emerging Infectious Diseases 10:117-120.

Valenzuela, R. K., S. N. Forbes, P. Keim, and P. M. Service. 2004. Quantitative trait loci affecting life span in replicated populations of Drosophila melanogaster. II. Response to selection. Genetics 168:313-324.

Van Ert, M. N., S. A. Hofstadler, Y. Jiang, J. D. Busch, D. M. Wagner, J. J. Drader, D. J. Ecker, J. C. Hannis, L. Y. Huynh, J. M. Schupp, T. S. Simonson, and P. Keim. 2004. Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis. Biotechniques 37:642-644, 646, 648 passim.

Vodkin, L. O., A. Khanna, R. Shealy, S. J. Clough, D. O. Gonzalez, R. Philip, G. Zabala, F. Thibaud-Nissen, M. Sidarous, M. V. Stromvik, E. Shoop, C. Schmidt, E. Retzel, J. Erpelding, R. C. Shoemaker, A. M. Rodriguez-Huete, J. C. Polacco, V. Coryell, P. Keim, G. Gong, L. Liu, J. Pardinas, and P. Schweitzer. 2004. Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics 5:73.

Wagner, D. M., and L. C. Drickamer. 2004. Abiotic habitat correlates of Gunnison’s prairie dog in Arizona. Journal of Wildlife Management 68:188-197.

Drickamer, L. C., P. A. Gowaty, and D. M. Wagner. 2003a. Free mutual mate preferences in house mice affect reproductive success and offspring performance. Animal Behaviour 65:105-114.

Drickamer, L. C., D. M. Wagner, and A. S. Robinson. 2003b. Double captures of house mice (Mus musculus) with information on genetic relatedness. The American Midland Naturalist 150:308-320.

Faure, J. E., M. L. Rusche, A. Thomas, P. Keim, C. Dumas, H. L. Mogensen, M. Rougier, and A. Chaboud. 2003. Double fertilization in maize: the two male gametes from a pollen grain have the ability to fuse with egg cells. Plant Journal 33:1051-1062.

Price, L. B., A. Vogler, T. Pearson, J. D. Busch, J. M. Schupp, and P. Keim. 2003. In vitro selection and characterization of Bacillus anthracis mutants with high-level resistance to ciprofloxacin. Antimicrobial Agents and Chemotherapy 47:2362-2365.

Radnedge, L., P. G. Agron, K. K. Hill, P. J. Jackson, L. O. Ticknor, P. Keim, and G. L. Andersen. 2003. Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Applied and Environmental Microbiology 69:2755-2764.

Spurgiesz, R. S., T. N. Quitugua, K. L. Smith, J. Schupp, E. G. Palmer, R. A. Cox, and P. Keim. 2003. Molecular typing of Mycobacterium tuberculosis by using nine novel variable-number tandem repeats across the Beijing family and low-copy-number IS6110 isolates. Journal of Clinical Microbiology 41:4224-4230.

Farlow, J., D. Postic, K. L. Smith, Z. Jay, G. Baranton, and P. Keim. 2002. Strain typing of Borrelia burgdorferi, Borrelia afzelii, and Borrelia garinii by using multiple-locus variable-number tandem repeat analysis. Journal of Clinical Microbiology 40:4612-4618.

Fouet, A., K. L. Smith, C. Keys, J. Vaissaire, C. Le Doujet, M. Levy, M. Mock, and P. Keim. 2002. Diversity among French Bacillus anthracis isolates. Journal of Clinical Microbiology 40:4732-4734.

Granger, C., V. Coryell, A. Khanna, P. Keim, L. Vodkin, and R. C. Shoemaker. 2002. Identification, structure, and differential expression of members of a BURP domain containing protein family in soybean. Genome 45:693-701.

Keim, P., and K. L. Smith. 2002. Bacillus anthracis evolution and epidemiology. Current Topics in Microbiology and Immunology 271:21-32.

Lindstedt, S. L., T. E. Reich, P. Keim, and P. C. LaStayo. 2002. Do muscles function as adaptable locomotor springs? Journal of Experimental Biology 205:2211-2216.

Mock, K. E., T. C. Theimer, O. E. Rhodes, Jr., D. L. Greenberg, and P. Keim. 2002. Genetic variation across the historical range of the wild turkey (Meleagris gallopavo). Molecular Ecology 11:643-657.

Read, T. D., S. L. Salzberg, M. Pop, M. Shumway, L. Umayam, L. Jiang, E. Holtzapple, J. D. Busch, K. L. Smith, J. M. Schupp, D. Solomon, P. Keim, and C. M. Fraser. 2002. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296:2028-2033.

Shoemaker, R., P. Keim, L. Vodkin, E. Retzel, S. W. Clifton, R. Waterston, D. Smoller, V. Coryell, A. Khanna, J. Erpelding, X. Gai, V. Brendel, C. Raph-Schmidt, E. G. Shoop, C. J. Vielweber, M. Schmatz, D. Pape, Y. Bowers, B. Theising, J. Martin, M. Dante, T. Wylie, and C. Granger. 2002. A compilation of soybean ESTs: generation and analysis. Genome 45:329-338.

Vogler, A. J., J. D. Busch, S. Percy-Fine, C. Tipton-Hunton, K. L. Smith, and P. Keim. 2002. Molecular analysis of rifampin resistance in Bacillus anthracis and Bacillus cereus. Antimicrobial Agents and Chemotherapy 46:511-513.

Farlow, J., K. L. Smith, J. Wong, M. Abrams, M. Lytle, and P. Keim. 2001. Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis. Journal of Clinical Microbiology 39:3186-3192.

Keim, P., K. L. Smith, C. Keys, H. Takahashi, T. Kurata, and A. Kaufmann. 2001. Molecular investigation of the Aum Shinrikyo anthrax release in Kameido, Japan. Journal of Clinical Microbiology 39:4566-4567.

Klevytska, A. M., L. B. Price, J. M. Schupp, P. L. Worsham, J. Wong, and P. Keim. 2001. Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome. Journal of Clinical Microbiology 39:3179-3185.

Martinsen, G. D., T. G. Whitham, R. J. Turek, and P. Keim. 2001. Hybrid populations selectively filter gene introgression between species. Evolution 55:1325-1335.

Ticknor, L. O., A. B. Kolsto, K. K. Hill, P. Keim, M. T. Laker, M. Tonks, and P. J. Jackson. 2001. Fluorescent Amplified Fragment Length Polymorphism Analysis of Norwegian Bacillus cereus and Bacillus thuringiensis Soil Isolates. Applied and Environmental Microbiology 67:4863-4873.

Young, W. P., C. O. Ostberg, P. Keim, and G. H. Thorgaard. 2001. Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Molecular Ecology 10:921-930.

Adair, D. M., P. L. Worsham, K. K. Hill, A. M. Klevytska, P. J. Jackson, A. M. Friedlander, and P. Keim. 2000. Diversity in a variable-number tandem repeat from Yersinia pestis. Journal of Clinical Microbiology 38:1516-1519.

Ferreira, A. R., K. R. Foutz, and P. Keim. 2000. Soybean genetic map of RAPD markers assigned to an existing scaffold RFLP map. Journal of Heredity 91:392-396.

Keim, P., L. B. Price, A. M. Klevytska, K. L. Smith, J. M. Schupp, R. Okinaka, P. J. Jackson, and M. E. Hugh-Jones. 2000. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. Journal of Bacteriology 182:2928-2936.

Schupp, J. M., A. M. Klevytska, G. Zinser, L. B. Price, and P. Keim. 2000. vrrB, a hypervariable open reading frame in Bacillus anthracis. Journal of Bacteriology 182:3989-3997.

Smith, K. L., V. DeVos, H. Bryden, L. B. Price, M. E. Hugh-Jones, and P. Keim. 2000. Bacillus anthracis diversity in Kruger National Park. Journal of Clinical Microbiology 38:3780-3784.

Wagner, D. M., G. A. Feldhamer, and J. A. Newman. 2000. Microhabitat selection by golden mice (Ochrotomys nuttalli) at arboreal nest sites. The American Midland Naturalist 144:220-225.

Jackson, P. J., K. K. Hill, M. T. Laker, L. O. Ticknor, and P. Keim. 1999. Genetic comparison of Bacillus anthracis and its close relatives using amplified fragment length polymorphism and polymerase chain reaction analysis. Journal of Applied Microbiology 87:263-269.

Keim, P., A. M. Klevytska, L. B. Price, J. M. Schupp, G. Zinser, K. L. Smith, M. E. Hugh-Jones, R. Okinaka, K. K. Hill, and P. J. Jackson. 1999. Molecular diversity in Bacillus anthracis. Journal of Applied Microbiology 87:215-217.

Okinaka, R., K. Cloud, O. Hampton, A. Hoffmaster, K. Hill, P. Keim, T. Koehler, G. Lamke, S. Kumano, D. Manter, Y. Martinez, D. Ricke, R. Svensson, and P. Jackson. 1999a. Sequence, assembly and analysis of pX01 and pX02. Journal of Applied Microbiology 87:261-262.

Okinaka, R. T., K. Cloud, O. Hampton, A. R. Hoffmaster, K. K. Hill, P. Keim, T. M. Koehler, G. Lamke, S. Kumano, J. Mahillon, D. Manter, Y. Martinez, D. Ricke, R. Svensson, and P. J. Jackson. 1999b. Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. Journal of Bacteriology 181:6509-6515.

Price, L. B., M. Hugh-Jones, P. J. Jackson, and P. Keim. 1999. Genetic diversity in the protective antigen gene of Bacillus anthracis. Journal of Bacteriology 181:2358-2362.

Schupp, J. M., L. B. Price, A. Klevytska, and P. Keim. 1999. Internal and flanking sequence from AFLP fragments using ligation-mediated suppression PCR. Biotechniques 26:905-910, 912.

Smith, K. L., V. De Vos, H. B. Bryden, M. E. Hugh-Jones, A. Klevytska, L. B. Price, P. Keim, and D. T. Scholl. 1999. Meso-scale ecology of anthrax in southern Africa: a pilot study of diversity and clustering. Journal of Applied Microbiology 87:204-207.

Jackson, P. J., M. E. Hugh-Jones, D. M. Adair, G. Green, K. K. Hill, C. R. Kuske, L. M. Grinberg, F. A. Abramova, and P. Keim. 1998. PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: the presence of multiple Bacillus anthracis strains in different victims. Proceedings of the National Academy of Sciences USA 95:1224-1229.

Willardson, B. M., J. F. Wilkins, T. A. Rand, J. M. Schupp, K. K. Hill, P. Keim, and P. J. Jackson. 1998. Development and testing of a bacterial biosensor for toluene-based environmental contaminants. Applied and Environmental Microbiology 64:1006-1012.

Jackson, P. J., E. A. Walthers, A. S. Kalif, K. L. Richmond, D. M. Adair, K. K. Hill, C. R. Kuske, G. L. Andersen, K. H. Wilson, M. Hugh-Jones, and P. Keim. 1997. Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates. Applied and Environmental Microbiology 63:1400-1405.

Keim, P., A. Kalif, J. Schupp, K. Hill, S. E. Travis, K. Richmond, D. M. Adair, M. Hugh-Jones, C. R. Kuske, and P. Jackson. 1997. Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. Journal of Bacteriology 179:818-824.

Morgante, M., I. Jurman, L. Shi, T. Zhu, P. Keim, and J. A. Rafalski. 1997. The STR120 satellite DNA of soybean: organization, evolution and chromosomal specificity. Chromosome Research 5:363-373.

Rusche, M. L., H. L. Mogensen, L. Shi, P. Keim, M. Rougier, A. Chaboud, and C. Dumas. 1997. B chromosome behavior in maize pollen as determined by a molecular probe. Genetics 147:1915-1921.

Danna, K. J., R. Workman, V. Coryell, and P. Keim. 1996. 5S rRNA genes in tribe Phaseoleae: array size, number, and dynamics. Genome 39:445-455.

Kimberling, D. N., A. R. Ferreira, S. M. Shuster, and P. Keim. 1996. RAPD marker estimation of genetic structure among isolated northern leopard frog populations in the south-western USA. Molecular Ecology 5:521-529.

Shi, L., T. Zhu, and P. Keim. 1996a. Ribosomal RNA genes in soybean and common bean: chromosomal organization, expression, and evolution. Theoretical and Applied Genetics 93:136-141.

Shi, L., T. Zhu, H. L. Mogensen, and P. Keim. 1996b. Sperm Identification in Maize by Fluorescence in Situ Hybridization. Plant Cell 8:815-821.

Shi, L., T. Zhu, M. Morgante, J. A. Rafalski, and P. Keim. 1996c. Soybean chromosome painting: a strategy for somatic cytogenetics. Journal of Heredity 87:308-313.

Travis, S. E., J. Maschinski, and P. Keim. 1996. An analysis of genetic variation in Astragalus cremnophylax var. cremnophylax, a critically endangered plant, using AFLP markers. Molecular Ecology 5:735-745.

Zhu, T., I. Shi, R. P. Funke, P. M. Gresshoff, and P. Keim. 1996. Characterization and application of soybean YACs to molecular cytogenetics. Molecular Genetics and Genomics 252:483-488.

Christensen, K. M., T. G. Whitham, and P. Keim. 1995. Herbivory and tree mortality across a pinyon pine hybrid zone. Oecologia 101:29-36.

Schupp, J. M., S. E. Travis, L. B. Price, R. F. Shand, and P. Keim. 1995. Rapid bacterial permeabilization reagent useful for enzyme assays. Biotechniques 19:18-20.

Vahedian, M., L. Shi, T. Zhu, R. Okimoto, K. Danna, and P. Keim. 1995. Genomic organization and evolution of the soybean SB92 satellite sequence. Plant Molecular Biology 29:857-862.

Webb, D. M., B. M. Baltazar, A. P. Rao-Arelli, J. Schupp, K. Clayton, P. Keim, and W. D. Beavis. 1995. Genetic mapping of soybean cyst nematode race-3 resistance loci in the soybean PI 437.654. Theoretical and Applied Genetics 91:574-581.

Zhu, T., L. Shi, J. J. Doyle, and P. Keim. 1995. A single nuclear locus phylogeny of soybean based on DNA sequence. Theoretical and Applied Genetics 90:991-999.

Sobral, B. W., D. P. Braga, E. S. Lahood, and P. Keim. 1994. Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. subtribe of the Andropogoneae Dumort. tribe. Theoretical and Applied Genetics 87:843-853.

Zhu, T., J. M. Schupp, A. Oliphant, and P. Keim. 1994. Hypomethylated sequences: characterization of the duplicate soybean genome. Molecular Genetics and Genomics 244:638-645.

Blackett, R. S., and P. Keim. 1992. Big game species identification by deoxyribonucleic acid (DNA) probes. Journal of Forensic Sciences 37:590-596.

Diers, B. W., P. Keim, W. R. Fehr, and R. C. Shoemaker. 1992. RFLP analysis of soybean seed protein and oil content. Theoretical and Applied Genetics 83:608-612.

Keim, P., W. Beavis, J. Schupp, and R. Freestone. 1992. Evaluation of soybean RFLP marker diversity in adapted germ plasm. Theoretical and Applied Genetics 85:205-212

Muehlbauer, G. J., P. E. Staswick, J. E. Specht, G. L. Graef, R. C. Shoemaker, and P. Keim. 1991. RFLP mapping using near-isogenic lines in the soybean [Glycine max (L.) Merr]. Theoretical and Applied Genetics 81:189-198.

Keim, P., B. W. Diers, T. C. Olson, and R. C. Shoemaker. 1990a. RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735-742.

Keim, P., B. W. Diers, and R. C. Shoemaker. 1990b. Genetic analysis of soybean hard seededness with molecular markers. Theoretical and Applied Genetics 79:465-469.

Keim, P., and K. G. Lark. 1990. The RecE recombination pathway mediates recombination between partially homologous DNA sequences: structural analysis of recombination products. Journal of Structural Biology 104:97-106.

Close, P. S., R. C. Shoemaker, and P. Keim. 1989. Distribution of restriction site polymorphism within the chloroplast genome of the genus Glycine, subgenus Soja. Theoretical and Applied Genetics 77:768-776.

Keim, P., K. N. Paige, T. G. Whitham, and K. G. Lark. 1989a. Genetic analysis of an interspecific hybrid swarm of Populus: occurrence of unidirectional introgression. Genetics 123:557-565.

Keim, P., R. C. Shoemaker, and R. G. Palmer. 1989b. Restriction fragment length polymorphism diversity in soybean. Theoretical and Applied Genetics 77:786-792.

Keim, P. 1987. Isolation of nuclei from soybean suspension cultures. Methods in Enzymology 148:535-541.

Keim, P., and K. G. Lark. 1987. The sequence of the 3.3-kilobase repetitive element from Dipodomys ordii suggests a mechanism for its amplification and interspersion. Journal of Molecular Evolution 25:65-73.