Adair, D. M. and Worsham, P. L. and Hill, K. K. and Klevytska, A. M. and Jackson, P. J. and Friedlander, A. M. and Keim, P. (2000) Diversity in a variable-number tandem repeat from Yersinia pestis. Journal of Clinical Microbiology, 38 (4). pp. 1516-1519. ISSN 1098-660X
Auerbach, Raymond K. and Tuanyok, Apichai and Probert, William S. and Kenefic, Leo and Vogler, Amy J. and Bruce, David C. and Munk, Christine and Brettin, Thomas S. and Eppinger, Mark and Ravel, Jacques and Wagner, David M. and Keim, Paul (2007) Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS One, 8. e770. ISSN 1932-6203
Baker, Anthony and Pearson, Talima and Price, Erin P. and Dale, Julia and Keim, Paul and Hornstra, Heidie and Greenhill, Andrew and Padilla, Gabriel and Warner, Jeffrey (2011) Molecular phylogeny of Burkholderia pseudomallei from a remote region of Papua New Guinea. PLoS ONE, 6 (3). e18343. ISSN 1932-6203
Barns, Susan M. and Grow, Christy C. and Okinaka, Richard T. and Keim, Paul and Kuske, Cheryl R. (2005) Detection of diverse new francisella-like bacteria in environmental samples. Applied and Environmental Microbiology, 71 (9). pp. 5494-5500. ISSN 1098-5336
Beckstrom-Sternberg, Stephen M. and Auerbach, Raymond K. and Godbole, Shubhada and Pearson, John V. and Beckstrom-Sternberg, James S. and Deng, Zuoming and Munk, Christine and Kubota, Kristy and Zhou, Yan and Bruce, David and Noronha, Jyothi and Scheuermann, Richard H. and Wang, Aihui and Wei, Xianying and Wang, Jianjun and Hao, Jicheng and Wagner, David M. and Brettin, Thomas S. and Brown, Nancy and Gilna, Paul and Keim, Paul S. (2007) Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis. PLoS ONE, 9. e947. ISSN 1932-6203
Birdsell, Dawn N. and Vogler, Amy J. and Buchhagen, Jordan and Clare, Ashley and Kaufman, Emily and Naumann, Amber and Driebe, Elizabeth and Wagner, David M. and Keim, Paul S. (2014) TaqMan real-time PCR assays for single-nucleotide polymorphisms which identify Francisella tularensis and its subspecies and subpopulations. PloS One, 9 (9). e10796. ISSN 1932-6203
Bowers, Jolene R. and Engelthaler, David M. and Ginther, Jennifer L and Pearson, Talima and Peacock, Sharon J. and Tuanyok, Apichai and Wagner, David M. and Currie, Bart J. and Keim, Paul S. (2010) BurkDiff: A real-time PCR allelic discrimination assay for Burkholderia pseudomallei and B. mallei. PLoS ONE, 5 (11). e15413. ISSN 1932-6203
Caporaso, J. Gregory and Knight, Rob and Kelley, Scott T. (2011) Host-associated and free-living phage communities differ profoundly in phylogenetic composition. PLoS ONE, 6 (2). e16900. ISSN 1932-6203
Champion, Mia D. and Zeng, Qiandong and Nix, Eli B. and Nano, Francis E. and Keim, Paul S and Kodira, Chinnappa D. and Borowsky, Mark and Young, Sarah and Koehrsen, Michael and Engels, Reinhard and Pearson, Matthew and Howarth, Clint and Larson, Lisa and White, Jared and Alvarado, Lucia and Forsman, Mats and Bearden, Scott W. and Sjoestedt, Anders and Titball, Richard and Michell, Stephen L. and Birren, Bruce and Galagan, James (2009) Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies. PLoS Pathogens, 5 (5). e1000459. ISSN 1553-7366
Chapman, Samantha K. and Newman, Gregory S. and Hart, Stephen C. and Schweitzer, Jennifer A. and Koch, George W. (2013) Leaf litter mixtures alter microbial community development: Mechanisms for non-additive effects in litter decomposition. PLoS ONE, 8 (4). e62671. ISSN 1932-6203
Clingenpeel, Scott R. and Moan, Jaina L and McGrath, Danielle M and Hungate, Bruce A. and Watwood, Mary E. (2012) Stable carbon isotope fractionation in chlorinated ethene degradation by bacteria expressing three toluene oxygenases. Frontiers in microbiology, 3. p. 63. ISSN 1664-302X
Cope, Emily K. and Goldstein-Daruech, Natalia and Kofonow, Jennifer M. and Christensen, Lanette and McDermott, Bridget and Monroy, Fernando and Palmer, James N. and Chiu, Alexander G. and Shirtliff, Mark E. and Cohen, Noam A. and Leid, Jeff G. (2011) Regulation of virulence gene expression resulting from Streptococcus pneumoniae and nontypeable Haemophilus influenzae interactions in chronic disease. PLoS ONE, 6 (12). e28523. ISSN 1932-6203
Cummings, Craig A. and Chung, Christina A. Bormann and Fang, Rixun and Barker, Melissa and Brzoska, Pius and Williamson, Phillip C. and Beaudry, Jodi and Matthews, Molly and Schupp, James and Wagner, David M. and Birdsell, Dawn and Vogler, Amy J. and Furtado, Manohar R. and Keim, Paul and Budowle, Bruce (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). 1/14/2015. ISSN 2041-2223
Dale, Julia and Price, Erin P. and Hornstra, Heidie and Busch, Joseph D. and Mayo, Mark and Godoy, Daniel and Wuthiekanun, Vanaporn and Baker, Anthony and Foster, Jeffrey T. and Wagner, David M. and Tuanyok, Apichai and Warner, Jeffrey and Spratt, Brian G. and Peacock, Sharon J. and Currie, Bart J. and Keim, Paul and Pearson, Talima (2011) Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei. PLoS Neglected Tropical Diseases, 5 (12). e1381. ISSN 1935-2727
Deng, Xiangyu and Shariat, Nikki and Driebe, Elizabeth M. and Roe, Chandler C. and Tolar, Beth and Trees, Eija and Keim, Paul and Zhang, Wei and Dudley, Edward G. and Fields, Patricia I. and Engelthaler, David M. (2015) Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis. Journal of Clinical Microbiology, 53 (1). pp. 212-218. ISSN 1098-660X
Easterday, W. Ryan and Van Ert, Matthew N. and Simonson, Tatum S. and Wagner, David M. and Kenefic, Leo J. and Allender, Christopher J. and Keim, Paul (2005) Use of single nucleotide polymorphisms in the plcR gene for specific identification of Bacillus anthracis. Journal of Clinical Microbiology, 43 (4). pp. 1995-1997. ISSN 1098-660X
Engelthaler, David M. and Bowers, Jolene and Schupp, James A. and Pearson, Talima and Ginther, Jennifer and Hornstra, Heidie M. and Dale, Julia and Stewart, Tasha and Sunenshine, Rebecca and Waddell, Victor and Levy, Craig and Gillece, John and Price, Lance B. and Contente, Tania and Beckstrom-Sternberg, Stephen M. and Blaney, David D. and Wagner, David M. and Mayo, Mark and Currie, Bart J. and Keim, Paul and Tuanyok, Apichai (2011) Molecular investigations of a locally acquired case of melioidosis in southern AZ, USA. PLoS Neglected Tropical Diseases, 5 (10). e1347. ISSN 1935-2727
Engelthaler, David M. and Hicks, Nathan D. and Gillece, John D. and Roe, Chandler C. and Schupp, James M. and Driebe, Elizabeth M. and Gilgado, Felix and Carriconde, Fabian and Trilles, Luciana and Firacative, Carolina and Ngamskulrungroj, Popchai and Castañeda, Elizabeth and Lazera, Marcia dos Santos and Melhem, Marcia S. C. and Pérez-Bercoff, Asa and Huttley, Gavin and Sorrell, Tania C. and Voelz, Kerstin and May, Robin C. and Fisher, Matthew C. and Thompson, George R. and Lockhart, Shawn R. and Keim, Paul and Meyer, Wieland (2014) Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. mBio, 5 (4). pp. 1-18. ISSN 2150-7511
Eppinger, Mark and Pearson, Talima and Koenig, Sara S K and Pearson, Ofori and Hicks, Nathan and Agrawal, Sonia and Sanjar, Fatemeh and Galens, Kevin and Daugherty, Sean and Crabtree, Jonathan and Hendriksen, Rene S and Price, Lance B and Upadhyay, Bishnu P and Shakya, Geeta and Fraser, Claire M and Ravel, Jacques and Keim, Paul S (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 (6). e01721-14. ISSN 2150-7511
Farlow, Jason and Postic, Danielle and Smith, Kimothy L. and Jay, Zack and Baranton, Guy and Keim, Paul (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 (12). pp. 4612-4618. ISSN 1098-660X
Farlow, Jason and Smith, Kimothy L. and Wong, Jane and Abrams, Michelle and Lytle, Michael and Keim, Paul (2001) Francisella tularensis strain typing using multiple-locus, variable-number tandem repeat analysis. Journal of Clinical Microbiology, 39 (9). pp. 3186-3192. ISSN 1098-660X
Flores, Gilberto E. and Caporaso, J. Gregory and Henley, Jessica B. and Rideout, Jai Ram and Domogala, Daniel David and Chase, John and Leff, Jonathan W. and Vazquez-Baeza, Yoshiki and Gonzalez, Antonio and Knight, Rob and Dunn, Robert R. and Fierer, Noah (2014) Temporal variability is a personalized feature of the human microbiome. Genome Biology, 15 (12). p. 531. ISSN 1465-6914
Foster, Jeffrey T. and Okinaka, Richard T. and Svensson, Rita and Shaw, Kathryn and De, Barun K. and Robison, Richard A. and Probert, William S. and Kenefic, Leo J. and Brown, William D. and Keim, Paul (2008) Real-time PCR assays of single-nucleotide polymorphisms defining the major Brucella clades. Journal of Clinical Microbiology, 46 (1). pp. 296-301. ISSN 1098-660X
Fouet, Agnès and Smith, Kimothy L. and Keys, Chris and Vaissaire, Josée and Le Doujet, Claudine and Levy, Martine and Mock, Michèle and Keim, Paul (2002) Diversity among French Bacillus anthracis isolates. Journal of Clinical Microbiology, 40 (12). pp. 4732-4734. ISSN 1098-660X
Fox, David T. and Schmidt, Emily N. and Tian, Hongzhao and Dhungana, Suraj and Valentine, Michael C. and Warrington, Nicole V. and Phillips, Paul D. and Finney, Kellan B. and Cope, Emily K. and Leid, Jeff G. and Testa, Charles A. and Koppisch, Andrew T. (2014) Sub-inhibitory fosmidomycin exposures elicits oxidative stress in Salmonella enterica Serovar typhimurium LT2. Plos One, 9 (4). e95271. ISSN 1932-6203
Greenberg, David L. and Busch, Joseph D. and Keim, Paul and Wagner, David M. (2010) Identifying experimental surrogates for Bacillus anthracis spores: a review. Investigative Genetics, 1 (1). p. 4. ISSN 2041-2223
Hansen, Cristina M. and Vogler, Amy J. and Keim, Paul and Wagner, David M. and Hueffer, Karsten (2011) Tularemia in Alaska, 1938-2010. Acta Veterinaria Scandinavica, 53 (61). ISSN 1751-0147
Harbeck, Michaela and Seifert, Lisa and Hänsch, Stephanie and Wagner, David M. and Birdsell, Dawn and Parise, Katy L. and Wiechmann, Ingrid and Grupe, Gisela and Thomas, Astrid and Keim, Paul and Zöller, Lothar and Bramanti, Barbara and Riehm, Julia M. and Scholz, Holger C. (2013) Yersinia pestis DNA from skeletal remains from the 6th century AD reveals insights into Justinianic plague. PLoS Pathogens, 9 (5). e1003349. ISSN 1553-7366
Hendriksen, Rene S. and Price, Lance B. and Schupp, James M. and Gillece, John D. and Kaas, Rolf S. and Engelthaler, David M. and Bortolaia, Valeria and Pearson, Talima Ross and Waters, Andrew E. and Upadhyay, Bishnu Prasad and Shrestha, Sirjana Devi and Adhikari, Shailaja and Shakya, Geeta and Keim, Paul S. and Aarestrup, Frank M. (2011) Population genetics of Vibrio cholerae from Nepal in 2010: Evidence on the origin of the Haitian outbreak. mBio, 2 (4). e00157-11. ISSN 2150-7511
Hill, Karen K. and Ticknor, Lawrence O. and Okinaka, Richard T. and Asay, Michelle and Blair, Heather and Bliss, Katherine A. and Laker, Mariam and Pardington, Paige E. and Richardson, Amber P. and Tonks, Melinda and Beecher, Douglas J. and Kemp, John D. and Kolstø, Anne-Brit and Wong, Amy C. Lee and Keim, Paul S and Jackson, Paul J. (2004) Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates. Applied and Environmental Microbiology, 70 (2). pp. 1068-1080. ISSN 1098-5336
Hornstra, Heidie M. and Priestley, Rachael A. and Georgia, Shalamar M. and Kachur, Sergey and Birdsell, Dawn N. and Hilsabeck, Remy and Gates, Lauren T. and Samuel, James E. and Heinzen, Robert A. and Kersh, Gilbert J. and Keim, Paul and Massung, Robert F. and Pearson, Talima (2011) Rapid typing of Coxiella burnetii. PLoS ONE, 6 (11). e26201. ISSN 1932-6203
Hou, Weiguo and Wang, Shang and Dong, Hailiang and Jiang, Hongchen and Briggs, Brandon R. and Peacock, Joseph P. and Huang, Qiuyuan and Huang, Liuqin and Wu, Geng and Zhi, Xiaoyang and Li, Wenjun and Dodsworth, Jeremy A. and Hedlund, Brian P. and Zhang, Chuanlun and Hartnett, Hilairy E. and Dijkstra, Paul and Hungate, Bruce A (2013) A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing. PLoS ONE, 8 (1). e53350. ISSN 1932-6203
Jackson, Paul J. and Walthers, Eliza A. and Kalif, Abdullahi S. and Richmond, Kara L. and Adair, Debra M. and Hill, Karen K. and Kuske, Cheryl R. and Andersen, Gary L. and Wilson, Kenneth H. and Hugh-Jones, Martin and Keim, Paul (1997) Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates. Applied and Environmental Microbiology, 63 (4). pp. 1400-1405. ISSN 1098-5336
Kaestli, Mirjam and Richardson, Leisha J. and Colman, Rebecca E. and Tuanyok, Apichai and Price, Erin P. and Bowers, Jolene R. and Mayo, Mark and Kelley, Erin and Seymour, Meagan L. and Sarovich, Derek S. and Pearson, Talima and Engelthaler, David M. and Wagner, David M. and Keim, Paul S. and Schupp, James M. and Currie, Bart J. (2012) Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens. Journal of Clinical Microbiology, 50 (6). pp. 2059-2062. ISSN 1098-660X
Kenefic, Leo J. and Pearson, Talima and Okinaka, Richard T. and Schupp, James M. and Wagner, David M. and Hoffmaster, Alex R. and Trim, Carla P. and Chung, Wai-Kwan and Beaudry, Jodi A. and Jiang, L. and Gajer, P. and Foster, Jeffrey T. and Mead, James I. and Ravel, Jacques and Keim, Paul (2009) Pre-columbian origins for North American anthrax. PLos One, 4 (March). e4813. ISSN 1932-6203
Khmaladze, Ekaterine and Birdsell, Dawn N. and Naumann, Amber A. and Hochhalter, Christian B. and Seymour, Meagan L. and Nottingham, Roxanne and Beckstrom-Sternberg, Stephen M. and Beckstrom-Sternberg, James and Nikolich, Mikeljon P. and Chanturia, Gvantsa and Zhgenti, Ekaterine and Zakalashvili, Mariam and Malania, Lile and Babuadze, Giorgi and Tsertsvadze, Nikoloz and Abazashvili, Natalia and Kekelidze, Merab and Tsanava, Shota and Imnadze, Paata and Ganz, Holly H. and Getz, Wayne M. and Pearson, Ofori and Gajer, Pawel and Eppinger, Mark and Ravel, Jacques and Wagner, David M. and Okinaka, Richard T. and Schupp, James M. and Keim, Paul and Pearson, Talima (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 (7). e102651. ISSN 1932-6203
Larsson, Pär and Elfsmark, Daniel and Svensson, Kerstin and Wikström, Per and Forsman, Mats and Brettin, Thomas and Keim, Paul and Johansson, Anders (2009) Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen. PLoS Pathogens, 5 (6). e1000472. ISSN 1553-7366
Liang, Winnie S. and Craig, David W. and Carpten, John and Borad, Mitesh J. and Demeure, Michael J. and Weiss, Glen J. and Izatt, Tyler and Sinari, Shripad and Christoforides, Alexis and Aldrich, Jessica and Kurdoglu, Ahmet and Barrett, Michael and Phillips, Lori and Benson, Hollie and Tembe, Waibhav and Braggio, Esteban and Kiefer, Jeffrey A. and Legendre, Christophe and Posner, Richard and Hostetter, Galen H. and Baker, Angela and Egan, Jan B. and Han, Haiyong and Lake, Douglas and Stites, Edward C. and Ramanathan, Ramesh K. and Fonseca, Rafael and Stewart, A. Keith and Von Hoff, Daniel (2012) Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing. PLoS ONE, 7 (10). e43192. ISSN 1932-6203
Limmathurotsakul, Direk and Dance, David A. B. and Wuthiekanun, Vanaporn and Kaestli, Mirjam and Mayo, Mark and Warner, Jeffrey and Wagner, David M. and Tuanyok, Apichai and Wertheim, Heiman and Cheng, Tan Yoke and Mukhopadhyay, Chiranjay and Puthucheary, Savithiri and Day, Nicholas P. J. and Steinmetz, Ivo and Currie, Bart J. and Peacock, Sharon J. (2013) Systematic review and consensus guidelines for environmental sampling of Burkholderia pseudomallei. PLoS Neglected Tropical Diseases, 7 (3). e2105. ISSN 1935-2727
Liu, Cindy M. and Hungate, Bruce A and Tobian, Aaron A. R. and Serwadda, David and Ravel, Jacques and Lester, Richard and Kigozi, Godfrey and Aziz, Maliha and Galiwango, Ronald M. and Nalugoda, Fred and Contente-Cuomo, Tania L. and Wawer, Maria J. and Keim, Paul and Gray, Ronald H. and Price, Lance B. (2013) Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria. mBio, 4 (2). e00076-13. ISSN 2150-7511
Losada, Liliana and Ronning, Catherine M. and DeShazer, David and Woods, Donald and Fedorova, Natalie and Kim, H. Stanley and Shabalina, Svetlana A. and Pearson, Talima R. and Brinkac, Lauren and Tan, Patrick and Nandi, Tannistha and Crabtree, Jonathan and Badger, Jonathan and Beckstrom-Sternberg, Stephen M. and Saqib, Muhammad and Schutzer, Steven E. and Keim, Paul and Nierman, William C. (2010) Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biology and Evolution, 2. pp. 102-116. ISSN 1759-6653
Maho, Angaya and Rossano, Alexandra and Haechler, Herbert and Holzer, Anita and Schelling, Esther and Zinsstag, Jakob and Hassane, Mahamat H and Toguebaye, Bhen S and Akakpo, Ayayi J and Van Ert, Matthew and Keim, Paul S and Kenefic, Leo and Frey, Joachim and Perreten, Vincent (2006) Antibiotic susceptibility and molecular diversity of Bacillus anthracis strains in Chad: Detection of a new phylogenetic subgroup. Journal of Clinical Microbiology, 44 (9). pp. 3422-3425. ISSN 1098-660X
Michelou, Vanessa K. and Caporaso, J. Gregory and Knight, Rob and Palumbi, Stephen R. (2013) The ecology of microbial communities associated with Macrocystis pyrifera. PLoS ONE, 8 (6). e67480. ISSN 1932-6203
Millman, Jack M and Waits, Kara and Grande, Heidi and Marks, Ann R and Marks, Jane C and Price, Lance B and Hungate, Bruce A (2013) Prevalence of antibiotic-resistant E. coli in retail chicken: comparing conventional, organic, kosher, and raised without antibiotics. F1000Research, 2. p. 155. ISSN 2046-1402
Okinaka, Richard and Pearson, Talima and Keim, Paul (2006) Anthrax, but not Bacillus anthracis? PLoS Pathogens, 2 (11). e122. ISSN 1553-7366
Okinaka, Richard T. and Challacombe, Jean and Drees, Kevin and Birdsell, Dawn N. and Janke, Nicolette and Naumann, Amber and Seymour, Meagan and Hornstra, Heidie and Schupp, James and Sahl, Jason and Foster, Jeffrey T. and Pearson, Talima and Turnbull, Peter and Keim, Paul (2014) Genome sequence of Bacillus anthracis STI, a sterne-like Georgian/Soviet vaccine strain. Genome Announcements, 2 (5). e00853-14. ISSN 2169-8287
Pomajbikova, Katerina and Obornik, Miroslav and Horak, Ales and Petrzelkova, Klara J. and Grim, J. Norman and Levecke, Bruno and Todd, Angelique and Mulama, Martin and Kiyang, John and Modry, David (2013) Novel Insights into the Genetic Diversity of Balantidium and Balantidium-like Cyst-forming Ciliates. Plos Neglected Tropical Diseases, 7 (3). e2140. ISSN 1935-2727
Price, Erin P. and Hornstra, Heidie M. and Limmathurotsakul, Direk and Max, Tamara L. and Sarovich, Derek S. and Vogler, Amy J. and Dale, Julia L. and Ginther, Jennifer L. and Leadem, Benjamin and Colman, Rebecca E. and Foster, Jeffrey T. and Tuanyok, Apichai and Wagner, David M. and Peacock, Sharon J. and Pearson, Talima and Keim, Paul (2010) Within-host evolution of Burkholderia pseudomallei in four cases of acute melioidosis. PLoS Pathogens, 6 (1). e1000725. ISSN 1553-7366
Price, Lance B. and Johnson, James R. and Aziz, Maliha and Clabots, Connie and Johnston, Brian and Tchesnokova, Veronika and Nordstrom, Lora and Billig, Maria and Chattopadhyay, Sujay and Stegger, Marc and Andersen, Paal S. and Pearson, Talima and Riddell, Kim and Rogers, Peggy and Scholes, Delia and Kahl, Barbara and Keim, Paul and Sokurenko, Evgeni V. (2013) The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. mBio, 4 (6). 00377-13. ISSN 2150-7511
Price, Lance B. and Liu, Cindy M and Melendez, Johan H. and Frankel, Yelena M. and Engelthaler, David and Aziz, Maliha and Bowers, Jolene and Rattray, Rogan and Ravel, Jacques and Kingsley, Chris and Keim, Paul S. and Lazarus, Gerald S. and Zenilman, Jonathan M. (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 (7). e6462. ISSN 1932-6203
Price, Lance B. and Stegger, Marc and Hasman, Henrik and Aziz, Maliha and Larsen, Jesper and Andersen, Paal Skytt and Pearson, Talima and Waters, Andrew E. and Foster, Jeffrey T. and Schupp, James and Gillece, John and Driebe, Elizabeth and Liu, Cindy M. and Springer, Burkhard and Zdovc, Irena and Battisti, Antonio and Franco, Alessia and Żmudzki, Jacek and Schwarz, Stefan and Butaye, Patrick and Jouy, Eric and Pomba, Constanca and Porrero, M. Concepción and Ruimy, Raymond and Smith, Tara C. and Robinson, D. Ashley and Weese, J. Scott and Arriola, Carmen Sofia and Yu, Fangyou and Laurent, Frederic and Keim, Paul and Skov, Robert and Aarestrup, Frank M. (2012) Staphylococcus aureus CC398: Host adaptation and emergence of methicillin resistance in livestock. mBio, 3 (1). e00305-11. ISSN 2150-7511
Radnedge, Lyndsay and Agron, Peter G. and Hill, Karen K. and Jackson, Paul J. and Ticknor, Lawrence O. and Keim, Paul and Andersen, Gary L. (2003) Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Applied and Environmental Microbiology, 69 (5). pp. 2755-2764. ISSN 1098-5336
Sahl, Jason W. and Caporaso, J. Gregory and Rasko, David A. and Keim, Paul (2014) The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ, 2 (e332). ISSN 2167-8359
Sahl, Jason W. and Gillece, John D. and Schupp, James M. and Waddell, Victor G. and Driebe, Elizabeth M. and Engelthaler, David M. and Keim, Paul (2013) Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in acinetobacter. PLoS ONE, 8 (1). e54287. ISSN 1932-6203
Sahl, Jason W. and Morris, Carolyn R. and Emberger, Jennifer and Fraser, Claire M. and Ochieng, John Benjamin and Juma, Jane and Fields, Barry and Breiman, Robert F. and Gilmour, Matthew and Nataro, James P. and Rasko, David A. (2015) Defining the phylogenomics of Shigella species: A pathway to diagnostics. Journal of Clinical Microbiology, 53 (3). pp. 951-960. ISSN 1098-660X
Sahl, Jason W. and Stone, Joshua K. and Gelhaus, H. Carl and Warren, Richard L. and Cruttwell, Caroline J. and Funnell, Simon G. and Keim, Paul and Tuanyok, Apichai (2013) Genome sequence of Burkholderia pseudomallei NCTC 13392. Genome Announcements, 1 (3). e00183. ISSN 2169-8287
Sarovich, Derek S. and Price, Erin P. and Schulze, Alex T. Von and Cook, James M. and Mayo, Mark and Watson, Lindsey M. and Richardson, Leisha and Seymour, Meagan L. and Tuanyok, Apichai and Engelthaler, David M. and Pearson, Talima and Peacock, Sharon J. and Currie, Bart J. and Keim, Paul and Wagner, David M. (2012) Characterization of ceftazidime resistance mechanisms in clinical isolates of Burkholderia pseudomallei from Australia. PLoS ONE, 7 (2). e30789. ISSN 1932-6203
Scholz, Holger C. and Pearson, Talima and Hornstra, Heidie and Projahn, Michaela and Terzioglu, Rahime and Wernery, Renate and Georgi, Enrico and Riehm, Julia M. and Wagner, David M. and Keim, Paul S. and Joseph, Marina and Johnson, Bobby and Kinne, Joerg and Jose, Shanti and Hepp, Crystal M. and Witte, Angela and Wernery, Ulrich (2014) Genotyping of burkholderia mallei from an outbreak of glanders in bahrain suggests multiple introduction events. PLoS Neglected Tropical Diseases, 8 (9). e3195. ISSN 1935-2727
Schwartz, Egbert (2007) Characterization of growing microorganisms in soil by stable isotope probing with H218O. Applied & Environmental Microbiology, 73 (8). pp. 2541-2546. ISSN 1098-5336
Schwarzberg, Karen and Le, Rosalin and Bharti, Balambal and Lindsay, Suzanne and Casaburi, Giorgio and Salvatore, Francesco and Saber, Mohamed H. and Alonaizan, Faisal and Slots, Jørgen and Gottlieb, Roberta A. and Caporaso, J. Gregory and Kelley, Scott T. (2014) The personal human oral microbiome obscures the effects of treatment on periodontal disease. PLoS ONE, 9 (1). e86708. ISSN 1932-6203
Shade, Ashley and Jones, Stuart E. and Caporaso, J. Gregory and Handelsman, Jo and Knight, Rob and Fierer, Noah and Gilbert, Jack A. (2014) Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio, 5 (4). ISSN 2150-7511
Shuey, Megan M. and Drees, Kevin P. and Lindner, Daniel L. and Keim, Paul S and Foster, Jeffrey T. (2014) Highly sensitive quantitative PCR for the detection and differentiation of Pseudogymnoascus destructans and other Pseudogymnoascus species. Applied & Environmental Microbiology, 80 (5). pp. 1726-1731. ISSN 1098-5336
Sinclair, Ryan and Boone, Stephanie A. and Greenberg, David and Keim, Paul S and Gerba, Charles P. (2008) Persistence of category A select agents in the environment. Applied & Environmental Microbiology, 74 (3). pp. 555-563. ISSN 1098-5336
Smith, K. L. and DeVos, V. and Bryden, H. and Price, L. B. and Hugh-Jones, M. E. and Keim, P. (2000) Bacillus anthracis diversity in Kruger National Park [South Africa]. Journal of Clinical Microbiology, 38 (10). pp. 3780-3784. ISSN 1098-660X
Spurgiesz, R. Scott and Quitugua, Teresa N. and Smith, Kimothy L. and Schupp, James and Palmer, Eldon G. and Cox, Rebecca A. and Keim, Paul (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 (9). pp. 4224-4230. ISSN 1098-660X
Stegger, Marc and Driebe, Elizabeth M. and Roe, Chandler and Lemmer, Darrin and Bowers, Jolene R. and Engelthaler, David M. and Keim, Paul and Andersen, Paal S. (2013) Genome sequence of Staphylococcus aureus strain CA-347, a USA600 methicillin-resistant isolate. Genome Announcements, 1 (4). e00517. ISSN 2169-8287
Stone, Nathan E and Olafson, Pia U. and Davey, Ronald B. and Buckmeier, Greta and Bodine, Deanna and Sidak-Loftis, Lindsay C. and Giles, John R. and Duhaime, Roberta and Miller, Robert J. and Mosqueda, Juan and Scoles, Glen A. and Wagner, David M. and Busch, Joseph D. (2014) 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 (456). pp. 1-14. ISSN 1756-3305
Taylor, Andrea C. and Walker, Faith M. and Goldingay, Ross L. and Ball, Tina and van der Ree, Rodney (2011) Degree of landscape fragmentation influences genetic isolation among populations of a gliding mammal. PLoS ONE, 6 (10). e26651. ISSN 1932-6203
Ticknor, Lawrence O. and Kolstø, Anne-Brit and Hill, Karen K. and Keim, Paul and Laker, Miriam T. and Tonks, Melinda and Jackson, Paul J. (2001) Fluorescent amplified fragment length polymorphism analysis of Norwegian Bacillus cereus and Bacillus thuringiensis soil isolates. Applied and Environmental Microbiology, 67 (10). pp. 4863-4873. ISSN 1098-5336
Tiller, Rebekah V. and De, Barun K. and Boshra, Marie and Huynh, Lynn Y. and Ert, Matthew N. Van and Wagner, David M. and Klena, John and Mohsen, T. S. and El-Shafie, S. S. and Keim, Paul and Hoffmaster, Alex R. and Wilkins, Patricia P. and Pimentel, Guillermo (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 (7). pp. 2226-2231. ISSN 1098-660X
Touchman, Jeffrey W. and Wagner, David M. and Hao, Jicheng and Mastrian, Stephen D. and Shah, Maulik K. and Vogler, Amy J. and Allender, Christopher J. and Clark, Erin A. and Benitez, Debbie S. and Youngkin, David J. and Girard, Jessica M. and Auerbach, Raymond K. and Beckstrom-Sternberg, Stephen M. and Keim, Paul (2007) A North American Yersinia pestis draft genome sequence: SNPs and phylogenetic analysis. PLoS ONE, 2 (2). e220. ISSN 1932-6203
Trunck, Lily A. and Propst, Katie L. and Wuthiekanun, Vanaporn and Tuanyok, Apichai and Beckstrom-Sternberg, Stephen M and Beckstrom-Sternberg, James S. and Peacock, Sharon J. and Keim, Paul and Dow, Steven W. and Schweizer, Herbert P. (2009) Molecular basis of rare aminoglycoside susceptibility and pathogenesis of Burkholderia pseudomallei clinical isolates from Thailand. PLoS Neglected Tropical Diseases, 3 (9). e0000519. ISSN 1935-2727
Tuanyok, Apichai and Stone, Joshua K. and Mayo, Mark and Kaestli, Mirjam and Gruendike, Jeffrey and Georgia, Shalamar and Warrington, Stephanie and Mullins, Travis and Allender, Christopher J. and Wagner, David M. and Chantratita, Narisara and Peacock, Sharon J. and Currie, Bart J. and Keim, Paul (2012) The genetic and molecular basis of O-antigenic diversity in Burkholderia pseudomallei Lipopolysaccharide. PLoS Neglected Tropical Diseases, 6 (1). e1453. ISSN 1935-2727
U'ren, Jana M. and Hornstra, Heidie and Pearson, Talima and Schupp, James M. and Leadem, Benjamin and Georgia, Shalamar and Sermswan, Rasana W. and Keim, Paul (2007) Fine-scale genetic diversity among Burkholderia pseudomallei soil isolates in northeast Thailand. Applied & Environmental Microbiology, 73 (20). pp. 6678-6681. ISSN 1098-5336
Van Ert, Matthew N. and Easterday, W. Ryan and Simonson, Tatum S. and U'Ren, Jana M. and Pearson, Talima and Kenefic, Leo J. and Busch, Joseph D. and Huynh, Lynn Y. and Dukerich, Megan and Trim, Carla B. and Beaudry, Jodi and Welty-Bernard, Amy and Read, Timothy and Fraser, Claire M. and Ravel, Jacques and Keim, Paul (2007) Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain. Journal of Clinical Microbiology, 45 (1). pp. 47-53. ISSN 1098-660X
Van Zandt, Kristopher E. and Tuanyok, Apichai and Keim, Paul S. and Warren, Richard L. and Gelhaus, H. Carl (2012) An objective approach for Burkholderia pseudomallei strain selection as challenge material for medical countermeasures efficacy testing. Frontiers in Cellular and Infection Microbiology, 2. 9 pp.. ISSN 2235-2988
Vogler, Amy J. and Chan, Fabien and Wagner, David M. and Roumagnac, Philippe and Lee, Judy and Nera, Roxanne and Eppinger, Mark and Ravel, Jacques and Rahalison, Lila and Rasoamanana, Bruno W. and Beckstrom-Sternberg, Stephen M. and Achtman, Mark and Chanteau, Suzanne and Keim, Paul (2011) Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS Neglected Tropical Diseases, 5 (9). e1319. ISSN 1935-2727
Wahab, Tara and Birdsell, Dawn N. and Hjertqvist, Marika and Mitchell, Cedar L. and Wagner, David M. and Keim, Paul S. and Hedenström, Ingela and Löfdahl, Sven (2014) Insights to genetic characterization tools for epidemiological tracking of Francisella tularensis in Sweden. PLoS ONE, 9 (11). e112167. ISSN 1932-6203
Willardson, Barry M. and Wilkins, Jon F. and Rand, Timothy A. and Schupp, James M. and Hill, Karen K. and Keim, Paul and Jackson, Paul J. (1998) Development and testing of a bacterial biosensor for toluene-based environmental contaminants. Applied and Environmental Microbiology, 64 (3). pp. 1006-1012. ISSN 1098-5336
Woods, Angela and Watwood, Maribeth and Schwartz, Egbert (2011) Identification of a toluene-degrading bacterium from a soil sample through H218O DNA stable isotope probing. Applied & Environmental Microbiology, 77 (17). pp. 5995-5999. ISSN 1098-5336
Yang, Ruifu and Keim, Paul (2012) Microbial forensics: A powerful tool for pursuing bioterrorism perpetrators and the need for an international database. Journal of Bioterrorism and Biodefense, 2 (S3). ISSN 2157-2526
Heitkamp, Rae and Sahl, Jason and Summers, Amy and Roth, Amanda L and Kirkcup, Benjaman C (2014) Resolving antagonistic interactions among clinical isolates of Acinetobacter baumannii with phylogenetic analysis. In: American Society for Microbiology General Meeting, May 17-20th, 2014, Boston, Massachusetts.
Chuckran, Peter (2022) A multi-omics approach to assessing growth, stress, and disturbance in soil microbial communities. Doctoral thesis, Northern Arizona University.
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